ORF STATUS Function Best COG Functional category Pathways and functional systems
r_klactV2444 good KL KOG2807 Replication, recombination and repair RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1
r_klactV2444 good KL KOG2807 Transcription RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1
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_klactV2444 851587 853050 488
(488 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
YLR005w [KL] KOG2807 RNA polymerase II transcription initiation/... 683 0.0
SPCC1682.07 [KL] KOG2807 RNA polymerase II transcription initiat... 412 e-115
Hs6681762 [KL] KOG2807 RNA polymerase II transcription initiatio... 305 8e-83
At1g05050 [KL] KOG2807 RNA polymerase II transcription initiatio... 300 3e-81
CE29053 [KL] KOG2807 RNA polymerase II transcription initiation/... 250 3e-66
7296597 [KL] KOG2807 RNA polymerase II transcription initiation/... 243 4e-64
ECU04g0280 [KL] KOG2807 RNA polymerase II transcription initiati... 143 7e-34
>YLR005w [KL] KOG2807 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH subunit SSL1
Length = 461
Score = 683 bits (1763), Expect = 0.0
Identities = 319/444 (71%), Positives = 371/444 (82%), Gaps = 5/444 (1%)
Query: 40 RTKETADSDGAGNGNSSDDEEDERVHSQLXXXXXXXXXXXXXXXXXXXXXNLQGVNGGYA 99
RTK DG G DD D++ NLQG NGGYA
Sbjct: 21 RTKRQVHFDGEG-----DDRVDQQQQQHSSSHRDRDKHVQRKKKKRLSNRNLQGSNGGYA 75
Query: 100 WEDDIQRSWDLVKVDDEGNIAAIVASIVEARKKRAAEKTVTPYQRGIIRTLILVLDCSEA 159
WED+I+RSWDLVKVDDEG++A++VASIVEARKKR A+K +TPYQRGIIR+LIL LDCSEA
Sbjct: 76 WEDEIKRSWDLVKVDDEGDMASLVASIVEARKKRTAKKNITPYQRGIIRSLILTLDCSEA 135
Query: 160 MMEKDLRPNRYAMTVQYAVDFIHEYFDQNPISQIGVVVMRDGLAQLISQVSGNPQEHIDA 219
M+EKDLRPNR+AM +QYA+DF+HE+FDQNPISQ+G+++MR+GLAQL+SQVSGNPQ+HIDA
Sbjct: 136 MLEKDLRPNRHAMIIQYAIDFVHEFFDQNPISQMGIIIMRNGLAQLVSQVSGNPQDHIDA 195
Query: 220 LKMLRRQEPKGNASLQNALEMARGLLLHVPAHCTREVLIVFGALSTTDPGDIHQTIGSLV 279
LK +R+QEPKGN SLQNALEMARGLLL VPAHCTREVLIVFG+LSTTDPGDIHQTI SLV
Sbjct: 196 LKSIRKQEPKGNPSLQNALEMARGLLLPVPAHCTREVLIVFGSLSTTDPGDIHQTIDSLV 255
Query: 280 HENIRAKVIGLSAQVSVCKELCKQTNYGDNSYYGIILNDHHFKELFTSAVTPLPVSKVNK 339
E IR KV+GLSAQV++CKELCK TNYGD S+Y I+L++ H KELF AVTPLPV+K+NK
Sbjct: 256 SEKIRVKVLGLSAQVAICKELCKATNYGDESFYKILLDETHLKELFNEAVTPLPVNKINK 315
Query: 340 GFTLVKMGFPTRVFEDTPSFCACHSTLVHGGYVCPNCKTKVCSLPTVCPSCDLMLILSTH 399
GFTLVKMGFPTR+FEDTP+FC+CHS LV+GGY CPNC +KVCSLPTVCP CDLMLILSTH
Sbjct: 316 GFTLVKMGFPTRIFEDTPTFCSCHSKLVYGGYFCPNCHSKVCSLPTVCPCCDLMLILSTH 375
Query: 400 LARSYHHLMPLKTFQEVPVSDSFPTDYCFGCQKRFPTLRNNKTGELLTSSRYRCEECDQD 459
LARSYHHLMPLKTF EVP ++ F ++ CF CQ RFP L+N+K G+LLTSSRYRCE+C Q+
Sbjct: 376 LARSYHHLMPLKTFAEVPTTEKFRSEDCFSCQSRFPILKNHKNGKLLTSSRYRCEDCKQE 435
Query: 460 FCIDCDVFIHETLHNCPGCESKPI 483
FC+DCDVFIHE LHNCPGCESKP+
Sbjct: 436 FCVDCDVFIHEILHNCPGCESKPV 459
>SPCC1682.07 [KL] KOG2807 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH subunit SSL1
Length = 421
Score = 412 bits (1059), Expect = e-115
Identities = 189/386 (48%), Positives = 266/386 (67%), Gaps = 3/386 (0%)
Query: 95 NGGYAWEDDIQRSWDLVKVDDEGNIAAIVASIVEARKKRAAEKTVTPYQRGIIRTLILVL 154
N GY WE + QRSWD+V+ D EG++ ++A ++++ K++ + TP QRGIIR ++LVL
Sbjct: 34 NEGYTWEGEYQRSWDIVQEDAEGSLVGVIAGLIQSGKRKRLLRDTTPLQRGIIRHMVLVL 93
Query: 155 DCSEAMMEKDLRPNRYAMTVQYAVDFIHEYFDQNPISQIGVVVMRDGLAQLISQVSGNPQ 214
D S +M E+D R+ + ++YA +F+ E+F+QNPISQ+ ++ + DG+A I+ + GNPQ
Sbjct: 94 DLSNSMEERDFHHKRFDLQIKYASEFVLEFFEQNPISQLSIIGVMDGIAHRITDLHGNPQ 153
Query: 215 EHIDALKMLRRQEPKGNASLQNALEMARGLLLHVPAHCTREVLIVFGALSTTDPGDIHQT 274
HI LK LR + GN SLQNALEMAR L H+ +H TREVLI+FG++ ++DPGDI +T
Sbjct: 154 SHIQKLKSLR--DCSGNFSLQNALEMARASLSHIASHGTREVLIIFGSILSSDPGDIFKT 211
Query: 275 IGSLVHENIRAKVIGLSAQVSVCKELCKQTNYGDNSYYGIILNDHHFKELFT-SAVTPLP 333
I +LVH++IR +++GL+A+V++CKE+C +TN + YG+++++ HF+EL S + P
Sbjct: 212 IDALVHDSIRVRIVGLAAEVAICKEICNKTNSSTKNAYGVVISEQHFRELLLESTIPPAT 271
Query: 334 VSKVNKGFTLVKMGFPTRVFEDTPSFCACHSTLVHGGYVCPNCKTKVCSLPTVCPSCDLM 393
S +LV MGFP++V E PS CACHS GG+ CP CK KVC+LP CPSC L+
Sbjct: 272 DSAKTTDASLVMMGFPSKVVEQLPSLCACHSIPSRGGFHCPRCKAKVCTLPIECPSCSLV 331
Query: 394 LILSTHLARSYHHLMPLKTFQEVPVSDSFPTDYCFGCQKRFPTLRNNKTGELLTSSRYRC 453
LILSTHLARSYHHL PLK + E+P S + + +CF CQ FP + E +S RY C
Sbjct: 332 LILSTHLARSYHHLFPLKNWSEIPWSANPKSTHCFACQLPFPKPPVSPFDESTSSMRYAC 391
Query: 454 EECDQDFCIDCDVFIHETLHNCPGCE 479
C FC+DCDVF HE LH C GC+
Sbjct: 392 PSCKNHFCLDCDVFAHEQLHECYGCQ 417
>Hs6681762 [KL] KOG2807 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH subunit SSL1
Length = 395
Score = 305 bits (782), Expect = 8e-83
Identities = 158/394 (40%), Positives = 229/394 (58%), Gaps = 28/394 (7%)
Query: 100 WEDDIQRSWDLVKVDDEGNIAAIVASIVEARKKRAAEKTVTPYQRGIIRTLILVLDCSEA 159
WE +R+W+++K D+ G++ A + I+ K++ + + G++R L +V+D S
Sbjct: 11 WEGGYERTWEILKEDESGSLKATIEDILFKAKRKRVFEHHGQVRLGMMRHLYVVVDGSRT 70
Query: 160 MMEKDLRPNRYAMTVQYAVDFIHEYFDQNPISQIGVVVMRDGLAQLISQVSGNPQEHIDA 219
M ++DL+PNR T++ F+ EYFDQNPISQIG++V + A+ ++++SGNP++HI +
Sbjct: 71 MEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITS 130
Query: 220 LKMLRRQEPKGNASLQNALEMARGLLLHVPAHCTREVLIVFGALSTTDPGDIHQTIGSLV 279
LK G SL N+L +A L H+P H +REVLI+F +L+T DP +I+ I +L
Sbjct: 131 LKKAVDMTCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLK 190
Query: 280 HENIRAKVIGLSAQVSVCKELCKQTNYGDNSYYGIILNDHHFKELFTSAVTPLPVSKVNK 339
IR VIGLSA+V VC L ++T Y +IL++ H+KEL T V+P P S ++
Sbjct: 191 AAKIRVSVIGLSAEVRVCTVLARET----GGTYHVILDESHYKELLTHHVSPPPASSSSE 246
Query: 340 GFTLVKMGFPTRVF------EDTPSFCACH------STLVHGGYVCPNCKTKVCSLPTVC 387
+L++MGFP + PSF H L GGY CP C+ K C LP C
Sbjct: 247 -CSLIRMGFPQHTIASLSDQDAKPSFSMAHLDGNTEPGLTLGGYFCPQCRAKYCELPVEC 305
Query: 388 PSCDLMLILSTHLARSYHHLMPLKTFQEVPVSDSFPTDYCFGCQKRFPTLRNNKTGELLT 447
C L L+ + HLARSYHHL PL FQE+P+ + +C+GCQ GEL
Sbjct: 306 KICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQ-----------GELKD 354
Query: 448 SSRYRCEECDQDFCIDCDVFIHETLHNCPGCESK 481
Y C C FC+DCDVF+H++LH CPGC K
Sbjct: 355 QHVYVCAVCQNVFCVDCDVFVHDSLHCCPGCIHK 388
>At1g05050 [KL] KOG2807 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH subunit SSL1
Length = 421
Score = 300 bits (768), Expect = 3e-81
Identities = 167/404 (41%), Positives = 239/404 (58%), Gaps = 29/404 (7%)
Query: 99 AWEDDIQRSWDLVKVDDEGNIAAIVAS-IVEARKKR-----AAEKTVTPYQRGIIRTLIL 152
A+ DD RSW+ ++ D+ G + I S I A+ +R +A T Q+G+IR L +
Sbjct: 29 AYVDD--RSWEELQEDESGLLRPIDNSAIYHAQYRRRLRMLSAAAAGTRIQKGLIRYLYI 86
Query: 153 VLDCSEAMMEKDLRPNRYAMTVQYAVDFIHEYFDQNPISQIGVVVMRDGLAQLISQVSGN 212
V+D S A E D RP+R A+ ++ FI E+FDQNP+SQIG+V +++G+A ++ + G+
Sbjct: 87 VIDFSRAAAEMDFRPSRMAIMAKHVEAFIREFFDQNPLSQIGLVSIKNGVAHTLTDLGGS 146
Query: 213 PQEHIDALKMLRRQEPKGNASLQNALEMARGLLLHVPAHCTREVLIVFGALSTTDPGDIH 272
P+ HI AL + + E G++SLQNALE+ L VP++ REVLI++ AL T DPGDI
Sbjct: 147 PETHIKAL--MGKLEALGDSSLQNALELVHEHLNQVPSYGHREVLILYSALCTCDPGDIM 204
Query: 273 QTIGSLVHENIRAKVIGLSAQVSVCKELCKQTNYGDNSYYGIILNDHHFKELFTSAVTPL 332
+TI +R VIGLSA++ +CK LC++T Y + +++ H K+L P
Sbjct: 205 ETIQKCKKSKLRCSVIGLSAEMFICKHLCQET----GGLYSVAVDEVHLKDLLLEHAPPP 260
Query: 333 PVSKVNKGFTLVKMGFPTRVFEDTPSFCACHSTL-VHGGYVCPNCKTKVCSLPTVCPSCD 391
P L+KMGFP R E + + C+CH + + GY+CP CK +VC LPT C C
Sbjct: 261 PAIAEFAIANLIKMGFPQRAAEGSMAICSCHKEVKIGAGYMCPRCKARVCDLPTECTICG 320
Query: 392 LMLILSTHLARSYHHLMPLKTFQEVPVSDSFPTD------YCFGCQKRFPTLRNNKTGEL 445
L L+ S HLARSYHHL P+ F EVP S + CFGCQ+ NK
Sbjct: 321 LTLVSSPHLARSYHHLFPIAPFDEVPALSSLNDNRRKLGKSCFGCQQSL-IGAGNKPVPC 379
Query: 446 LTSSRYRCEECDQDFCIDCDVFIHETLHNCPGCES--KPINVNI 487
+T C +C FC+DCD++IHE+LHNCPGCES +P +V++
Sbjct: 380 VT-----CRKCKHYFCLDCDIYIHESLHNCPGCESIHRPKSVSL 418
>CE29053 [KL] KOG2807 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH subunit SSL1
Length = 376
Score = 250 bits (639), Expect = 3e-66
Identities = 135/389 (34%), Positives = 211/389 (53%), Gaps = 28/389 (7%)
Query: 97 GYAWEDDIQRSWDL--VKVDDEGNIA--AIVASIVEARKKRAAEKTVTPYQRGIIRTLIL 152
GY WE ++ V V+DEG +I + ++++K K + GI+R +++
Sbjct: 8 GYTWEAGYAEGLNINDVLVEDEGGSIEKSIAKYVADSKRKARLTKRPERIRLGIMRHVMI 67
Query: 153 VLDCSEAMMEKDLRPNRYAMTVQYAVDFIHEYFDQNPISQIGVVVMRDGLAQLISQVSGN 212
V+DCS M K + P+R+ + ++ F+ +F+QNPI+QIG++ +D A ++ ++GN
Sbjct: 68 VIDCSRFMTSKAMPPSRFVVVMKALQTFLDRFFEQNPIAQIGLITCKDRKADRLTMMTGN 127
Query: 213 PQEHIDALKMLRRQEPKGNASLQNALEMARGLLLHVPAHCTREVLIVFGALSTTDPGDIH 272
+ ++L L G+ SLQNAL++A L +P H +REV++V ALST DPG+I+
Sbjct: 128 IRVLKESLNTLTEAFCGGDFSLQNALQLACANLKGMPGHVSREVVLVISALSTIDPGNIY 187
Query: 273 QTIGSLVHENIRAKVIGLSAQVSVCKELCKQTNYGDNSYYGIILNDHHFKELFTSAVTPL 332
TI ++ NIR IGLSA++ VCKE+ K T Y + L+ H + LF+ P
Sbjct: 188 STIETMKRMNIRCSAIGLSAEMFVCKEMAKAT----KGEYSVALDPDHLQLLFSKHTLP- 242
Query: 333 PVSKVNKGFTLVKMGFPTRVFEDTPSFCACH---STLVHGGYVCPNCKTKVCSLPTVCPS 389
P S + + +GFP T SFC CH + G++C C + CS+P CP
Sbjct: 243 PSSAKSSECNAIHVGFPHHELITTRSFCVCHPDTKPISSRGFICTQCGARHCSIPAECPV 302
Query: 390 CDLMLILSTHLARSYHHLMPLKTFQEVPVSDSFPTDYCFGCQKRFPTLRNNKTGELLTSS 449
C L L+ + LAR++ HL PL F+++ V+ F C+ C+ R L+
Sbjct: 303 CKLTLVAAPQLARAFRHLQPLSAFEQIEVTRGF----CYACETR------------LSGE 346
Query: 450 RYRCEECDQDFCIDCDVFIHETLHNCPGC 478
+RC C FC+DCD +HE+LH CPGC
Sbjct: 347 GFRCGSCQLVFCLDCDTLLHESLHVCPGC 375
>7296597 [KL] KOG2807 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH subunit SSL1
Length = 362
Score = 243 bits (621), Expect = 4e-64
Identities = 128/332 (38%), Positives = 195/332 (58%), Gaps = 17/332 (5%)
Query: 98 YAWEDDIQRSWDLVKVDDEGNIAAIVASIVEARKKRAAEKTVTPYQRGIIRTLILVLDCS 157
Y WE +++W+ +K D++G + +A I++ K++ + + G++R + +VLDCS
Sbjct: 12 YRWETGYEKTWEAIKDDEDGMLDGAIAEIIQKAKRQRQAQKSKQNRLGMMRHMFVVLDCS 71
Query: 158 EAMMEKDLRPNRYAMTVQYAVDFIHEYFDQNPISQIGVVVMRDGLAQLISQVSGNPQEHI 217
E+M DL+P R TV+ FI E+FDQNPISQ+G++ ++ A+ +++++G + H+
Sbjct: 72 ESMSVPDLKPTRLRCTVKLLELFIEEFFDQNPISQLGLIALKAKRAEKVTELTGTSRVHL 131
Query: 218 DALKMLRRQEPKGNASLQNALEMARGLLLHVPAHCTREVLIVFGALSTTDPGDIHQTIGS 277
AL+ L SLQN L++A L VP+H +RE++I+ G+L+T DP DI+ TI
Sbjct: 132 KALESLANVSLTSEPSLQNGLDLALKSLKVVPSHASREIVIIMGSLTTCDPVDINLTIDE 191
Query: 278 LVHENIRAKVIGLSAQVSVCKELCKQTNYGDNSYYGIILNDHHFKELFTSAVTPLPVSKV 337
L E IR VI LSA++ V + L +QT +G +L+D HF++ S V P P +K
Sbjct: 192 LKKEGIRCSVISLSAEIHVARYLTQQT----MGTFGAVLDDAHFRDQLMSQVDPPPAAKT 247
Query: 338 NKGFTLVKMGFPTRVFE----DTP-SFCACH-------STLVHGGYVCPNCKTKVCSLPT 385
+L++MGFP E D P S C CH S L G+ CP C +K C LP
Sbjct: 248 QHN-SLIRMGFPHTKNEVEGKDAPLSMCMCHIENLEEPSELTTTGHHCPQCNSKYCELPV 306
Query: 386 VCPSCDLMLILSTHLARSYHHLMPLKTFQEVP 417
C SC L L+ + HLARSYHHL P+ F+E+P
Sbjct: 307 ECQSCGLTLVSAPHLARSYHHLFPVPNFEELP 338
>ECU04g0280 [KL] KOG2807 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH subunit SSL1
Length = 340
Score = 143 bits (360), Expect = 7e-34
Identities = 108/391 (27%), Positives = 175/391 (44%), Gaps = 68/391 (17%)
Query: 98 YAWEDDIQRSWDLVKVDDEGNIAAIVASIVEARKKRAAE---KTVTPY---QRGIIRTLI 151
++WE + +R+W+ + ++ E +T PY ++GI+R L
Sbjct: 5 FSWEQEYKRTWE------------------DRNDRKVNEFNLETEAPYSNNRKGIVRHLH 46
Query: 152 LVLDCSEAMMEKDLRPNRYAMTVQYAVDFIHEYFDQNPISQIGVVVMRDGLAQLISQVSG 211
+++D SEA+ + D P A + FI ++ +NP+S + + +RD + S +
Sbjct: 47 IIIDVSEAIDKSDFLPTFRANVTKVLEGFIPSFYSENPLSTLSFLSIRDVCVKYTSSMD- 105
Query: 212 NPQEHIDALKMLRRQEPKGNASLQNALEMARGLL---LHVPAHCTREVLIVFGALSTTDP 268
ID L + K SL N LE + ++ +HV +E+L++ + ST DP
Sbjct: 106 -----IDIHAFLGQTGSKW-FSLLNGLEGSIEVMKNTMHV-----KEILVIVASTSTRDP 154
Query: 269 GDIHQTIGSLVHENIRAKVIGLSAQVSVCKELCKQTNYGDNSYYGIILNDHHFKELFTSA 328
+ + L NI+ I L ++++ K + K T + +Y + ++ H +
Sbjct: 155 HGYAEVLAKLRAYNIKVHFISLCGEITLYKSISKAT---EGRFY-VPVDAGHLSAIMREL 210
Query: 329 VTPLPVSKVNKGFTLVKMGFPTRVFEDTPSFCACHSTLVHGGYVCPNCKTKVCSLPTVCP 388
P + +LVK+GFP+ + E PS CACH + GY CP CKT VCSLP CP
Sbjct: 211 SHPTDFNGTK--LSLVKIGFPSPMME--PSVCACHLEVKGAGYECPVCKTMVCSLPISCP 266
Query: 389 SCDLMLILSTHLARSYHHLMPLKTFQEVPVSDSFPTDYCFGCQKRFPTLRNNKTGELLTS 448
C L+ + +L++S L PL+ F E C CQ +
Sbjct: 267 ICSTQLVSTLNLSKSLRFLYPLRPFVEKAEGT------CRVCQGK--------------- 305
Query: 449 SRYRCEECDQDFCIDCDVFIHETLHNCPGCE 479
Y+CE C FC C+ IH TL C CE
Sbjct: 306 GAYQCELCKSTFCSYCNRLIHNTLSFCIYCE 336
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
0.320 0.136 0.413
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,817,533
Number of Sequences: 60738
Number of extensions: 1207359
Number of successful extensions: 7299
Number of sequences better than 1.0e-05: 7
Number of HSP's better than 0.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 7268
Number of HSP's gapped (non-prelim): 9
length of query: 488
length of database: 30,389,216
effective HSP length: 110
effective length of query: 378
effective length of database: 23,708,036
effective search space: 8961637608
effective search space used: 8961637608
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)