BLASTP 2.0.10 [Aug-26-1999]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= PAB2410 (rpoD) DE:DNA-directed RNA polymerase, subunit D (rpoD)
(259 letters)
Database: ./suso.pep; /banques/blast2/nr.pep
598,487 sequences; 189,106,746 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
pir||E75171 DNA-directed RNA polymerase, chain D (rpod) PAB2410 ... 523 e-147
sp|O59303|RPOD_PYRHO DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gi|7... 491 e-138
gi|11499863 DNA-directed RNA polymerase, subunit D (rpoD) [Archa... 160 1e-38
sp|O26144|RPOD_METTH DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gi|7... 155 4e-37
gb|AAG19520.1| (AE005043) DNA-directed RNA polymerase II; Rpb3 [... 153 1e-36
pir||T43940 RNA-polymerase chain D [imported] - Halobacterium sa... 142 4e-33
sp|Q00813|RPOD_HALMA DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gi|3... 140 1e-32
emb|CAC12159.1| (AL445066) DNA-dependent RNA polymerase, subunit... 136 3e-31
sp|Q57648|RPOD_METJA DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gi|2... 125 4e-28
gb|AAK40433.1| DNA-directed RNA polymerase, subunit D (rpoD) [Su... 125 7e-28
sp|P95989|RPOD_SULSO DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gi|7... 125 7e-28
pir||D72557 probable DNA-directed RNA polymerase subunit D APE17... 116 3e-25
emb|CAB38635.1| (AJ133650) RNA polymerase II p33 subunit [Drosop... 112 4e-24
sp|P39471|RPOD_SULAC DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gi|6... 112 5e-24
sp|Q39211|RP3A_ARATH DNA-DIRECTED RNA POLYMERASE II 36 KDA POLYP... 107 2e-22
gi|6325367 RNA polymerase III (C) subunit; Rpc40p [Saccharomyces... 106 2e-22
gi|6322168 45 kDa subunit of RNA polymerase II; Rpb3p [Saccharom... 102 6e-21
gb|AAA34889.1| (M27496) RNA polymerase II (EC 2.7.7.6) [Saccharo... 101 7e-21
gb|AAD22284.1|AC006920_8 (AC006920) DNA-directed RNA polymerase ... 101 1e-20
gi|4505943 polymerase (RNA) II (DNA directed) polypeptide C (33k... 100 2e-20
gi|11431274 polymerase (RNA) II (DNA directed) polypeptide C (33... 100 2e-20
pir||T49627 probable DNA-directed RNA polymerase [imported] - Ne... 99 6e-20
pir||T39358 DNA-directed RNA polymerase (EC 2.7.7.6) chain Rpc40... 98 1e-19
emb|CAA71570.1| (Y10542) homologous to 40kD subunit of RNA-polym... 98 1e-19
pir||S71177 DNA-directed RNA polymerase (EC 2.7.7.6) II 35.5K ch... 96 3e-19
gi|6677797 RNA polymerase II 3 [Mus musculus] >gi|2829844|sp|P97... 95 7e-19
sp|P37382|RPB3_SCHPO DNA-DIRECTED RNA POLYMERASE II 33 KD POLYPE... 92 8e-18
dbj|BAA09315.1| (D50661) RNA polymerase II subunit 3 [Schizosacc... 92 8e-18
pir||T40975 dna-directed rna polymerase ii subunit - fission yea... 92 8e-18
dbj|BAA09316.1| (D50662) RNA polymerase II subunit 3 [Schizosacc... 91 1e-17
>pir||E75171 DNA-directed RNA polymerase, chain D (rpod) PAB2410 - Pyrococcus
abyssi (strain Orsay) >gi|5457962|emb|CAB49452.1|
(AJ248284) DNA-directed RNA polymerase, subunit D (rpoD)
[Pyrococcus abyssi]
Length = 259
Score = 523 bits (1332), Expect = e-147
Identities = 259/259 (100%), Positives = 259/259 (100%)
Query: 1 MVEIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIA 60
MVEIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIA
Sbjct: 1 MVEIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIA 60
Query: 61 HRLAMIPLKTPVDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKPANPDIPI 120
HRLAMIPLKTPVDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKPANPDIPI
Sbjct: 61 HRLAMIPLKTPVDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKPANPDIPI 120
Query: 121 VKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTYYKYFTRIHISKEIEGWEKLKKLAKKRGL 180
VKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTYYKYFTRIHISKEIEGWEKLKKLAKKRGL
Sbjct: 121 VKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTYYKYFTRIHISKEIEGWEKLKKLAKKRGL 180
Query: 181 PVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYVFVVETNGELPVEEIVKIAL 240
PVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYVFVVETNGELPVEEIVKIAL
Sbjct: 181 PVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYVFVVETNGELPVEEIVKIAL 240
Query: 241 KILMRKADRFINELQGLAG 259
KILMRKADRFINELQGLAG
Sbjct: 241 KILMRKADRFINELQGLAG 259
>sp|O59303|RPOD_PYRHO DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gi|7437637|pir||E71043
probable DNA-directed RNA polymerase subunit D -
Pyrococcus horikoshii >gi|3258066|dbj|BAA30749.1|
(AP000006) 261aa long hypothetical DNA-directed RNA
polymerase subunit D [Pyrococcus horikoshii]
Length = 261
Score = 491 bits (1251), Expect = e-138
Identities = 242/259 (93%), Positives = 249/259 (95%)
Query: 1 MVEIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIA 60
MV+IKILKKT+DSITFILEGV VAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIA
Sbjct: 3 MVKIKILKKTEDSITFILEGVSVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIA 62
Query: 61 HRLAMIPLKTPVDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKPANPDIPI 120
HRLAMIPLKTP DRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKP PDIPI
Sbjct: 63 HRLAMIPLKTPTDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKPVTPDIPI 122
Query: 121 VKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTYYKYFTRIHISKEIEGWEKLKKLAKKRGL 180
VKLAKGQRLVFNA+AKLGRGKDHAKWQPGFTYYKYFTR+HISK+I GWEKL KLAKKRGL
Sbjct: 123 VKLAKGQRLVFNAYAKLGRGKDHAKWQPGFTYYKYFTRVHISKKINGWEKLAKLAKKRGL 182
Query: 181 PVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYVFVVETNGELPVEEIVKIAL 240
P KENE EVIVETIKPFYIPKEFEEYEGK IWEEIVP+TYVFVVETNGELPVEEIVKIAL
Sbjct: 183 PTKENEEEVIVETIKPFYIPKEFEEYEGKEIWEEIVPDTYVFVVETNGELPVEEIVKIAL 242
Query: 241 KILMRKADRFINELQGLAG 259
+ILMRKADRFINELQ LAG
Sbjct: 243 RILMRKADRFINELQRLAG 261
>gi|11499863 DNA-directed RNA polymerase, subunit D (rpoD) [Archaeoglobus
fulgidus] >gi|3122769|sp|O28002|RPOD_ARCFU DNA-DIRECTED
RNA POLYMERASE SUBUNIT D >gi|7434685|pir||B69535
DNA-directed RNA polymerase, subunit D (rpoD) homolog -
Archaeoglobus fulgidus >gi|2648239|gb|AAB88973.1|
(AE000947) DNA-directed RNA polymerase, subunit D (rpoD)
[Archaeoglobus fulgidus]
Length = 264
Score = 160 bits (401), Expect = 1e-38
Identities = 99/265 (37%), Positives = 149/265 (55%), Gaps = 12/265 (4%)
Query: 1 MVEIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIA 60
M EI+IL++ D I FIL+ A AN+ RR + EVP AVD V+ Y N S +DE+IA
Sbjct: 2 MPEIEILEEKDFKIKFILKNASPALANSFRRAMKAEVPAMAVDYVDIYLNSSYFYDEVIA 61
Query: 61 HRLAMIPLKTPVDRFELDA------LELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKPA 114
HRLAM+P+KT +DRF + + + ++ L EGP +VYSGD SDDPDV A
Sbjct: 62 HRLAMLPIKTYLDRFNMQSECSCGGEGCPNCQISFRLNVEGPKVVYSGDFISDDPDVVFA 121
Query: 115 NPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQP-GFTYYKYFTRIHISKEIEGWEKLKK 173
+IP+++L +GQ+L+ A A+LG G++HAK+QP YK I +++ G +
Sbjct: 122 IDNIPVLELFEGQQLMLEAVARLGTGREHAKFQPVSVCVYKIIPEIVVNENCNGCGDCIE 181
Query: 174 LAKKRGLPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYVFVVETNGELPVE 233
+ +++ ++V V+ + + E E N ++F VE G LPV
Sbjct: 182 ACPRN--VFEKDGDKVRVKNVMACSMCGECVEVCEMNAISVNETNNFLFTVEGTGALPVR 239
Query: 234 EIVKIALKILMRKAD---RFINELQ 255
E++K AL+IL KA+ + I E+Q
Sbjct: 240 EVMKKALEILRSKAEEMNKIIEEIQ 264
>sp|O26144|RPOD_METTH DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gi|7434684|pir||G69147
DNA-dependent RNA polymerase, subunit D -
Methanobacterium thermoautotrophicum (strain Delta H)
>gi|2621073|gb|AAB84545.1| (AE000796) DNA-dependent RNA
polymerase, subunit D [Methanobacterium
thermoautotrophicum]
Length = 264
Score = 155 bits (389), Expect = 4e-37
Identities = 92/265 (34%), Positives = 150/265 (55%), Gaps = 12/265 (4%)
Query: 2 VEIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAH 61
++I + +KTD + F++ GV V F NA+RR + EVP A++ V Y ND+ +FDE++AH
Sbjct: 1 MDIALKEKTDTEMVFVVSGVTVPFINAIRRICMMEVPKLAIEYVNMYRNDAKMFDEVLAH 60
Query: 62 RLAMIPLKTPVDRFEL----DALELDDY----TVTLSLEAEGPGIVYSGDLKSDDPDVKP 113
RL ++PL + E + + ++Y +V+L+L +GPG+VYSGDL S+ P VKP
Sbjct: 61 RLGLVPLAADPEFAESLKMPEECDCEEYCSECSVSLTLRKKGPGVVYSGDLVSETPAVKP 120
Query: 114 ANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQPGFT-YYKYFTRIHISKEIEGWEKLK 172
PDIP+VKL L A A+LG G++HAKW+P YKY+ RI S++ + E L+
Sbjct: 121 VYPDIPLVKLGDDDELELEAVAQLGVGREHAKWEPTTACAYKYYPRIEFSEDCD--ECLE 178
Query: 173 KL-AKKRGLPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYVFVVETNGELP 231
+ A R + +E+ V+V+ + + I ++F +ET+G +
Sbjct: 179 CIEACPRDVLGEESGKPVVVDLENCSMCKSCVRACDKRAIDVGYEEGKFIFRIETDGSVD 238
Query: 232 VEEIVKIALKILMRKADRFINELQG 256
++++ A IL KA++ I +G
Sbjct: 239 PKDVLLKACDILRDKAEQVITFCEG 263
>gb|AAG19520.1| (AE005043) DNA-directed RNA polymerase II; Rpb3 [Halobacterium sp.
NRC-1]
Length = 248
Score = 153 bits (384), Expect = 1e-36
Identities = 91/261 (34%), Positives = 145/261 (54%), Gaps = 28/261 (10%)
Query: 3 EIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHR 62
+++ + + D F++ + AFAN +RR IL +VPT ++D V F EN S +FDE + R
Sbjct: 7 DVEFVDRDDREARFVVRNITPAFANGIRRAILVDVPTLSIDTVRFVENSSVMFDEQLGLR 66
Query: 63 LAMIPLKTPVDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKPANPDIPIVK 122
L ++PL TP D +A VTL+L+ EGPG YSGDL S+DP+V+ A+ +IPI++
Sbjct: 67 LGLVPLTTPEDYAAGEA-------VTLALDVEGPGTAYSGDLVSNDPEVEAADENIPIIE 119
Query: 123 LAKGQRLVFNAFAKLGRGKDHAKWQPGFTY-YKYFTRIHISKEIEGW-----EKLKKLAK 176
L QRL A A +G G+DHAK Q G Y++ R+H+ + + + L+ + +
Sbjct: 120 LKDDQRLELEADAVMGHGRDHAKHQGGVAVGYRHLQRVHVVGDSPEYADDDPQMLRGVIE 179
Query: 177 KRG--LPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYVFVVETNGELPVEE 234
+ +P + +N++ Y GK + E V +VF VE++G +PVEE
Sbjct: 180 EDDELVPTDDFDNDLTT-------------RYPGKEVEIEDVDGAFVFHVESDGSMPVEE 226
Query: 235 IVKIALKILMRKADRFINELQ 255
+V A+ L+ +AD +Q
Sbjct: 227 LVLRAVDTLVDRADELEQAVQ 247
>pir||T43940 RNA-polymerase chain D [imported] - Halobacterium salinarum
>gi|6172230|dbj|BAA85898.1| (AB030282) RNA-polymerase D
[Halobacterium halobium]
Length = 249
Score = 142 bits (355), Expect = 4e-33
Identities = 90/266 (33%), Positives = 143/266 (52%), Gaps = 37/266 (13%)
Query: 3 EIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHR 62
+++ + + D F++ + AFAN +RR IL +VPT ++D V F EN S +FDE + R
Sbjct: 7 DVEFVDRDDREARFVVRNITPAFANGIRRAILVDVPTLSIDTVRFVENSSVMFDEQLGLR 66
Query: 63 LAMIPLKTPVDRFELDALELDDYT---VTLSLEAEGPGIVYSGDLKSDDPDVKPANPDIP 119
L ++PL TP +DY VTL+L+ EGPG Y GDL S+DP+V+ A+ +IP
Sbjct: 67 LGLVPLTTP-----------EDYPAGEVTLALDVEGPGTAYPGDLVSNDPEVEAADENIP 115
Query: 120 IVKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTY-YKY--FTRIHISKEIEGW-----EKL 171
I++L QRL A A G G+DHAK Q G Y++ R+H+ + + + L
Sbjct: 116 IIELKDDQRLELEADAVDGHGRDHAKHQGGVAVGYRHLQLQRVHVVGDSPEYADDDPQML 175
Query: 172 KKLAKKRG--LPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYVFVVETNGE 229
+ + ++ +P + +N++ Y GK + E V +VF VE++G
Sbjct: 176 RGVIEEDDELVPTDDFDNDLTT-------------RYPGKEVEIEDVDGAFVFHVESDGS 222
Query: 230 LPVEEIVKIALKILMRKADRFINELQ 255
+PVEE+V A+ L+ +AD +Q
Sbjct: 223 MPVEELVLRAVDTLVDRADELEQAVQ 248
>sp|Q00813|RPOD_HALMA DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gi|322340|pir||D44126
DNA-directed RNA polymerase II chain RpB3 homolog
Rp-alpha - Haloarcula marismortui
>gi|148773|gb|AAA73212.1| (M87833) ribosomal protein
HmaRp-alpha subunit [Haloarcula marismortui]
Length = 259
Score = 140 bits (350), Expect = 1e-32
Identities = 86/259 (33%), Positives = 137/259 (52%), Gaps = 12/259 (4%)
Query: 3 EIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHR 62
E++ +++ + ++ G+ AFAN +RR ++ +VPTF++D V EN S +F+E I R
Sbjct: 6 EVEFVERGEREARILVRGITPAFANGIRRAMVADVPTFSIDTVRVIENTSVMFNEQIGLR 65
Query: 63 LAMIPLKTPVDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKPANPDIPIVK 122
L ++PL T +D FE+ VTLSL +GP YS DL S DP V+ A+ +IPI+
Sbjct: 66 LGLVPLTTDLDDFEIGD------EVTLSLSVDGPSTAYSSDLVSSDPMVEAADDNIPIID 119
Query: 123 LAKGQRLVFNAFAKLGRGKDHAKWQPGFTY-YKYFTRIHISKEIEGWEKLKKLAKKRGLP 181
L +GQRL A A L G++HAK Q G Y++ ++ + ++ +E + +
Sbjct: 120 LKEGQRLEVEADAVLDTGREHAKHQGGVAVGYRHLQQVEVVGDLGEFEDDDPNILRGVIE 179
Query: 182 VKENENEVIVETIKPFYIPKEFE-----EYEGKGIWEEIVPNTYVFVVETNGELPVEEIV 236
+ E+ T EF+ Y GK + VPN +VF VET+G EE+V
Sbjct: 180 EQAAEHAAGDATNGELVATDEFDNDLRNRYPGKDVEVSDVPNAFVFHVETDGSFTTEELV 239
Query: 237 KIALKILMRKADRFINELQ 255
A++ L +A + +Q
Sbjct: 240 LRAVETLRDRATELKDAVQ 258
>emb|CAC12159.1| (AL445066) DNA-dependent RNA polymerase, subunit D related protein
[Thermoplasma acidophilum]
Length = 271
Score = 136 bits (339), Expect = 3e-31
Identities = 91/273 (33%), Positives = 140/273 (50%), Gaps = 24/273 (8%)
Query: 2 VEIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEF------------YE 49
+++KI K +D I F ++G+ + ANALRRT++ ++P A++ V F Y+
Sbjct: 1 MDVKIFKLSDKYIRFEIDGITPSQANALRRTLINDIPKLAIENVTFHHGEIRDSEGNVYD 60
Query: 50 NDSALFDEIIAHRLAMIPLKTPV-----DRFELDALELDDYTVTLSLEAEGPGIVYSGDL 104
+ LFDE++AHRL +IPLKT + D+ TVT S+ GP V+S DL
Sbjct: 61 SSLPLFDEMVAHRLGLIPLKTDLTMNFRDQCSCGGKGCSLCTVTYSINKLGPSTVFSSDL 120
Query: 105 KS-DDPDVKPANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQ-PGFTYYKYFTRIHIS 162
++ PD+ P + +IPIVKL Q ++ A A LG K+HAKWQ YKY H+S
Sbjct: 121 QAVSHPDLIPVDGEIPIVKLGPKQAILITAEAILGTAKEHAKWQVTSGVSYKYHREFHVS 180
Query: 163 -KEIEGWEKLKKLAKKRGLPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYV 221
K+ E W+KLK K + E + E++ E +G + E+ + ++
Sbjct: 181 KKDFEDWQKLKGACPKS--VMSETDTEIVFTDDFGCNDLNVLFESDGVNMIED--DSRFI 236
Query: 222 FVVETNGELPVEEIVKIALKILMRKADRFINEL 254
F ET+G L +E + AL L + D + L
Sbjct: 237 FQFETDGSLTAKETLLYALNRLKDRWDILVESL 269
>sp|Q57648|RPOD_METJA DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gi|2127867|pir||A64324
DNA-directed RNA polymerase (EC 2.7.7.6) subunit D -
Methanococcus jannaschii >gi|1590937|gb|AAB98172.1|
(U67475) DNA-directed RNA polymerase, subunit D (rpoD)
[Methanococcus jannaschii]
Length = 191
Score = 125 bits (312), Expect = 4e-28
Identities = 89/257 (34%), Positives = 127/257 (48%), Gaps = 72/257 (28%)
Query: 1 MVEIKILKKTDDSITFILE-GVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEII 59
M+ IK +KT FI ++F+NA+RR ++ EVPTFA+++V YEN S++ DEI+
Sbjct: 1 MITIKEKRKTRIGEEFIFSLKAPISFSNAIRRIMISEVPTFAIEDVYIYENSSSMDDEIL 60
Query: 60 AHRLAMIPLK-TPVDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKPANPDI 118
AHRL +IP+K P+ L++ +T +LE EGP VYS DLKS++ +V A +I
Sbjct: 61 AHRLGLIPIKGKPL---------LENEVITFTLEKEGPCTVYSSDLKSENGEV--AFKNI 109
Query: 119 PIVKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTYYKYFTRIHISKEIEGWEKLKKLAKKR 178
PIVKL KGQR+ A G GK HAKWQP YK
Sbjct: 110 PIVKLGKGQRIQIECEAIPGIGKVHAKWQPCNAVYK------------------------ 145
Query: 179 GLPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYVFVVETNGELPVEEIVKI 238
+ ++E E VET G++ EEI++
Sbjct: 146 --QIADDEVEFFVETF---------------------------------GQMEAEEILEE 170
Query: 239 ALKILMRKADRFINELQ 255
A+KIL KA+ F+ +L+
Sbjct: 171 AVKILKNKAESFLQQLE 187
>gb|AAK40433.1| DNA-directed RNA polymerase, subunit D (rpoD) [Sulfolobus
solfataricus]
Length = 265
Score = 125 bits (310), Expect = 7e-28
Identities = 87/266 (32%), Positives = 139/266 (51%), Gaps = 19/266 (7%)
Query: 2 VEIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAH 61
+ I +L K D I + EG + F NA+RR + VP AVD+V F EN+S L+DEI+AH
Sbjct: 1 MSINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAH 60
Query: 62 RLAMIPLKT----PVDRFELDALELDD-----YTVTLSLEAEGPG---IVYSGDLKSDDP 109
RLA+IP + R+ + +E + YT + +EAE P ++YS D+KS+DP
Sbjct: 61 RLALIPFMSEEALDTYRWPEECIECTENCEKCYT-KIYIEAEAPNEPRMIYSKDIKSEDP 119
Query: 110 DVKPANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQP-GFTYYKYFTRIHISKEIEGW 168
V P + DIPIV L Q++ A +LG GK+HAK+ P + +Y+ ++ I +
Sbjct: 120 SVVPISGDIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLSVVRYYPKVEI---LANC 176
Query: 169 EKLKKLAKKRGLPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYVFVVETNG 228
EK + + +K + ++ V+ + +E Y I V + Y+ +E+ G
Sbjct: 177 EKAVNVCPEGVFELK--DGKLSVKNELSCTLCEECLRYCNGSIRISFVEDKYILEIESVG 234
Query: 229 ELPVEEIVKIALKILMRKADRFINEL 254
L E I+ A K ++RK + +L
Sbjct: 235 SLKPERILLEAGKSIIRKIEELEKKL 260
>sp|P95989|RPOD_SULSO DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gi|7434682|pir||S75417
probable DNA-directed RNA polymerase (EC 2.7.7.6) chain
D - Sulfolobus solfataricus >gi|1707823|emb|CAA69531.1|
(Y08257) DNA-directed RNA polymerase subunit D
[Sulfolobus solfataricus]
Length = 265
Score = 125 bits (310), Expect = 7e-28
Identities = 87/266 (32%), Positives = 139/266 (51%), Gaps = 19/266 (7%)
Query: 2 VEIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAH 61
+ I +L K D I + EG + F NA+RR + VP AVD+V F EN+S L+DEI+AH
Sbjct: 1 MSINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAH 60
Query: 62 RLAMIPLKT----PVDRFELDALELDD-----YTVTLSLEAEGPG---IVYSGDLKSDDP 109
RLA+IP + R+ + +E + YT + +EAE P ++YS D+KS+DP
Sbjct: 61 RLALIPFMSEEALDTYRWPEECIECTENCEKCYT-KIYIEAEAPNEPRMIYSKDIKSEDP 119
Query: 110 DVKPANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQP-GFTYYKYFTRIHISKEIEGW 168
V P + DIPIV L Q++ A +LG GK+HAK+ P + +Y+ ++ I +
Sbjct: 120 SVVPISGDIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLSVVRYYPKVEI---LANC 176
Query: 169 EKLKKLAKKRGLPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYVFVVETNG 228
EK + + +K + ++ V+ + +E Y I V + Y+ +E+ G
Sbjct: 177 EKAVNVCPEGVFELK--DGKLSVKNELSCTLCEECLRYCNGSIRISFVEDKYILEIESVG 234
Query: 229 ELPVEEIVKIALKILMRKADRFINEL 254
L E I+ A K ++RK + +L
Sbjct: 235 SLKPERILLEAGKSIIRKIEELEKKL 260
>pir||D72557 probable DNA-directed RNA polymerase subunit D APE1744 - Aeropyrum
pernix (strain K1) >gi|5105432|dbj|BAA80745.1|
(AP000062) 290aa long hypothetical DNA-directed RNA
polymerase subunit D [Aeropyrum pernix]
Length = 290
Score = 116 bits (288), Expect = 3e-25
Identities = 80/259 (30%), Positives = 134/259 (50%), Gaps = 19/259 (7%)
Query: 18 LEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRLAMIPLKT--PVDRF 75
+ G V F NA+RRT+L +VPT AVD ++N +A++DE++AHRL ++ L + V+++
Sbjct: 27 IRGYPVVFVNAIRRTVLSDVPTMAVDYAYIFDNTTAVYDEMVAHRLGLVVLDSNEAVEKY 86
Query: 76 ----ELDALEL--DDYTVTLSLEAEGPG------IVYSGDLKSDDPDVKPANPDIPIVKL 123
E E +D V +SLEAE + +GDL DP VKP P+ P++ +
Sbjct: 87 RRPEECAGKEPSEEDCFVEVSLEAEVDAEGETGRYITAGDLSISDPQVKPVYPETPLIYV 146
Query: 124 AKGQRLVFNAFAKLGRGKDHAKWQPGFTYYKYFTRIHISKEIEGWEKLKKLAKKRGLPVK 183
A GQR+ AFA+LGRGK+H KW P +T I I + ++ + V+
Sbjct: 147 APGQRIHVQAFARLGRGKEHTKWSPASLSVLRYTPILIYDSSKAGDECLECLSAYPQVVE 206
Query: 184 E----NENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYV-FVVETNGELPVEEIVKI 238
+ +++E ++ + E +G E ++ + VE+ G L E+IV++
Sbjct: 207 ALKSGGKGSLVLEGLRRTSGLRYCAETACRGAVEVRYDSSNLDLEVESTGALRPEKIVEL 266
Query: 239 ALKILMRKADRFINELQGL 257
A++ L K RF ++ +
Sbjct: 267 AIRELEEKVKRFAEAVESV 285
>emb|CAB38635.1| (AJ133650) RNA polymerase II p33 subunit [Drosophila melanogaster]
>gi|7287788|gb|AAF44826.1|AE003406_31 (AE003416)
symbol=RpII33; synonym=BG:DS00941.10;
cDNA=method:''sim4'', score:''1000.0'', desc:''LD09978
LD Drosophila melanogaster embryo BlueScript Drosophila
melanogaster cDNA clone LD09978 full-length mRNA
sequence from BDGP''; match=method:''BLASTX>
>gi|7298103|gb|AAF53342.1| (AE003641) RpII33 gene
product [Drosophila melanogaster]
Length = 275
Score = 112 bits (278), Expect = 4e-24
Identities = 85/282 (30%), Positives = 132/282 (46%), Gaps = 57/282 (20%)
Query: 4 IKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRL 63
++I + TDD++ F+LE +++ AN+LRR + E PT A+D V+ N + L DE +AHR+
Sbjct: 9 VQITELTDDNVKFVLEDTELSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFLAHRI 68
Query: 64 AMIPLKTP--VDRFEL--DALELD-------DYTVTLSLEAEGPGIVYSGDLKSDDPDVK 112
+IPL + V+R + D + LD ++T+ + E V + DLKS + V
Sbjct: 69 GLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTADLKSSNAKVL 128
Query: 113 P---------------ANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQPG----FTYY 153
P +N +I I+KL KGQ L A+AK G GK+HAKW P F Y
Sbjct: 129 PVTSRNQGEEDNEYGESNDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPTAGVCFEYD 188
Query: 154 KYFTRIH-ISKEIEGWEKLKKLAKKRGLPVKENENEVIVETIKPFYIPKEFEEYEGKGIW 212
+ H + + + W K + + E ++YE W
Sbjct: 189 PDNSMRHTLYPKPDEWPKSE-------------------------HTELEDDQYEAPYNW 223
Query: 213 EEIVPNTYVFVVETNGELPVEEIVKIALKILMRKADRFINEL 254
E PN + F VE+ G L E IV + +++L K +L
Sbjct: 224 -EAKPNKFFFNVESAGALKPENIVVMGVQVLKNKLSNLQTQL 264
>sp|P39471|RPOD_SULAC DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gi|629417|pir||S47023
DNA-directed RNA polymerase (EC 2.7.7.6) chain D -
Sulfolobus acidocaldarius >gi|517290|emb|CAA56480.1|
(X80194) RNA polymerase subunit D [Sulfolobus
acidocaldarius]
Length = 264
Score = 112 bits (277), Expect = 5e-24
Identities = 81/264 (30%), Positives = 138/264 (51%), Gaps = 17/264 (6%)
Query: 4 IKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRL 63
I ++++ + +LE + F N++RR + VP AVDEV F EN+S L+DEI+AHRL
Sbjct: 3 ISLIERNGLRLRLVLENYPLEFVNSIRRASILYVPVMAVDEVYFIENNSPLYDEILAHRL 62
Query: 64 AMIPL---------KTPVDRFELDALELDDYT-VTLSLEAEGPGI-VYSGDLKSDDPDVK 112
A++P + P + E Y V L +EA+ + +YS DLKS+D +
Sbjct: 63 ALVPFVSDEALEHYRPPEECAECKENCDGCYNRVYLDVEAKDQSLMIYSRDLKSEDQMIT 122
Query: 113 PANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQP-GFTYYKYFTRIHISKEIEGWEKL 171
P + IPIV L Q++ A +LG GK+H K+ P + +Y+ ++ + + EK
Sbjct: 123 PVSGAIPIVLLGSKQKISLEARLRLGYGKEHIKYSPVSVSIVRYYPKVTV---LGNCEKA 179
Query: 172 KKLAKKRGLPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYVFVVETNGELP 231
++ + G+ EN N+++V+ + +E +Y + E V N ++ +E+ G L
Sbjct: 180 VEVCPE-GVFAMEN-NKLVVKNELSCILCEECLKYCAGSVSIESVENKFILEIESVGSLK 237
Query: 232 VEEIVKIALKILMRKADRFINELQ 255
E I+ A K L+RK ++L+
Sbjct: 238 PERILIEASKSLLRKLSELKSKLE 261
>sp|Q39211|RP3A_ARATH DNA-DIRECTED RNA POLYMERASE II 36 KDA POLYPEPTIDE A (RNA POLYMERASE
II SUBUNIT 3) >gi|2129726|pir||S71176 DNA-directed RNA
polymerase (EC 2.7.7.6) II 35.5K chain A - Arabidopsis
thaliana >gi|514318|gb|AAB03741.1| (L34770) RNA
polymerase II third largest subunit [Arabidopsis
thaliana] >gi|4544370|gb|AAD22281.1|AC006920_5
(AC006920) DNA-directed RNA polymerase II, third largest
subunit [Arabidopsis thaliana]
Length = 319
Score = 107 bits (264), Expect = 2e-22
Identities = 93/284 (32%), Positives = 133/284 (46%), Gaps = 38/284 (13%)
Query: 3 EIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHR 62
+IKI + DD F L DV+ ANALRR ++ EVPT A+D VE N S L DE IAHR
Sbjct: 11 KIKIRELKDDYAKFELRETDVSMANALRRVMISEVPTVAIDLVEIEVNSSVLNDEFIAHR 70
Query: 63 LAMIPL---KTPVDRFELDALELD----------DYTVTLSLEAEGPGIVYSGDLKSDDP 109
L +IPL + RF D D ++ ++ + V S DL S DP
Sbjct: 71 LGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFRLSSKCVTDQTLDVTSRDLYSADP 130
Query: 110 DVKPA-------------NPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTY-YKY 155
V P + I IVKL +GQ L A A+ G GKDHAKW P T + Y
Sbjct: 131 TVTPVDFTIDSSVSDSSEHKGIIIVKLRRGQELKLRAIARKGIGKDHAKWSPAATVTFMY 190
Query: 156 FTRIHISKE-IEGWEKLKKLAKKRGLPVK-----ENENEVIVETIKPFYIPKEF---EEY 206
I I+++ ++ +K+ P K +V+V + + +E E
Sbjct: 191 EPDIIINEDMMDTLSDEEKIDLIESSPTKVFGMDPVTRQVVVVDPEAYTYDEEVIKKAEA 250
Query: 207 EGKGIWEEIVP--NTYVFVVETNGELPVEEIVKIALKILMRKAD 248
GK EI P ++++F VE+ G + ++V A+ +L +K D
Sbjct: 251 MGKPGLIEISPKDDSFIFTVESTGAVKASQLVLNAIDLLKQKLD 294
>gi|6325367 RNA polymerase III (C) subunit; Rpc40p [Saccharomyces cerevisiae]
>gi|133369|sp|P07703|RPC5_YEAST DNA-DIRECTED RNA
POLYMERASES I AND III 40 KD POLYPEPTIDE (AC40)
>gi|82995|pir||A25968 DNA-directed RNA polymerase (EC
2.7.7.6) 40K chain - yeast (Saccharomyces cerevisiae)
>gi|172474|gb|AAA34999.1| (M15499) RNA polymerase C-40
[Saccharomyces cerevisiae] >gi|914981|gb|AAB68080.1|
(U32445) RNA Polymerases I and III 40 kD subunit (Swiss
Prot. accession number P07703) [Saccharomyces
cerevisiae]
Length = 335
Score = 106 bits (263), Expect = 2e-22
Identities = 87/291 (29%), Positives = 134/291 (45%), Gaps = 42/291 (14%)
Query: 3 EIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHR 62
E+ I F L +D + ANA RR ++ EVP+ A + V F+ N S + DE++AHR
Sbjct: 41 EVNISSLDAREANFDLINIDTSIANAFRRIMISEVPSVAAEYVYFFNNTSVIQDEVLAHR 100
Query: 63 LAMIPLKTPVDRFEL-------DALELDDYTVTLSL------------------EAEGPG 97
+ ++PLK D D D+ T+ LSL E
Sbjct: 101 IGLVPLKVDPDMLTWVDSNLPDDEKFTDENTIVLSLNVKCTRNPDAPKGSTDPKELYNNA 160
Query: 98 IVYSGDLKSD----------DPDVKPANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQ 147
VY+ DLK + D V PA+PDI + KL GQ + A LG G DHAK+
Sbjct: 161 HVYARDLKFEPQGRQSTTFADCPVVPADPDILLAKLRPGQEISLKAHCILGIGGDHAKFS 220
Query: 148 PGFT-YYKYFTRIHISKEIEG--WEKLKKLAKKRGLPVKENENEVIVETIKPFYIPKE-- 202
P T Y+ +I+I + I+G + +K + + E +E V+ + + +E
Sbjct: 221 PVSTASYRLLPQINILQPIKGESARRFQKCFPPGVIGIDEGSDEAYVKDARKDTVSREVL 280
Query: 203 -FEEYEGKGIWEEIVPNTYVFVVETNGELPVEEIVKIALKILMRKADRFIN 252
+EE+ K + V N ++F VE+ G + EEI +++IL KA+ N
Sbjct: 281 RYEEFADK-VKLGRVRNHFIFNVESAGAMTPEEIFFKSVRILKNKAEYLKN 330
>gi|6322168 45 kDa subunit of RNA polymerase II; Rpb3p [Saccharomyces
cerevisiae] >gi|730603|sp|P16370|RPB3_YEAST DNA-DIRECTED
RNA POLYMERASE II 45 KD POLYPEPTIDE (B44.5)
>gi|1077100|pir||S49961 DNA-directed RNA polymerase (EC
2.7.7.6) II chain RPB3 [validated] - yeast
(Saccharomyces cerevisiae) >gi|599978|emb|CAA86971.1|
(Z46881) RNA polymerase II [Saccharomyces cerevisiae]
Length = 318
Score = 102 bits (251), Expect = 6e-21
Identities = 85/269 (31%), Positives = 125/269 (45%), Gaps = 46/269 (17%)
Query: 3 EIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHR 62
++KI + + D++ FIL VD+A AN+LRR ++ E+PT A+D VE N + L DE IAHR
Sbjct: 7 QVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHR 66
Query: 63 LAMIPLKTPVDRFELDALE----------LDDYTVTLSL----EAEGPGIVYSGDL---- 104
L +IPL++ +++ LE D +V L+L E+E VYS DL
Sbjct: 67 LGLIPLQS----MDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS 122
Query: 105 -----KSDDPDVKPANPD-IPIVKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTYYKYFTR 158
P ++ + + I KL KGQ L AK G K+HAKW P
Sbjct: 123 NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAA------- 175
Query: 159 IHISKEIEGWEKLKKLAK-KRGLPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVP 217
I E + W KLK KE E P P E + ++ K
Sbjct: 176 --IEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDP---PNEGDPFDYKA-----QA 225
Query: 218 NTYVFVVETNGELPVEEIVKIALKILMRK 246
+T+ VE+ G +PV+++V + L +K
Sbjct: 226 DTFYMNVESVGSIPVDQVVVRGIDTLQKK 254
>gb|AAA34889.1| (M27496) RNA polymerase II (EC 2.7.7.6) [Saccharomyces cerevisiae]
Length = 318
Score = 101 bits (250), Expect = 7e-21
Identities = 85/269 (31%), Positives = 125/269 (45%), Gaps = 46/269 (17%)
Query: 3 EIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHR 62
++KI + + D++ FIL VD+A AN+LRR ++ E+PT A+D VE N + L DE IAHR
Sbjct: 7 QVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHR 66
Query: 63 LAMIPLKTPVDRFELDALE----------LDDYTVTLSL----EAEGPGIVYSGDL---- 104
L +IPL++ +++ LE D +V L+L E+E VYS DL
Sbjct: 67 LGLIPLQS----MDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS 122
Query: 105 -----KSDDPDVKPANPD-IPIVKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTYYKYFTR 158
P ++ + + I KL KGQ L AK G K+HAKW P
Sbjct: 123 NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPA--------- 173
Query: 159 IHISKEIEGWEKLKKLAK-KRGLPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVP 217
I E + W KLK KE E P P E + ++ K
Sbjct: 174 AGIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDP---PNEGDPFDYKA-----QA 225
Query: 218 NTYVFVVETNGELPVEEIVKIALKILMRK 246
+T+ VE+ G +PV+++V + L +K
Sbjct: 226 DTFYMNVESVGSIPVDQVVVRGIDTLQKK 254
>gb|AAD22284.1|AC006920_8 (AC006920) DNA-directed RNA polymerase II, third largest subunit
[Arabidopsis thaliana]
Length = 319
Score = 101 bits (249), Expect = 1e-20
Identities = 91/283 (32%), Positives = 131/283 (46%), Gaps = 38/283 (13%)
Query: 4 IKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRL 63
+KI + DD F L DV+ ANALRR ++ EVPT A+ V+ N S L DE IA RL
Sbjct: 12 VKIRELKDDYAKFELRETDVSMANALRRVMISEVPTMAIHLVKIEVNSSVLNDEFIAQRL 71
Query: 64 AMIPL---KTPVDRFELDALELD----------DYTVTLSLEAEGPGIVYSGDLKSDDPD 110
++IPL + RF D + + ++ ++ + V S DL S DP
Sbjct: 72 SLIPLTSERAMSMRFCQDCEDCNGDEHCEFCSVEFPLSAKCVTDQTLDVTSRDLYSADPT 131
Query: 111 VKPA-------------NPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTY-YKYF 156
V P + I I KL +GQ L A A+ G GKDHAKW P T Y Y
Sbjct: 132 VTPVDFTSNSSTSDSSEHKGIIIAKLRRGQELKLKALARKGIGKDHAKWSPAATVTYMYE 191
Query: 157 TRIHISKEI------EGWEKLKKLAKKRGLPVKENENEVIVETIKPFYIPKEF---EEYE 207
I I++E+ E L + + + + +V+V + + +E E
Sbjct: 192 PDIIINEEMMNTLTDEEKIDLIESSPTKVFGIDPVTGQVVVVDPEAYTYDEEVIKKAEAM 251
Query: 208 GKGIWEEIVP--NTYVFVVETNGELPVEEIVKIALKILMRKAD 248
GK EI P +++VF VE+ G L ++V A+ IL +K D
Sbjct: 252 GKPGLIEIHPKHDSFVFTVESTGALKASQLVLNAIDILKQKLD 294
>gi|4505943 polymerase (RNA) II (DNA directed) polypeptide C (33kD) [Homo
sapiens] >gi|105877|pir||A36264 DNA-directed RNA
polymerase (EC 2.7.7.6) II 33K chain - human
>gi|337497|gb|AAA36586.1| (J05448) RNA polymerase
subunit hRPB 33 [Homo sapiens]
>gi|2920709|emb|CAA11842.1| (AJ224143) RNA polymerase II
subunit [Homo sapiens] >gi|2920711|emb|CAA11843.1|
(AJ224144) RNA polymerase subunit [Homo sapiens]
Length = 275
Score = 100 bits (246), Expect = 2e-20
Identities = 63/170 (37%), Positives = 90/170 (52%), Gaps = 25/170 (14%)
Query: 4 IKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRL 63
++I + TD+++ FI+E D+A AN++RR + EVP A+D V+ N S L DE IAHRL
Sbjct: 9 VRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRL 68
Query: 64 AMIPLKTP--VDR-------------------FELDALELDDYT---VTLSLEAEGPGIV 99
+IPL + VD+ F LD +D T + L + P ++
Sbjct: 69 GLIPLISDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVI 128
Query: 100 -YSGDLKSDDPDVKPANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQP 148
+ + +DP+ DI IVKL KGQ L A+AK G GK+HAKW P
Sbjct: 129 PVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP 178
>gi|11431274 polymerase (RNA) II (DNA directed) polypeptide C (33kD) [Homo
sapiens] >gi|3915850|sp|P19387|RPB3_HUMAN DNA-DIRECTED
RNA POLYMERASE II 33 KDA POLYPEPTIDE (RPB3) (RPB33)
(RPB31) >gi|2266931|gb|AAC14355.1| (AF008443) RNA
polymerase II subunit hRPB33 [Homo sapiens]
>gi|3252823|gb|AAC24309.1| (AC004382) RNA polymerase II
subunit hRPB33 [Homo sapiens]
Length = 275
Score = 100 bits (246), Expect = 2e-20
Identities = 63/170 (37%), Positives = 90/170 (52%), Gaps = 25/170 (14%)
Query: 4 IKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRL 63
++I + TD+++ FI+E D+A AN++RR + EVP A+D V+ N S L DE IAHRL
Sbjct: 9 VRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRL 68
Query: 64 AMIPLKTP--VDR-------------------FELDALELDDYT---VTLSLEAEGPGIV 99
+IPL + VD+ F LD +D T + L + P ++
Sbjct: 69 GLIPLISDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVI 128
Query: 100 -YSGDLKSDDPDVKPANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQP 148
+ + +DP+ DI IVKL KGQ L A+AK G GK+HAKW P
Sbjct: 129 PVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP 178
>pir||T49627 probable DNA-directed RNA polymerase [imported] - Neurospora crassa
>gi|7801032|emb|CAB91428.1| (AL355932) probable
DNA-directed RNA polymerase [Neurospora crassa]
Length = 337
Score = 98.7 bits (242), Expect = 6e-20
Identities = 84/275 (30%), Positives = 127/275 (45%), Gaps = 44/275 (16%)
Query: 4 IKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRL 63
+KI + + + F L +++FAN+LRR +L E+PT A+D VE N S L DE IAHRL
Sbjct: 18 VKISQADNTRVKFELSNTELSFANSLRRVMLAEIPTIAIDLVEIEANSSVLADEFIAHRL 77
Query: 64 AMIPLKTPVDRFELDA--LELDDY----TVTLSLEAEGPG----------IVYSGDLKSD 107
+IPL L + + D+Y +VTL+L A+ G +V GD +
Sbjct: 78 GLIPLNAEGIEQLLYSRDCDCDEYCEHCSVTLNLHAKCTGDDIMQVCARDLVPVGDRVNQ 137
Query: 108 ---DPDVKPANPDIP-IVKLAKGQRLVFNAFAKLGRGKDHAKWQP----GFTYYKYFTRI 159
P + P I+KL GQ + AK G K+H+KW P GF Y + ++
Sbjct: 138 VLGSPIINDPEGQGPLILKLRHGQEIKLQCIAKKGIAKEHSKWAPSAAIGFEYDPH-NKL 196
Query: 160 HISKEIEGWEKLKKLAKKRGLPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNT 219
H ++ W + K+ P E Y E EG+ + VP
Sbjct: 197 H---HLDLWYEQD---PKKEWPPSE-------------YADWEEPPQEGEPFDYDAVPQR 237
Query: 220 YVFVVETNGELPVEEIVKIALKILMRKADRFINEL 254
+ + VET G +P + IV +K++ +K I+EL
Sbjct: 238 FYYNVETAGPIPPDAIVTEGIKVIQQKLAGLIHEL 272
>pir||T39358 DNA-directed RNA polymerase (EC 2.7.7.6) chain Rpc40 [validated] -
fission yeast (Schizosaccharomyces pombe)
>gi|4490662|emb|CAB38687.1| (AL035675) dna-directed rna
polymerases i and iii polypeptide. [Schizosaccharomyces
pombe] >gi|4760696|dbj|BAA77385.1| (AB021859) RPA42
[Schizosaccharomyces pombe]
>gi|5531859|gb|AAD44503.1|AF082512_1 (AF082512) RNA
polymerase subunit Rpc40 [Schizosaccharomyces pombe]
Length = 348
Score = 97.9 bits (240), Expect = 1e-19
Identities = 81/302 (26%), Positives = 139/302 (45%), Gaps = 46/302 (15%)
Query: 2 VEIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAH 61
+++ I +++ F + G+D + ANA RR ++ E+PT A + V N S + DE+++H
Sbjct: 46 LKVSITSLDQETMVFEISGIDASIANAFRRILIAEIPTLAFEFVYIINNTSIIQDEVLSH 105
Query: 62 RLAMIPLKTPVDRFE--------LDALELDDYTVTLSL------------EAEGP----- 96
R+ ++P+ D F+ +A D TV SL + + P
Sbjct: 106 RIGLVPISADPDMFKWFQHPLPGQEATHTDYDTVVFSLNKKCEFNKNAATDEKDPKRLYV 165
Query: 97 -GIVYSGDL----------KSDDPDVKPANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAK 145
VYSGDL + D ++ NPDI + KL GQ + A A LG G+DHAK
Sbjct: 166 NSEVYSGDLIWKPQGRQEERFADNPIRVVNPDIVVAKLRPGQEIDLEAHAILGIGQDHAK 225
Query: 146 WQPGFT-YYKYFTRIHISKEIEGWE--KLKKLAKKRGLPVKE---NENEVIVETIKPFYI 199
+ P T Y+ IHI IEG + K +K K + ++E + + V ++ +
Sbjct: 226 FSPVATASYRLLPTIHILSPIEGEDAVKFQKCFPKGVIELEEGPDGKKQARVADVRKDTV 285
Query: 200 PKE---FEEYEGKGIWEEIVPNTYVFVVETNGELPVEEIVKIALKILMRKADRFINELQG 256
+E E+ K + V + Y+F VE+ G + + + ++ +L K + LQ
Sbjct: 286 SRECLRHPEFADK-VQLGRVRDHYLFSVESTGIMKPDVLFIKSIAVLKSKCLAVKSSLQN 344
Query: 257 LA 258
++
Sbjct: 345 IS 346
>emb|CAA71570.1| (Y10542) homologous to 40kD subunit of RNA-polymerase I and III
[Cricetulus griseus]
Length = 347
Score = 97.5 bits (239), Expect = 1e-19
Identities = 81/301 (26%), Positives = 138/301 (44%), Gaps = 46/301 (15%)
Query: 2 VEIKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAH 61
+++ I +++ F + G+D + ANA RR ++ E+PT A + V N S + DE+++H
Sbjct: 45 LKVSITSLDQETMVFEISGIDASIANAFRRILIAEIPTLAFEFVYIINNTSIIQDEVLSH 104
Query: 62 RLAMIPLKTPVDRFE--------LDALELDDYTVTLSL------------EAEGP----- 96
R+ ++P+ D F+ +A D TV SL + + P
Sbjct: 105 RIGLVPISADPDMFKWFQHPLPGQEATHTDYDTVVFSLNKKCEFNKNAATDEKDPKRLYV 164
Query: 97 -GIVYSGDL----------KSDDPDVKPANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAK 145
VYSGDL + D ++ NPDI + KL GQ + A A LG G+DHAK
Sbjct: 165 NSEVYSGDLIWKPQGRQEERFADNPIRVVNPDIVVAKLRPGQEIDLEAHAILGIGQDHAK 224
Query: 146 WQPGFT-YYKYFTRIHISKEIEGWE--KLKKLAKKRGLPVKE---NENEVIVETIKPFYI 199
+ P T Y+ IHI IEG + K +K K + ++E + + V ++ +
Sbjct: 225 FSPVATASYRLLPTIHILSPIEGEDAVKFQKCFPKGVIELEEGPDGKKQARVADVRKDTV 284
Query: 200 PKE---FEEYEGKGIWEEIVPNTYVFVVETNGELPVEEIVKIALKILMRKADRFINELQG 256
+E E+ K + V + Y+F VE+ G + + + ++ +L K + LQ
Sbjct: 285 SRECLRHPEFADK-VQLGRVRDHYLFSVESTGIMKPDVLFIKSIAVLKSKCLAVKSSLQN 343
Query: 257 L 257
+
Sbjct: 344 I 344
>pir||S71177 DNA-directed RNA polymerase (EC 2.7.7.6) II 35.5K chain B -
Arabidopsis thaliana >gi|514320|gb|AAB03740.1| (L34771)
RNA polymerase II third largest subunit [Arabidopsis
thaliana]
Length = 319
Score = 96.3 bits (236), Expect = 3e-19
Identities = 89/283 (31%), Positives = 129/283 (45%), Gaps = 38/283 (13%)
Query: 4 IKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRL 63
+KI + DD F L DV+ ANALRR ++ EVPT A+ V+ N S L DE IA RL
Sbjct: 12 VKIRELKDDYAKFELRETDVSMANALRRVMISEVPTMAIHLVKIEVNSSVLNDEFIAQRL 71
Query: 64 AMIPL---KTPVDRFELDALELD----------DYTVTLSLEAEGPGIVYSGDLKSDDPD 110
++IPL + RF D + + ++ ++ + V S DL S DP
Sbjct: 72 SLIPLTSERAMSMRFCQDCEDCNGDEHCEFCSVEFPLSAKCVTDQTLDVTSRDLYSADPT 131
Query: 111 VKPA-------------NPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTY-YKYF 156
V P + I I KL +GQ L A A+ G GKDHAKW P T Y Y
Sbjct: 132 VTPVDFTSNSSTSDSSEHKGIIIAKLRRGQELKLKALARKGIGKDHAKWSPAATVTYMYE 191
Query: 157 TRIHISKEI------EGWEKLKKLAKKRGLPVKENENEVIVETIKPFYIPKEF---EEYE 207
I I++E+ E L + + + + +V+V + + +E E
Sbjct: 192 PDIIINEEMMNTLTDEEKIDLIESSPTKVFGIDPVTGQVVVVDPEAYTYDEEVIKKAEAM 251
Query: 208 GKGIWEEIVP--NTYVFVVETNGELPVEEIVKIALKILMRKAD 248
GK EI P +++V V + G L ++V A+ IL +K D
Sbjct: 252 GKPGLIEIHPKHDSFVLSVHSTGALKASQLVLNAIDILKQKLD 294
>gi|6677797 RNA polymerase II 3 [Mus musculus] >gi|2829844|sp|P97760|RPB3_MOUSE
DNA-DIRECTED RNA POLYMERASE II 33 KDA POLYPEPTIDE (RPB3)
(RNA POLYMERASE II SUBUNIT 3) (RPB33) (RPB31)
>gi|7434683|pir||JC6181 RNA polymerase II 31.3K chain -
mouse >gi|1850789|dbj|BAA12205.1| (D83999) the third
largest RNA polymerase II subunit [Mus musculus]
Length = 275
Score = 95.2 bits (233), Expect = 7e-19
Identities = 60/170 (35%), Positives = 88/170 (51%), Gaps = 25/170 (14%)
Query: 4 IKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRL 63
++I + T++++ FI+E D+A AN++RR + EVP A+D V+ N S L DE IAHRL
Sbjct: 9 VRITELTEENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDGNSSVLHDEFIAHRL 68
Query: 64 AMIPLKTP--VDR-------------------FELDALELDDYT---VTLSLEAEGPGIV 99
+IPL + VD+ F LD +D T + L + P ++
Sbjct: 69 GLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVI 128
Query: 100 -YSGDLKSDDPDVKPANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQP 148
+ + +DP+ DI IVKL KGQ L A+ K GK+HAKW P
Sbjct: 129 PVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYVKKRSGKEHAKWNP 178
>sp|P37382|RPB3_SCHPO DNA-DIRECTED RNA POLYMERASE II 33 KD POLYPEPTIDE (RNA POLYMERASE II
SUBUNIT 3) >gi|626066|pir||S43201 DNA-directed RNA
polymerase (EC 2.7.7.6) II chain 3 - fission yeast
(Schizosaccharomyces pombe) (fragment)
Length = 296
Score = 91.7 bits (224), Expect = 8e-18
Identities = 80/273 (29%), Positives = 113/273 (41%), Gaps = 38/273 (13%)
Query: 4 IKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRL 63
I I + +S+ F+L +A AN+LRR +L E+PT A+D VE N S + DE +AHRL
Sbjct: 7 ITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRL 66
Query: 64 AMIPLKT-------PVDRFELDALELDDYTVTLSLE--------AEGPGIVYSGDLKSDD 108
MIPL + PV + D Y S+E EG +Y+ DL
Sbjct: 67 GMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVSS 126
Query: 109 PD-------VKPANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTYYKYFTRIHI 161
P + I KL K Q + AK G K+HAKW P +
Sbjct: 127 NSSLGHPILADPKSRGPLICKLRKEQEISLRCIAKKGIAKEHAKWSPTSA---------V 177
Query: 162 SKEIEGWEKLKKLAKKRGLPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYV 221
+ E + W KL+ EN+ E K E EG+ + P +
Sbjct: 178 AFEYDPWNKLQHTD-------YWFENDADAEWPKSKNADWEEPPREGEPFNFQEEPRRFY 230
Query: 222 FVVETNGELPVEEIVKIALKILMRKADRFINEL 254
VE+ G +P EI+ L+IL K + +L
Sbjct: 231 MDVESVGSIPPNEIMVQGLRILQEKLAVLVRDL 263
>dbj|BAA09315.1| (D50661) RNA polymerase II subunit 3 [Schizosaccharomyces pombe]
Length = 296
Score = 91.7 bits (224), Expect = 8e-18
Identities = 81/273 (29%), Positives = 113/273 (40%), Gaps = 38/273 (13%)
Query: 4 IKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRL 63
I I + DS+ F+L +A AN+LRR +L E+PT A+D VE N S + DE +AHRL
Sbjct: 7 ITIRNISRDSVDFVLTNSSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRL 66
Query: 64 AMIPLKT-------PVDRFELDALELDDYTVTLSLE--------AEGPGIVYSGDLKSDD 108
MIPL + PV + D Y S+E EG +Y+ DL
Sbjct: 67 DMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVSS 126
Query: 109 PD-------VKPANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTYYKYFTRIHI 161
P + I KL K Q + AK G K+HAKW P +
Sbjct: 127 NSSLGHPILADPKSRGPLICKLRKEQEISLRCIAKKGIAKEHAKWSPTSA---------V 177
Query: 162 SKEIEGWEKLKKLAKKRGLPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYV 221
+ E + W KL+ EN+ E K E EG+ + P +
Sbjct: 178 AFEYDPWNKLQHTD-------YWFENDADAEWPKSKNADWEEPPREGEPFNFQEEPRRFY 230
Query: 222 FVVETNGELPVEEIVKIALKILMRKADRFINEL 254
VE+ G +P EI+ L+IL K + +L
Sbjct: 231 MDVESVGSIPPNEIMVQGLRILQEKLAVLVRDL 263
>pir||T40975 dna-directed rna polymerase ii subunit - fission yeast
(Schizosaccharomyces pombe) >gi|2465184|dbj|BAA22566.1|
(D15070) polymerase II third largest subunit (subunit 3)
[Schizosaccharomyces pombe] >gi|3790255|emb|CAA21444.1|
(AL031966) dna-directed rna polymerase ii subunit
[Schizosaccharomyces pombe]
Length = 297
Score = 91.7 bits (224), Expect = 8e-18
Identities = 80/273 (29%), Positives = 113/273 (41%), Gaps = 38/273 (13%)
Query: 4 IKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRL 63
I I + +S+ F+L +A AN+LRR +L E+PT A+D VE N S + DE +AHRL
Sbjct: 7 ITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRL 66
Query: 64 AMIPLKT-------PVDRFELDALELDDYTVTLSLE--------AEGPGIVYSGDLKSDD 108
MIPL + PV + D Y S+E EG +Y+ DL
Sbjct: 67 GMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVSS 126
Query: 109 PD-------VKPANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTYYKYFTRIHI 161
P + I KL K Q + AK G K+HAKW P +
Sbjct: 127 NSSLGHPILADPKSRGPLICKLRKEQEISLRCIAKKGIAKEHAKWSPTSA---------V 177
Query: 162 SKEIEGWEKLKKLAKKRGLPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYV 221
+ E + W KL+ EN+ E K E EG+ + P +
Sbjct: 178 AFEYDPWNKLQHTD-------YWFENDADAEWPKSKNADWEEPPREGEPFNFQEEPRRFY 230
Query: 222 FVVETNGELPVEEIVKIALKILMRKADRFINEL 254
VE+ G +P EI+ L+IL K + +L
Sbjct: 231 MDVESVGSIPPNEIMVQGLRILQEKLAVLVRDL 263
>dbj|BAA09316.1| (D50662) RNA polymerase II subunit 3 [Schizosaccharomyces pombe]
Length = 296
Score = 90.9 bits (222), Expect = 1e-17
Identities = 78/265 (29%), Positives = 110/265 (41%), Gaps = 38/265 (14%)
Query: 12 DSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRLAMIPLKT- 70
+S+ F+L +A AN+LRR +L E+PT A+D VE N S + DE +AHRL MIPL +
Sbjct: 15 NSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRLGMIPLDSS 74
Query: 71 ------PVDRFELDALELDDYTVTLSLE--------AEGPGIVYSGDLKSDDPD------ 110
PV + D Y S+E EG +Y+ DL
Sbjct: 75 NIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVSSNSSLGHPI 134
Query: 111 -VKPANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTYYKYFTRIHISKEIEGWE 169
P + I KL K Q + AK G K+HAKW P ++ E + W
Sbjct: 135 LADPKSRGPLICKLRKEQEISLRCIAKKGIAKEHAKWSPTSA---------VAFEYDPWN 185
Query: 170 KLKKLAKKRGLPVKENENEVIVETIKPFYIPKEFEEYEGKGIWEEIVPNTYVFVVETNGE 229
KL+ EN+ E K E EG+ + P + VE+ G
Sbjct: 186 KLQHTD-------YWFENDADAEWPKSKNADWEEPPREGEPFNFQEEPRRFYMDVESVGS 238
Query: 230 LPVEEIVKIALKILMRKADRFINEL 254
+P EI+ L+IL K + +L
Sbjct: 239 IPPNEIMVQGLRILQEKLAVLVRDL 263
Database: ./suso.pep
Posted date: Jul 6, 2001 5:57 PM
Number of letters in database: 840,471
Number of sequences in database: 2977
Database: /banques/blast2/nr.pep
Posted date: Dec 14, 2000 12:46 PM
Number of letters in database: 188,266,275
Number of sequences in database: 595,510
Lambda K H
0.318 0.141 0.404
Gapped
Lambda K H
0.270 0.0470 0.230
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 99907464
Number of Sequences: 2977
Number of extensions: 4451393
Number of successful extensions: 10050
Number of sequences better than 1.0e-10: 30
Number of HSP's better than 0.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 9993
Number of HSP's gapped (non-prelim): 31
length of query: 259
length of database: 189,106,746
effective HSP length: 55
effective length of query: 204
effective length of database: 156,189,961
effective search space: 31862752044
effective search space used: 31862752044
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 41 (21.7 bits)
S2: 164 (68.3 bits)