ORF STATUS Function Best COG Functional category Pathways and functional systems
r_klactII2143 good KL KOG2487 Replication, recombination and repair RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4
r_klactII2143 good KL KOG2487 Transcription RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4
Only best alignment is shown:
BLASTP 2.2.3 [May-13-2002]
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= r_klactII2143 757571 756561 -337
(337 letters)
Database: KOG eukaryal database 04/03
60,738 sequences; 30,389,216 total letters
Searching..................................................done
Color Key for Alignment Scores: 
Score E
Sequences producing significant alignments: (bits) Value
YPR056w [KL] KOG2487 RNA polymerase II transcription initiation/... 363 e-100
SPBC30B4.07c [KL] KOG2487 RNA polymerase II transcription initia... 177 3e-44
Hs19923732 [KL] KOG2487 RNA polymerase II transcription initiati... 106 5e-23
7296117 [KL] KOG2487 RNA polymerase II transcription initiation/... 89 1e-17
CE01686 [KL] KOG2487 RNA polymerase II transcription initiation/... 76 6e-14
At1g18340_1 [KL] KOG2487 RNA polymerase II transcription initiat... 59 1e-08
>YPR056w [KL] KOG2487 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH subunit TFB4
Length = 338
Score = 363 bits (933), Expect = e-100
Identities = 189/343 (55%), Positives = 238/343 (69%), Gaps = 20/343 (5%)
Query: 1 MDAIADTVFQGTKSKTQEIEDTPSLLTVVVDTSIHSWVQLTKQQXXXXXXXXXXXKQLIE 60
MDAI+D F+ +S+ Q E++PSLLTV+++ + W ++ +I+
Sbjct: 1 MDAISDPTFKHARSRKQVTEESPSLLTVIIEIAPKLWTTFDEEGNEKGS--------IIK 52
Query: 61 ALKSIVVFLNAHLAFNSGNQVCLIAAHSEGMKYLYPSADS-----------KPSMSMVSS 109
L++++VFLNAHLAFNS N+V +IAA+S+G+KYLYP + S + + +++S
Sbjct: 53 VLEALIVFLNAHLAFNSANKVAVIAAYSQGIKYLYPESTSALKASESENKTRSDLKIINS 112
Query: 110 DMYRGFRNVDEIVVEQWYRLFKEELEGQESKVXXXXXXXXXXXXXXTYVNRILKENENTS 169
DMYR FRNVDE +VE+ Y+LF+ E + E TYVNRI KE+ TS
Sbjct: 113 DMYRRFRNVDETLVEEIYKLFELEKKQIEQN-SQRSTLAGAMSAGLTYVNRISKESVTTS 171
Query: 170 LRSRLLVITCGTSQGKDEIFQYIPIMNCIFSATKMKCSIDVVKIGGGIESTFLQQATDAT 229
L+SRLLV+TCG+ KDEIFQYIPIMNCIFSATKMKC IDVVKIGG ESTFLQQ TDAT
Sbjct: 172 LKSRLLVLTCGSGSSKDEIFQYIPIMNCIFSATKMKCPIDVVKIGGSKESTFLQQTTDAT 231
Query: 230 SGVYLHVENTRGLIQYLSTAMFIDPSLRNVIIKPNQGSVDFRTSCFLTGKVVAVGFXXXX 289
+GVYLHVE+T GLIQYL+TAMFIDPSLR +I+KPN GSVDFRTSC+LTG+VVAVGF
Sbjct: 232 NGVYLHVESTEGLIQYLATAMFIDPSLRPIIVKPNHGSVDFRTSCYLTGRVVAVGFICSV 291
Query: 290 XXXXXXXIPPGQKCPACDSPFDSKIIARLRRKPVLSNGVPKKK 332
IPPG KCPACDS FD +IA+L+RKPV+ KKK
Sbjct: 292 CLCVLSIIPPGNKCPACDSQFDEHVIAKLKRKPVVPRLKAKKK 334
>SPBC30B4.07c [KL] KOG2487 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH subunit TFB4
Length = 297
Score = 177 bits (448), Expect = 3e-44
Identities = 107/274 (39%), Positives = 155/274 (56%), Gaps = 30/274 (10%)
Query: 16 TQEIEDTPSLLTVVVDTSIHSWVQLTKQQXXXXXXXXXXXKQLIEALKSIVVFLNAHLAF 75
+++ DTPSLL V++D + SW L+K+ + + L I VFLNAHLAF
Sbjct: 16 SEDANDTPSLLVVILDANPASWYSLSKKV------------PVSKVLADITVFLNAHLAF 63
Query: 76 NSGNQVCLIAAHSEGMKYLYPSADSKPSMSMVS----SDMYRGFRNVDEIVVEQWYRLFK 131
+ N+V ++A+HS+ ++YLYPS + ++ V ++ YR FR VD++V+ RL
Sbjct: 64 HHDNRVAVLASHSDKVEYLYPSIAPEQKVAEVDPTKEANTYRKFREVDDLVLSGMKRLMS 123
Query: 132 EELEGQESKVXXXXXXXXXXXXXXTYVNRILKENENTSLRSRLLVITCGTSQGKDEIFQY 191
KV Y+N++ +N+NT LRSR+L+ S D QY
Sbjct: 124 ST-----DKVSRKTMISGALSRALAYINQV--QNKNT-LRSRILIF----SLTGDVALQY 171
Query: 192 IPIMNCIFSATKMKCSIDVVKIGGGIESTFLQQATDATSGVYLHVENTRGLIQYLSTAMF 251
IP MNCIF A K I+V I GG + FL+QA DAT G+YL V+N +GL+QYL ++F
Sbjct: 172 IPTMNCIFCAQKKNIPINVCNIEGG--TLFLEQAADATGGIYLKVDNPKGLLQYLMMSLF 229
Query: 252 IDPSLRNVIIKPNQGSVDFRTSCFLTGKVVAVGF 285
D +LR + PNQ +VDFR +CF KV+ +GF
Sbjct: 230 PDQNLRKHLNTPNQANVDFRATCFCHKKVLDIGF 263
>Hs19923732 [KL] KOG2487 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH subunit TFB4
Length = 308
Score = 106 bits (264), Expect = 5e-23
Identities = 84/319 (26%), Positives = 141/319 (43%), Gaps = 40/319 (12%)
Query: 20 EDTPSLLTVVVDTSIHSWVQLTKQQXXXXXXXXXXXKQLIEALKSIVVFLNAHLAFNSGN 79
ED +LL +VVD + W + ++ L + + +++V N+HL N N
Sbjct: 5 EDELNLLVIVVDANPIWWGKQALKESQFT---------LSKCIDAVMVLGNSHLFMNRSN 55
Query: 80 QVCLIAAHSEGMKYLYPSADSK---------------PSMSMVSSDMYRGFRNVDEIVVE 124
++ +IA+H + ++LYP + + PS S Y + +E++VE
Sbjct: 56 KLAVIASHIQESRFLYPGKNGRLGDFFGDPGNPPEFNPSGS--KDGKYELLTSANEVIVE 113
Query: 125 QWYRLF-KEELEGQESKVXXXXXXXXXXXXXXTYVNRILKE-NENTSLRSRLLVITCGTS 182
+ L K +++GQ ++ Y++R+ KE +N ++SR+LVI
Sbjct: 114 EIKDLMTKSDIKGQHTETLLAGSLAKAL----CYIHRMNKEVKDNQEMKSRILVIKAA-- 167
Query: 183 QGKDEIFQYIPIMNCIFSATKMKCSIDVVKIGGGIESTFLQQATDATSGVYLHVENTRGL 242
+D QY+ MN IF+A K ID + +S LQQA D T G+YL V L
Sbjct: 168 --EDSALQYMNFMNVIFAAQKQNILIDACVLDS--DSGLLQQACDITGGLYLKVPQMPSL 223
Query: 243 IQYLSTAMFIDPSLRNVIIKPNQGSVDFRTSCFLTGKVVAVGFXXXXXXXXXXXIPPGQK 302
+QYL D R+ +I P VD+R +CF ++ +G+ P
Sbjct: 224 LQYLLWVFLPDQDQRSQLILPPPVHVDYRAACFCHRNLIEIGYVCSVCLSIFCNFSP--I 281
Query: 303 CPACDSPFDSKIIARLRRK 321
C C++ F + L+ K
Sbjct: 282 CTTCETAFKISLPPVLKAK 300
>7296117 [KL] KOG2487 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH subunit TFB4
Length = 276
Score = 88.6 bits (218), Expect = 1e-17
Identities = 67/278 (24%), Positives = 121/278 (43%), Gaps = 25/278 (8%)
Query: 10 QGTKSKTQEIEDTPSLLTVVVDTSIHSWVQLTKQQXXXXXXXXXXXKQLIEALKSIVVFL 69
+ ++ ++E E LL +V+DT+ Q L + L++++ F
Sbjct: 2 EADQAASKEAESCIDLLVIVLDTNPSQHFVRQNPQ------------NLTQILEAVIAFG 49
Query: 70 NAHLAFNSGNQVCLIAAHSEGMKYLYPSADSKPSMSMVSSDMYRGFRNVDEIVVEQWYRL 129
NAHL + N++ +++ +LYP + + V Y F V++ V +Q +
Sbjct: 50 NAHLMQKAQNKLAVVSCSHHATNFLYPLPRRQVELRQVDGQ-YEAFNLVEKTVKQQLGSI 108
Query: 130 FKEELEGQESKVXXXXXXXXXXXXXXTYVNRILKE-NENTSLRSRLLVITCGTSQGKDEI 188
+ Y++R+ + + SR+LV+T G +E
Sbjct: 109 L---MNAPRLSAPCESLLAGSMSMALCYISRLQRNLAPGVKMHSRILVVT-----GSNEC 160
Query: 189 F-QYIPIMNCIFSATKMKCSIDVVKIGGGIESTFLQQATDATSGVYLHVENTRGLIQYLS 247
QY+ MN F+A K+ +ID + + + LQQ D TSG +L V GL+QYL
Sbjct: 161 ASQYMTFMNVFFTAQKLGITIDTCALDKTL--SLLQQGCDITSGQFLKVTQLDGLLQYLL 218
Query: 248 TAMFIDPSLRNVIIKPNQGSVDFRTSCFLTGKVVAVGF 285
P +R+ ++ P VD+R SCF +++ +G+
Sbjct: 219 WVFLPAPQIRHKLVLPPPPKVDYRASCFCHRELIDIGY 256
>CE01686 [KL] KOG2487 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH subunit TFB4
Length = 345
Score = 76.3 bits (186), Expect = 6e-14
Identities = 80/310 (25%), Positives = 121/310 (38%), Gaps = 34/310 (10%)
Query: 24 SLLTVVVDTSIHSWVQLTKQQXXXXXXXXXXXKQLIEALKSIVVFLNAHLAFNSGNQVCL 83
S L+V+++TS SW L L++IV F NAHL ++ NQ+ +
Sbjct: 51 STLSVLIETSSCSWGMLASAHGDRTIGII---------LRAIVSFCNAHLGQSANNQLLV 101
Query: 84 IA-AHSEGMKYLYPSADS----------KPSMSMVSSDMYRGFRNVDEIVVEQWYRLFKE 132
A + K +Y S K ++SSD + + F
Sbjct: 102 FAYGRNVDNKMIYSSTRCEDRNASFLVVKRLRELLSSDALTNDATIGAPLGPALAHAFCH 161
Query: 133 ELEGQESKVXXXXXXXXXXXXXXTYVNRILKENENTSLRSRLLVITCGTSQGKDEIFQYI 192
+ +S+V T E + +R +VI+ G + +
Sbjct: 162 MKK--DSRVVTADPCDDSLGPQTTSEQ---SETASEKATNRAVVISITPIMGSE----HG 212
Query: 193 PIMNCIFSATKMKCSIDVVKIGGGIESTFLQQATDATSGVYLHVENTRGLIQYLSTAMFI 252
+MN FSA K +DVV +G LQQA D T G +LH + + L++ L T M
Sbjct: 213 SLMNLFFSAAKQSICVDVVSMGDDFTGGILQQAADITGGSFLHAKKPQTLLKILMTNMLT 272
Query: 253 DPSLRNVIIKPNQGSVDFRTSCFLTGKVVAVGFXXXXXXXXXXXIPPGQKCPACDSPFDS 312
DP+ R V K + SVD+R SC ++V+ G+ P C C + F
Sbjct: 273 DPTHRAVFSKLSHNSVDYRASCACHHQLVSSGWVCSICLSVLCQYTP--ICKVCKAAF-- 328
Query: 313 KIIARLRRKP 322
IA L KP
Sbjct: 329 -TIANLPIKP 337
>At1g18340_1 [KL] KOG2487 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH subunit TFB4
Length = 289
Score = 58.9 bits (141), Expect = 1e-08
Identities = 62/240 (25%), Positives = 102/240 (41%), Gaps = 28/240 (11%)
Query: 16 TQEIEDTPSLLTVVVDTSIHSWVQLTKQQXXXXXXXXXXXKQLIEALKSIVVFLNAHLAF 75
+++ D SLL +++DT+ W + L ++ FLNA L
Sbjct: 6 SKQYSDDVSLLVLLLDTNPLFW--------------STTSITFSQFLSHVLAFLNAVLGL 51
Query: 76 NSGNQVCLIAAHSEGMKYLYPSADSKPSMSMVSSD-----MYRGFRNVDEIVVEQWYRLF 130
N NQV +IA Y+Y S+ + + S+ ++ E V + L
Sbjct: 52 NQLNQVVVIATGYSSCDYIYDSSLTSNHGNFESNGTGMPAIFGSLLKKLEEFVTKDEELS 111
Query: 131 KEELEGQESKVXXXXXXXXXXXXXXTYVNRILKENENTSLRSRLLVITCGTSQGKDEIFQ 190
KEE+ E ++ Y+ R+ + + + R+L + G+ G + Q
Sbjct: 112 KEEV--SEDRI-PSCLLSGSLSMALCYIQRVFRSG-HLHPQPRILCLQ-GSPDGPE---Q 163
Query: 191 YIPIMNCIFSATKMKCSIDVVKIGGGIESTFLQQATDATSGVYLHVENTRGLIQYLSTAM 250
Y+ +MN IFSA ++ ID IG S FLQQA+ T GV+ + GL QYL+ +
Sbjct: 164 YVAVMNSIFSAQRLMVPIDSCYIGVQ-NSAFLQQASYITGGVHHTPKQLDGLFQYLTVLL 222
Database: KOG eukaryal database 04/03
Posted date: Apr 14, 2003 1:07 PM
Number of letters in database: 30,389,216
Number of sequences in database: 60,738
Lambda K H
0.318 0.134 0.381
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,969,372
Number of Sequences: 60738
Number of extensions: 606240
Number of successful extensions: 1232
Number of sequences better than 1.0e-05: 6
Number of HSP's better than 0.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1212
Number of HSP's gapped (non-prelim): 7
length of query: 337
length of database: 30,389,216
effective HSP length: 107
effective length of query: 230
effective length of database: 23,890,250
effective search space: 5494757500
effective search space used: 5494757500
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)