ORF STATUS Function Best COG Functional category Pathways and functional systems
r_klactV3334 good KL KOG1123 Replication, recombination and repair RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2
r_klactV3334 good KL KOG1123 Transcription RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2
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_klactV3334 1156820 1154247 -858
(858 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
YIL143c [KL] KOG1123 RNA polymerase II transcription initiation/... 1280 0.0
SPAC17A5.06 [KL] KOG1123 RNA polymerase II transcription initiat... 1062 0.0
7294816 [KL] KOG1123 RNA polymerase II transcription initiation/... 768 0.0
Hs4557563 [KL] KOG1123 RNA polymerase II transcription initiatio... 765 0.0
At5g41370 [KL] KOG1123 RNA polymerase II transcription initiatio... 744 0.0
At5g41360 [KL] KOG1123 RNA polymerase II transcription initiatio... 739 0.0
CE28998 [KL] KOG1123 RNA polymerase II transcription initiation/... 731 0.0
ECU01g1060 [KL] KOG1123 RNA polymerase II transcription initiati... 729 0.0
>YIL143c [KL] KOG1123 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH 3'-5' helicase subunit SSL2
Length = 843
Score = 1280 bits (3313), Expect = 0.0
Identities = 646/767 (84%), Positives = 685/767 (89%), Gaps = 5/767 (0%)
Query: 96 AGSGMNHNLAAKDDILHAHLDDIPPDFEPDVVSGMFKTNDFSYLKLKPDHASRPLWISPN 155
A S MN A +L DIP DF PD VSGMF+++DFSYL+L+PDHASRPLWISP+
Sbjct: 78 ADSSMNQMDAKDKALLQDTNSDIPADFVPDSVSGMFRSHDFSYLRLRPDHASRPLWISPS 137
Query: 156 DGRVILESFSPLAEQAQDFLVTIAEPVSRPSHIHEYRITAYSLYAAVSVGLETEDIIAVL 215
DGR+ILESFSPLAEQAQDFLVTIAEP+SRPSHIHEY+ITAYSLYAAVSVGLET+DII+VL
Sbjct: 138 DGRIILESFSPLAEQAQDFLVTIAEPISRPSHIHEYKITAYSLYAAVSVGLETDDIISVL 197
Query: 216 DRLSKVPVAPSIINFIKSATVSYGKVKLVIKHNRYFVETSQADILQMLLNDQIIGNLRIX 275
DRLSKVPVA SIINFIK AT+SYGKVKLVIKHNRYFVET+QADILQMLLND +IG LRI
Sbjct: 198 DRLSKVPVAESIINFIKGATISYGKVKLVIKHNRYFVETTQADILQMLLNDSVIGPLRID 257
Query: 276 XXXXXXXXXXXXMANKMVDA----EGVDPNDVEAVFSAVVGANKELEEEDDDIDAVHAFE 331
A V+PNDVEAVFSAV+G + E EEEDDDIDAVH+FE
Sbjct: 258 SDHQVQPPEDVLQQQLQQTAGKPATNVNPNDVEAVFSAVIGGDNEREEEDDDIDAVHSFE 317
Query: 332 IDNASVEIVKKRCQELDYPVLEEYDFRNDRRNPDLDIDLKPSTQIRPYQEKSLSKMFGNG 391
I N SVE+VKKRCQE+DYPVLEEYDFRND RNPDLDIDLKPSTQIRPYQEKSLSKMFGNG
Sbjct: 318 IANESVEVVKKRCQEIDYPVLEEYDFRNDHRNPDLDIDLKPSTQIRPYQEKSLSKMFGNG 377
Query: 392 RARSGIIVLPCGAGKTLVGITAACTIKKSVIVLCTSSVSVMQWRQQFLQWCTLQPENVAV 451
RARSGIIVLPCGAGKTLVGITAACTIKKSVIVLCTSSVSVMQWRQQFLQWCTLQPEN AV
Sbjct: 378 RARSGIIVLPCGAGKTLVGITAACTIKKSVIVLCTSSVSVMQWRQQFLQWCTLQPENCAV 437
Query: 452 FTSDNKEMFQTESGLVVSTYSMVANTRNRSYDSQKVMDFLTGREWGFIILDEVHVVPAAM 511
FTSDNKEMFQTESGLVVSTYSMVANTRNRS+DSQKVMDFLTGREWGFIILDEVHVVPAAM
Sbjct: 438 FTSDNKEMFQTESGLVVSTYSMVANTRNRSHDSQKVMDFLTGREWGFIILDEVHVVPAAM 497
Query: 512 FRRVVSTIAAHAKLGLTATLVREDDKISDLNFLIGPKLYEANWMELSQKGHIANVQCAEV 571
FRRVVSTIAAHAKLGLTATLVREDDKI DLNFLIGPKLYEANWMELSQKGHIANVQCAEV
Sbjct: 498 FRRVVSTIAAHAKLGLTATLVREDDKIGDLNFLIGPKLYEANWMELSQKGHIANVQCAEV 557
Query: 572 WCPMTAEFYQEYLRENARKRMLLYIMNPTKFQACQFLIQYHEKRGDKIIVFSDNVYALQE 631
WCPMTAEFYQEYLRE ARKRMLLYIMNPTKFQACQFLIQYHE+RGDKIIVFSDNVYALQE
Sbjct: 558 WCPMTAEFYQEYLRETARKRMLLYIMNPTKFQACQFLIQYHERRGDKIIVFSDNVYALQE 617
Query: 632 YALKLGKPFIYGSTPQQERMNILQNFQYNDQINTIFLSKVGDTSIDLPEATCLIQISSHY 691
YALK+GKPFIYGSTPQQERMNILQNFQYNDQINTIFLSKVGDTSIDLPEATCLIQISSHY
Sbjct: 618 YALKMGKPFIYGSTPQQERMNILQNFQYNDQINTIFLSKVGDTSIDLPEATCLIQISSHY 677
Query: 692 GSRRQEAQRLGRILRAKRRNDEGFNAFFYSLVSKDTQEMYYSTKRQAFLVDQGYAFKVIT 751
GSRRQEAQRLGRILRAKRRNDEGFNAFFYSLVSKDTQEMYYSTKRQAFLVDQGYAFKVIT
Sbjct: 678 GSRRQEAQRLGRILRAKRRNDEGFNAFFYSLVSKDTQEMYYSTKRQAFLVDQGYAFKVIT 737
Query: 752 HLHGMENLPNLAYSSAXXXXXXXXXXXXKNEEAAGIEAGEDNDSYIWKNGGNKRPRNKSK 811
HLHGMEN+PNLAY+S KNEEAAGIE G+D D+ + + G N R KSK
Sbjct: 738 HLHGMENIPNLAYASPRERRELLQEVLLKNEEAAGIEVGDDADNSVGR-GSNGHKRFKSK 796
Query: 812 AVKSEGSLAGLAGGEDMAYLEYSSNKNKDLRDHHPLIRKMYYRSANK 858
AV+ EGSL+GLAGGEDMAY+EYS+NKNK+L++HHPLIRKMYY++ K
Sbjct: 797 AVRGEGSLSGLAGGEDMAYMEYSTNKNKELKEHHPLIRKMYYKNLKK 843
>SPAC17A5.06 [KL] KOG1123 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH 3'-5' helicase subunit SSL2
Length = 804
Score = 1062 bits (2746), Expect = 0.0
Identities = 540/743 (72%), Positives = 612/743 (81%), Gaps = 25/743 (3%)
Query: 127 VSGMFKTNDFS-YLKLKPDHASRPLWISPNDGRVILESFSPLAEQAQDFLVTIAEPVSRP 185
+S MF NDFS L LK DH +RPLWI+P DGR+ILE+FSPLAEQA DFLVTI+EPVSRP
Sbjct: 67 ISAMFGQNDFSNLLGLKLDHTARPLWINPIDGRIILEAFSPLAEQAIDFLVTISEPVSRP 126
Query: 186 SHIHEYRITAYSLYAAVSVGLETEDIIAVLDRLSKVPVAPSIINFIKSATVSYGKVKLVI 245
+ IHEYRITAYSLYAAVSVGL+TEDIIAVLDRLSK P+ PSI++FI++ TVSYGKVKLV+
Sbjct: 127 AFIHEYRITAYSLYAAVSVGLKTEDIIAVLDRLSKTPIPPSIVDFIRACTVSYGKVKLVL 186
Query: 246 KHNRYFVETSQADILQMLLNDQIIGNLRIXXXXXXXXXXXXXMANKM-----------VD 294
K NRYF+E+ A +L++LL D +IG LRI +N+
Sbjct: 187 KKNRYFIESGDASVLRLLLRDPVIGPLRIDYSTQSSKQKSSKPSNEDNVEDKKDITNDSS 246
Query: 295 AEGVDPNDVEAVFSAVVGANKELEEEDDDIDAVHAFEIDNASVEIVKKRCQELDYPVLEE 354
E + + + +FSAVVG L+EE+DD DAVH FEI ++SVE +KKRC E+DYP+LEE
Sbjct: 247 KETAEKSSSDELFSAVVG----LQEEEDDEDAVHLFEIKHSSVETIKKRCAEIDYPLLEE 302
Query: 355 YDFRNDRRNPDLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAA 414
YDFRND NPDL IDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAA
Sbjct: 303 YDFRNDNINPDLPIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAA 362
Query: 415 CTIKKSVIVLCTSSVSVMQWRQQFLQWCTLQPENVAVFTSDNKEMFQTESGLVVSTYSMV 474
CTIKKSVIVLCTSSVSVMQWRQQFLQW ++P+++AVFT+D+KE F +E+G+VVSTYSMV
Sbjct: 363 CTIKKSVIVLCTSSVSVMQWRQQFLQWSNIKPDHIAVFTADHKERFHSEAGVVVSTYSMV 422
Query: 475 ANTRNRSYDSQKVMDFLTGREWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVRE 534
ANTRNRSYDSQK+MDFLTGREWGFI+LDEVHVVPAAMFRRVV+TIAAH KLGLTATLVRE
Sbjct: 423 ANTRNRSYDSQKMMDFLTGREWGFILLDEVHVVPAAMFRRVVTTIAAHTKLGLTATLVRE 482
Query: 535 DDKISDLNFLIGPKLYEANWMELSQKGHIANVQCAEVWCPMTAEFYQEYLRENARKRMLL 594
DDKI DLNFLIGPK+YEANWM+L+QKGHIA VQCAEVWC MT EFY EYLREN+RKRMLL
Sbjct: 483 DDKIDDLNFLIGPKMYEANWMDLAQKGHIAKVQCAEVWCAMTTEFYNEYLRENSRKRMLL 542
Query: 595 YIMNPTKFQACQFLIQYHEKRGDKIIVFSDNVYALQEYALKLGKPFIYGSTPQQERMNIL 654
YIMNP KFQACQFLI YHEKRGDKIIVFSDNVYAL+ YA+KLGK FIYG TPQQERM IL
Sbjct: 543 YIMNPKKFQACQFLIDYHEKRGDKIIVFSDNVYALRAYAIKLGKYFIYGGTPQQERMRIL 602
Query: 655 QNFQYNDQINTIFLSKVGDTSIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRRNDEG 714
+NFQYN+ +NTIFLSKVGDTSIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRRNDEG
Sbjct: 603 ENFQYNELVNTIFLSKVGDTSIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRRNDEG 662
Query: 715 FNAFFYSLVSKDTQEMYYSTKRQAFLVDQGYAFKVITHLHGMENLPNLAYSSAXXXXXXX 774
FNAFFYSLVSKDTQEMYYS+KRQAFL+DQGYAFKVIT+L GMENLPNLAY+S
Sbjct: 663 FNAFFYSLVSKDTQEMYYSSKRQAFLIDQGYAFKVITNLKGMENLPNLAYASKAERLELL 722
Query: 775 XXXXXKNEEAAGIEAGEDNDSYIWKNGGNKRPRNKSKAVKSEGSLAGLAGGEDMAYLEYS 834
+NEEAA ++ GED G R +KA +S GSL+ LAG ++MAY+EY+
Sbjct: 723 QEVLLQNEEAADLDDGEDTSF-----GSRSLSRAPAKAKRSSGSLSTLAGADNMAYVEYN 777
Query: 835 SNKN----KDLRDHHPLIRKMYY 853
+ N KD ++HH L RK Y
Sbjct: 778 KSANKQLKKDSKEHHALFRKHLY 800
>7294816 [KL] KOG1123 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH 3'-5' helicase subunit SSL2
Length = 798
Score = 768 bits (1983), Expect = 0.0
Identities = 387/739 (52%), Positives = 510/739 (68%), Gaps = 41/739 (5%)
Query: 137 SYLKLKPDHASRPLWISPNDGRVILESFSPLAEQAQDFLVTIAEPVSRPSHIHEYRITAY 196
S ++L+PDH +RPLW++PN G V LESFSP+ + A DFL+ I+EPV RP HIHEY++TAY
Sbjct: 73 SQMQLRPDHGNRPLWVAPN-GHVFLESFSPVYKHAHDFLIAISEPVCRPEHIHEYKLTAY 131
Query: 197 SLYAAVSVGLETEDIIAVLDRLSKVPVAPSIINFIKSATVSYGKVKLVIKHNRYFVETSQ 256
SLYAAVSVGL+T DI+ L RLSK + I+ FI+ T+SYGKVKLV+KHN+YF+E+
Sbjct: 132 SLYAAVSVGLQTHDIVEYLKRLSKTSIPEGILEFIRLCTLSYGKVKLVLKHNKYFIESPH 191
Query: 257 ADILQMLLNDQIIGNLRIXXXXXXXXXXXXXMANKMVD-------------------AEG 297
++LQ LL D +I R+ + A G
Sbjct: 192 PEVLQKLLKDPVIQKCRLIRSEGEDFIQGTLDGKAITQFGTKLPPGATDKPTPDPAAAAG 251
Query: 298 VD-----PNDVEAVFSAVVGANKELEEEDDDIDAVHAFEIDNASVEIVKKRCQELDYPVL 352
D P D+ + + +KE E+ED+ +FE+ +E+++KRC E+++P+L
Sbjct: 252 ADGTTAVPEDITDFYEKI---DKEEEDEDEANLKTVSFEVAQEKIEVIQKRCIEIEHPLL 308
Query: 353 EEYDFRNDRRNPDLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGIT 412
EYDFRND NPD++IDLKP+ +RPYQEKSL KMFGNGRARSG+IVLPCGAGK+LVG+T
Sbjct: 309 AEYDFRNDTNNPDINIDLKPAAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVT 368
Query: 413 AACTIKKSVIVLCTSSVSVMQWRQQFLQWCTLQPENVAVFTSDNKEMFQTESGLVVSTYS 472
A CT++K +VLC S VSV QW+QQF W T + FTS+ K+ G++V+TYS
Sbjct: 369 ACCTVRKRALVLCNSGVSVEQWKQQFKMWSTADDSMICRFTSEAKDK-PMGCGILVTTYS 427
Query: 473 MVANTRNRSYDSQKVMDFLTGREWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLV 532
M+ +T+ RS+++++ M +L +EWG ++LDEVH +PA MFRRV++ + +H KLGLTATL+
Sbjct: 428 MITHTQKRSWEAEQTMRWLQEQEWGIMVLDEVHTIPAKMFRRVLTIVQSHCKLGLTATLL 487
Query: 533 REDDKISDLNFLIGPKLYEANWMELSQKGHIANVQCAEVWCPMTAEFYQEYLRENARKRM 592
REDDKI+DLNFLIGPKLYEANW+EL +KG+IA VQCAEVWCPM+ EFY+EYL K+M
Sbjct: 488 REDDKIADLNFLIGPKLYEANWLELQKKGYIARVQCAEVWCPMSPEFYREYLTTKTSKKM 547
Query: 593 LLYIMNPTKFQACQFLIQYHEKRGDKIIVFSDNVYALQEYALKLGKPFIYGSTPQQERMN 652
LLY+MNP+KF++CQFLI+YHE+RGDK IVFSDNV+AL+ YA+K+ KPFIYG T Q ER+
Sbjct: 548 LLYVMNPSKFRSCQFLIKYHEQRGDKTIVFSDNVFALKHYAIKMNKPFIYGPTSQNERIQ 607
Query: 653 ILQNFQYNDQINTIFLSKVGDTSIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKR-RN 711
ILQNF++N ++NTIF+SKV DTS DLPEA LIQISSH GSRRQEAQRLGRILRAK+
Sbjct: 608 ILQNFKFNSKVNTIFVSKVADTSFDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKGAI 667
Query: 712 DEGFNAFFYSLVSKDTQEMYYSTKRQAFLVDQGYAFKVITHLHGMENLPNLAYSSAXXXX 771
E +NAFFY+LVS+DT EM YS KRQ FLV+QGY++KVITHL GM+ +L Y +
Sbjct: 668 AEEYNAFFYTLVSQDTMEMSYSRKRQRFLVNQGYSYKVITHLKGMDTDSDLMYGTQEEQG 727
Query: 772 XXXXXXXXKNEEAAGIEAGEDNDSYIWKNGGNKRPRNKSKAVKSEGSLAGLAGGEDMAYL 831
++ E Y RP AV+ G L+ ++GG+D Y
Sbjct: 728 QLLQLVLSASDLDCEDEKLPGEPGY--------RPSGSGGAVRRVGGLSSMSGGDDAIYY 779
Query: 832 EYSSNKNKDLRDHHPLIRK 850
E+ + K++ HPL +K
Sbjct: 780 EH---RKKNIGSVHPLFKK 795
>Hs4557563 [KL] KOG1123 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH 3'-5' helicase subunit SSL2
Length = 782
Score = 765 bits (1975), Expect = 0.0
Identities = 403/731 (55%), Positives = 520/731 (71%), Gaps = 35/731 (4%)
Query: 139 LKLKPDHASRPLWISPNDGRVILESFSPLAEQAQDFLVTIAEPVSRPSHIHEYRITAYSL 198
+ LK DH SRPLW++P DG + LE+FSP+ + AQDFLV IAEPV RP+H+HEY++TAYSL
Sbjct: 65 MPLKDDHTSRPLWVAP-DGHIFLEAFSPVYKYAQDFLVAIAEPVCRPTHVHEYKLTAYSL 123
Query: 199 YAAVSVGLETEDIIAVLDRLSKVPVAPSIINFIKSATVSYGKVKLVIKHNRYFVETSQAD 258
YAAVSVGL+T DI L +LSK V I+ FIK TVSYGKVKLV+KHNRYFVE+ D
Sbjct: 124 YAAVSVGLQTSDITEYLRKLSKTGVPDGIMQFIKLCTVSYGKVKLVLKHNRYFVESCHPD 183
Query: 259 ILQMLLNDQIIGNLRI------XXXXXXXXXXXXXMANKMVDAEG-------VDP---ND 302
++Q LL D +I R+ +K ++ G DP +D
Sbjct: 184 VIQHLLQDPVIRECRLRNSEGEATELITETFTSKSAISKTAESSGGPSTSRVTDPQGKSD 243
Query: 303 VEA-VFSAVVGANKELEEEDDDIDAVHAFEIDNASVEIVKKRCQELDYPVLEEYDFRNDR 361
+ +F +K+ EEE+++ V +FE+ +E ++KRC L+YP+L EYDFRND
Sbjct: 244 IPMDLFDFYEQMDKD-EEEEEETQTV-SFEVKQEMIEELQKRCIHLEYPLLAEYDFRNDS 301
Query: 362 RNPDLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTIKKSV 421
NPD++IDLKP+ +RPYQEKSL KMFGNGRARSG+IVLPCGAGK+LVG+TAACT++K
Sbjct: 302 VNPDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRC 361
Query: 422 IVLCTSSVSVMQWRQQFLQWCTLQPENVAVFTSDNKEMFQTESGLVVSTYSMVANTRNRS 481
+VL S+VSV QW+ QF W T+ + FTSD K+ + +STYSM+ +T RS
Sbjct: 362 LVLGNSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDK-PIGCSVAISTYSMLGHTTKRS 420
Query: 482 YDSQKVMDFLTGREWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVREDDKISDL 541
+++++VM++L +EWG +ILDEVH +PA MFRRV++ + AH KLGLTATLVREDDKI DL
Sbjct: 421 WEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKIVDL 480
Query: 542 NFLIGPKLYEANWMELSQKGHIANVQCAEVWCPMTAEFYQEYLRENARKRMLLYIMNPTK 601
NFLIGPKLYEANWMEL G+IA VQCAEVWCPM+ EFY+EY+ +KR+LLY MNP K
Sbjct: 481 NFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNK 540
Query: 602 FQACQFLIQYHEKRGDKIIVFSDNVYALQEYALKLGKPFIYGSTPQQERMNILQNFQYND 661
F+ACQFLI++HE+R DKIIVF+DNV+AL+EYA++L KP+IYG T Q ERM ILQNF++N
Sbjct: 541 FRACQFLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNP 600
Query: 662 QINTIFLSKVGDTSIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKR-RNDEGFNAFFY 720
+INTIF+SKVGDTS DLPEA LIQISSH GSRRQEAQRLGR+LRAK+ E +NAFFY
Sbjct: 601 KINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFY 660
Query: 721 SLVSKDTQEMYYSTKRQAFLVDQGYAFKVITHLHGMENLPNLAYSSAXXXXXXXXXXXXK 780
SLVS+DTQEM YSTKRQ FLVDQGY+FKVIT L GME +LA+S+ +
Sbjct: 661 SLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEE-EDLAFST----------KEEQ 709
Query: 781 NEEAAGIEAGEDNDSYIWKNGGNKRPRNKSKAVKSEGSLAGLAGGEDMAYLEYSSNKNKD 840
+ + A D D+ G R+ S+A + G+++ ++G +D Y+EY S+++K
Sbjct: 710 QQLLQKVLAATDLDAEEEVVAGEFGSRS-SQASRRFGTMSSMSGADDTVYMEYHSSRSKA 768
Query: 841 LRDH-HPLIRK 850
H HPL ++
Sbjct: 769 PSKHVHPLFKR 779
>At5g41370 [KL] KOG1123 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH 3'-5' helicase subunit SSL2
Length = 755
Score = 744 bits (1922), Expect = 0.0
Identities = 401/747 (53%), Positives = 516/747 (68%), Gaps = 48/747 (6%)
Query: 129 GMFKTNDFSYLKLKPDHASRPLWISPNDGRVILESFSPLAEQAQDFLVTIAEPVSRPSHI 188
G K DF+ L+LKPDH +RPLW DGR+ LE+FSPL +QA DFL+ IAEPV RP +
Sbjct: 33 GEEKKRDFTKLELKPDHGNRPLWACA-DGRIFLETFSPLYKQAYDFLIAIAEPVCRPESM 91
Query: 189 HEYRITAYSLYAAVSVGLETEDIIAVLDRLSKVPVAPSIINFIKSATVSYGKVKLVIKHN 248
HEY +T +SLYAAVSVGLETE II+VL++LSK + +I FI ++T +YGKVKLV+K N
Sbjct: 92 HEYNLTPHSLYAAVSVGLETETIISVLNKLSKTKLPKEMIEFIHASTANYGKVKLVLKKN 151
Query: 249 RYFVETSQADILQMLLNDQIIGNLRIXXXXXXXXXXXXXMANKMVDAEGVDPNDV--EAV 306
RYF+E+ ++L+ LL+D +I R + P ++ EA
Sbjct: 152 RYFIESPFPEVLKRLLSDDVINRARFSSEPYYGGDGFS--VGRTCGELEAGPGELLNEAE 209
Query: 307 FSAVVGANKELEEEDDDIDAVHAFEIDNASVEIVKKRC--QELDYPVLEEYDFRNDRRNP 364
F+A EE++ H+FEID A VE VK+RC L+YP+LEEYDFRND NP
Sbjct: 210 FAAAA------EEKE-----THSFEIDPAQVENVKQRCLPNALNYPMLEEYDFRNDNVNP 258
Query: 365 DLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTIKKSVIVL 424
DLD++LKP Q RPYQEKSLSKMFGNGRARSGIIVLPCGAGK+LVG++AA IKKS + L
Sbjct: 259 DLDMELKPHAQPRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVSAAARIKKSCLCL 318
Query: 425 CTSSVSVMQWRQQFLQWCTLQPENVAVFTSDNKEMFQTESGLVVSTYSMVANTRNRSYDS 484
T++VSV QW QF W T++ + + FTSD+KE F+ +G+VV+TY+MVA RS +S
Sbjct: 319 ATNAVSVDQWAFQFKLWSTIRDDQICRFTSDSKERFRGNAGVVVTTYNMVAFGGKRSEES 378
Query: 485 QKVMDFLTGREWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVREDDKISDLNFL 544
+K+++ + REWG +++DEVHVVPA MFR+V+S +H KLGLTATLVRED++I+DLNFL
Sbjct: 379 EKIIEEMRNREWGLLLMDEVHVVPAHMFRKVISITKSHCKLGLTATLVREDERITDLNFL 438
Query: 545 IGPKLYEANWMELSQKGHIANVQCAEVWCPMTAEFYQEYL-RENARKRMLLYIMNPTKFQ 603
IGPKLYEANW++L + G IANVQCAEVWCPMT EF+ EYL +EN++K+ LY+MNP KF+
Sbjct: 439 IGPKLYEANWLDLVKGGFIANVQCAEVWCPMTKEFFAEYLKKENSKKKQALYVMNPNKFR 498
Query: 604 ACQFLIQYHE-KRGDKIIVFSDNVYALQEYALKLGKPFIYGSTPQQERMNILQNFQYNDQ 662
AC+FLI++HE +RGDKIIVF+DN++AL EYA+KL KP IYG+T ER IL+ F+ +
Sbjct: 499 ACEFLIRFHEQQRGDKIIVFADNLFALTEYAMKLRKPMIYGATSHIERTKILEAFKTSKD 558
Query: 663 INTIFLSKVGDTSIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRR-------NDEGF 715
+NT+FLSKVGD SID+PEA +IQISSH GSRRQEAQRLGRILRAK + E +
Sbjct: 559 VNTVFLSKVGDNSIDIPEANVIIQISSHAGSRRQEAQRLGRILRAKGKLEDRMAGGKEEY 618
Query: 716 NAFFYSLVSKDTQEMYYSTKRQAFLVDQGYAFKVITHLHGMENLPNLAYSSAXXXXXXXX 775
NAFFYSLVS DTQEMYYSTKRQ FL+DQGY+FKVIT L + +L+Y S
Sbjct: 619 NAFFYSLVSTDTQEMYYSTKRQQFLIDQGYSFKVITSLPPPDAGSSLSYHSQEEQLSLLG 678
Query: 776 XXXXKNEEAAGIE-AGEDNDSYIWKNGGNKRPRNKSKAVKSEGSLAGLAGGEDMAYLEYS 834
++ G+E ED D + KA +S GS++ ++G + M Y+EY+
Sbjct: 679 KVMNAGDDLVGLEQLEEDTDGMALQ-----------KARRSMGSMSVMSGSKGMVYMEYN 727
Query: 835 S---------NKNKDLRDHHPLIRKMY 852
S K KD H L +K Y
Sbjct: 728 SGRHKSGQQFKKPKDPTKRHNLFKKRY 754
>At5g41360 [KL] KOG1123 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH 3'-5' helicase subunit SSL2
Length = 754
Score = 739 bits (1908), Expect = 0.0
Identities = 396/747 (53%), Positives = 512/747 (68%), Gaps = 49/747 (6%)
Query: 129 GMFKTNDFSYLKLKPDHASRPLWISPNDGRVILESFSPLAEQAQDFLVTIAEPVSRPSHI 188
G K DF+ L+LKPDH +RPLW DG++ LE+FSPL +QA DFL+ IAEPV RP +
Sbjct: 33 GEEKRRDFTDLELKPDHGNRPLWACA-DGKIFLETFSPLYKQAYDFLIAIAEPVCRPESM 91
Query: 189 HEYRITAYSLYAAVSVGLETEDIIAVLDRLSKVPVAPSIINFIKSATVSYGKVKLVIKHN 248
HEY +T +SLYAAVSVGLETE II+VL++LSK + II+FI ++T +YGKVKLV+K N
Sbjct: 92 HEYNLTPHSLYAAVSVGLETETIISVLNKLSKTKLPGEIIDFIHASTANYGKVKLVLKKN 151
Query: 249 RYFVETSQADILQMLLNDQIIGNLRIXXX--XXXXXXXXXXMANKMVDAEGVDPNDVEAV 306
RYF+E+ ++L+ LL+D +I R + ++ G N+ E
Sbjct: 152 RYFIESPFPEVLKRLLSDDVINRARFTSEPYYGGDGFTIGKTSGELEAGPGELLNEAELA 211
Query: 307 FSAVVGANKELEEEDDDIDAVHAFEIDNASVEIVKKRC--QELDYPVLEEYDFRNDRRNP 364
+A EE++ H+FEID A VE VK+RC L+YP+LEEYDFRND NP
Sbjct: 212 AAA--------EEKE-----THSFEIDPALVENVKQRCLPNALNYPMLEEYDFRNDNVNP 258
Query: 365 DLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTIKKSVIVL 424
DLD++LKP Q RPYQEKSLSKMFGNGRARSGIIVLPCGAGK+LVG++AA IKKS + L
Sbjct: 259 DLDMELKPHAQPRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVSAAARIKKSCLCL 318
Query: 425 CTSSVSVMQWRQQFLQWCTLQPENVAVFTSDNKEMFQTESGLVVSTYSMVANTRNRSYDS 484
T++VSV QW QF W T++ + + FTSD+KE F+ +G+VV+TY+M+A RS ++
Sbjct: 319 ATNAVSVDQWAYQFKLWSTIKDDQICRFTSDSKERFRGNAGVVVTTYNMIAFGGKRSEEA 378
Query: 485 QKVMDFLTGREWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVREDDKISDLNFL 544
+K+++ + REWG +++DEVHVVPA MFR+V+S +H KLGLTATLVRED+KI+DLNFL
Sbjct: 379 EKIIEEMRNREWGLLLMDEVHVVPAHMFRKVISITKSHCKLGLTATLVREDEKITDLNFL 438
Query: 545 IGPKLYEANWMELSQKGHIANVQCAEVWCPMTAEFYQEYL-RENARKRMLLYIMNPTKFQ 603
IGPKLYEANW++L + G IANVQCAEVWCPMT EF+ EYL +EN++K+ LY+MNP KF+
Sbjct: 439 IGPKLYEANWLDLVKGGFIANVQCAEVWCPMTKEFFAEYLKKENSKKKQALYVMNPNKFR 498
Query: 604 ACQFLIQYHE-KRGDKIIVFSDNVYALQEYALKLGKPFIYGSTPQQERMNILQNFQYNDQ 662
AC+FLI++HE +RGDKIIVF+DN++AL EYA+KL KP IYG+T ER IL+ F+ +
Sbjct: 499 ACEFLIRFHEQQRGDKIIVFADNLFALTEYAMKLRKPMIYGATSHIERTKILEAFKTSKT 558
Query: 663 INTIFLSKVGDTSIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRR-------NDEGF 715
+NT+FLSKVGD SID+PEA +IQISSH GSRRQEAQRLGRILRAK + E +
Sbjct: 559 VNTVFLSKVGDNSIDIPEANVIIQISSHAGSRRQEAQRLGRILRAKGKLEDRMAGGKEEY 618
Query: 716 NAFFYSLVSKDTQEMYYSTKRQAFLVDQGYAFKVITHLHGMENLPNLAYSSAXXXXXXXX 775
NAFFYSLVS DTQEMYYSTKRQ FL+DQGY+FKVIT L + +L Y S
Sbjct: 619 NAFFYSLVSTDTQEMYYSTKRQQFLIDQGYSFKVITSLPPPDAGSSLGYHSQEEQLSLLG 678
Query: 776 XXXXKNEEAAGIE-AGEDNDSYIWKNGGNKRPRNKSKAVKSEGSLAGLAGGEDMAYLEYS 834
++ G+E ED D K +S GS++ ++G Y+EY+
Sbjct: 679 KVLNAGDDMVGLEQLEEDTDG------------KALKTRRSMGSMSAMSGANGRVYMEYN 726
Query: 835 ---------SNKNKDLRDHHPLIRKMY 852
S K KD H + +K Y
Sbjct: 727 SGRQKSGNQSKKPKDPTKRHNIFKKRY 753
>CE28998 [KL] KOG1123 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH 3'-5' helicase subunit SSL2
Length = 789
Score = 731 bits (1887), Expect = 0.0
Identities = 388/753 (51%), Positives = 509/753 (67%), Gaps = 45/753 (5%)
Query: 126 VVSGMFKTNDFSY-LKLKPDHASRPLWISPNDGRVILESFSPLAEQAQDFLVTIAEPVSR 184
V++ F D+ + LK D +RPLW++P DG + LESFSP+ + A+DFL+ I+EPV R
Sbjct: 51 VMTDEFGAKDYRKDMPLKGDFTARPLWVAP-DGHIFLESFSPVYKHARDFLIAISEPVCR 109
Query: 185 PSHIHEYRITAYSLYAAVSVGLETEDIIAVLDRLSKVPVAPSIINFIKSATVSYGKVKLV 244
P HIHEY++TAYSLYAAVSVGL+T+DII L+RLSK + +I F++ TVSYGKVKLV
Sbjct: 110 PQHIHEYQLTAYSLYAAVSVGLQTKDIIEYLERLSKSQLPKGVITFVQMCTVSYGKVKLV 169
Query: 245 IKHNRYFVETSQADILQMLLNDQIIGNLRIXXXXXXXXXXXXXMANKM------VDAEGV 298
+KHNRYFVE+ +D++Q LL D +I + + K+ + +GV
Sbjct: 170 LKHNRYFVESRHSDVMQKLLKDSVIQSCILDDRVQPAQQTELPAQEKIKFSHGNENEKGV 229
Query: 299 DPNDVEAVFSAVVGANKELEEE----------DDDIDA------VHAFEIDNASVEIVKK 342
+ + A +A + ++ + DD+ DA + FEI ++E V+K
Sbjct: 230 EKDGAAADGTAAAATDGKVPADIDEFYGKIDGDDEEDAEIRNLQLLTFEIKQETIETVQK 289
Query: 343 RCQELDYPVLEEYDFRNDRRNPDLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPC 402
RC EL+YP+L EYDFRND NP+L IDLKPST +RPYQEKSL KMFGN RARSG+IVLPC
Sbjct: 290 RCIELEYPLLAEYDFRNDTLNPNLGIDLKPSTTLRPYQEKSLRKMFGNSRARSGVIVLPC 349
Query: 403 GAGKTLVGITAACTIKKSVIVLCTSSVSVMQWRQQFLQWCTLQPENVAVFTSDNKE---- 458
GAGKTLVG+TA T+ K +VL S+VSV QWR QF W T+Q + + FT + K+
Sbjct: 350 GAGKTLVGVTAVTTVNKRCLVLANSNVSVEQWRAQFKLWSTIQDKQLVRFTREAKDPAPS 409
Query: 459 -MFQTESGLVVSTYSMVANTRNRSYDSQKVMDFLTGREWGFIILDEVHVVPAAMFRRVVS 517
T+ + +STYSMVA + R+ +++ M F+ +EWG ++LDEVH +PA MFRRV++
Sbjct: 410 GADATKPVVCISTYSMVAYSGRRTLQAEEAMKFIEKQEWGLLLLDEVHTIPAKMFRRVLT 469
Query: 518 TIAAHAKLGLTATLVREDDKISDLNFLIGPKLYEANWMELSQKGHIANVQCAEVWCPMTA 577
+ AH KLGLTATLVREDDKI+DLNFLIGPK+YEANWMEL + GHIA VQCAEVWCPMT+
Sbjct: 470 IVQAHCKLGLTATLVREDDKITDLNFLIGPKIYEANWMELQKAGHIAKVQCAEVWCPMTS 529
Query: 578 EFYQEYLRENARKRMLLYIMNPTKFQACQFLIQYHEKRGDKIIVFSDNVYALQEYALKLG 637
FY YLR +++LL +MNP KF+ CQFLI++HE+R DKIIVFSDNV+AL+ YA+++
Sbjct: 530 AFYSYYLRSQIARKLLLAVMNPNKFRICQFLIKFHERRNDKIIVFSDNVFALKRYAIEMQ 589
Query: 638 KPFIYGSTPQQERMNILQNFQYNDQINTIFLSKVGDTSIDLPEATCLIQISSHYGSRRQE 697
KPF+YG T Q ERM ILQNFQYN ++NTIF+SKV DTS DLPEA LIQIS+H GSRRQE
Sbjct: 590 KPFLYGETSQNERMKILQNFQYNPRVNTIFVSKVADTSFDLPEANVLIQISAHGGSRRQE 649
Query: 698 AQRLGRILRAKRRNDEGFNAFFYSLVSKDTQEMYYSTKRQAFLVDQGYAFKVITHLHGME 757
AQRLGRILRAK+ + + FNAFFYSLVS+DT EM YS KRQ FLV+QGYA+KV+ +L GME
Sbjct: 650 AQRLGRILRAKKHSTDQFNAFFYSLVSQDTVEMGYSRKRQRFLVNQGYAYKVVNNLPGME 709
Query: 758 NLPNLAYSSAXXXXXXXXXXXXKNEEAAGIEAGEDNDSYIWKNGGNKRPRNKSKAVKSEG 817
L +L +S ++ A E+ D G R + E
Sbjct: 710 -LEDLKLASKESQLQLLQQVLATSDADA-----EEEDVKEELADGTIR------ISRREA 757
Query: 818 SLAGLAGGEDMAYLEYSSNKNKDLRDHHPLIRK 850
++A ++GG+ Y +K K + + HPL ++
Sbjct: 758 TMASMSGGQGAQY----HSKAKAIAERHPLFKR 786
>ECU01g1060 [KL] KOG1123 RNA polymerase II transcription initiation/nucleotide
excision repair factor TFIIH 3'-5' helicase subunit SSL2
Length = 696
Score = 729 bits (1881), Expect = 0.0
Identities = 388/724 (53%), Positives = 485/724 (66%), Gaps = 66/724 (9%)
Query: 120 PDFEPDVVSGMFKTNDFSY--LKLKPDHASRPLWISPNDGRVILESFSPLAEQAQDFLVT 177
P+ V+ + F Y L LK D S P+W++ DG +ILE+F + QA DFL+
Sbjct: 23 PEMNEVVIPKKATKHQFPYEELVLKEDGESHPIWVN-YDGLIILETFRESSRQASDFLIA 81
Query: 178 IAEPVSRPSHIHEYRITAYSLYAAVSVGLETEDIIAVLDRLSKVPVAPSIINFIKSATVS 237
IAEP+SRP IHE++ITAYSLYAAVSVGL T DII LDR SK + S+ FI T+S
Sbjct: 82 IAEPMSRPLQIHEFQITAYSLYAAVSVGLTTSDIIETLDRFSKNFLPRSVRVFITECTLS 141
Query: 238 YGKVKLVIKHNRYFVETSQADILQMLLNDQIIGNLRIXXXXXXXXXXXXXMANKMVDAEG 297
YGKVKLV+K + +F+ET+ + +ML +D +I
Sbjct: 142 YGKVKLVMKESSFFLETANESVYKMLSSDAVIR--------------------------- 174
Query: 298 VDPNDVEAVFSAVVGANKELEEEDDDIDAVHAFEIDNASVEIVKKRCQELDYPVLEEYDF 357
S +G +KE I+ VE+VKKRC E+DYP++EEYDF
Sbjct: 175 ----------SHTIGKSKE----------GGGLSIEVEEVELVKKRCIEIDYPLIEEYDF 214
Query: 358 RNDRRNPDLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTI 417
RND+ L IDLKP+T IR YQE L+KMFGNGRARSGIIVLPCG+GKT+VGITA TI
Sbjct: 215 RNDKVLRSLQIDLKPTTIIRSYQEICLNKMFGNGRARSGIIVLPCGSGKTIVGITAISTI 274
Query: 418 KKSVIVLCTSSVSVMQWRQQFLQWCTLQPENVAVFTSDNKEMFQTESGLVVSTYSMVANT 477
KK+ +VLCTS+VSV QW+QQ LQ+ + P+ V FTSD+KE + +SG+V++TY+M+A T
Sbjct: 275 KKNCLVLCTSAVSVEQWKQQTLQFTNMAPDGVGRFTSDHKEWPKDDSGIVITTYTMLAYT 334
Query: 478 RNRSYDSQKVMDFLTGREWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVREDDK 537
RS+++QK+MD + EWG ++LDEVHVVPA MFRRV+S ++ H KLGLTATLVREDDK
Sbjct: 335 GKRSHEAQKIMDLIRRTEWGLLVLDEVHVVPAMMFRRVLSLVSHHCKLGLTATLVREDDK 394
Query: 538 ISDLNFLIGPKLYEANWMELSQKGHIANVQCAEVWCPMTAEFYQEYLRENARKRMLLYIM 597
I DLNFLIGPKLYEA+W +LS KGHIA V C EVWC MT +FY+EYL + R+R LL IM
Sbjct: 395 IEDLNFLIGPKLYEADWQDLSAKGHIARVSCIEVWCGMTGDFYREYLSQPTRRRRLLSIM 454
Query: 598 NPTKFQACQFLIQYHEKRGDKIIVFSDNVYALQEYALKLGKPFIYGSTPQQERMNILQNF 657
NPTKFQ C++LI HE RGDKIIVFSD+VYAL+ YALKLGKPFIYG T Q ERM IL+ F
Sbjct: 455 NPTKFQVCEYLINKHESRGDKIIVFSDSVYALKAYALKLGKPFIYGPTGQTERMRILKQF 514
Query: 658 QYNDQINTIFLSKVGDTSIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRRNDEGFNA 717
Q N INTIFLSKVGDTSIDLPEATCLIQISSH+GSRRQEAQRLGRILRAKRRND F
Sbjct: 515 QTNPVINTIFLSKVGDTSIDLPEATCLIQISSHFGSRRQEAQRLGRILRAKRRNDPDFKV 574
Query: 718 FFYSLVSKDTQEMYYSTKRQAFLVDQGYAFKVITHLHGMENLPNLAYSSAXXXXXXXXXX 777
+FYSLVSKDT EM+YS+KRQ FL+DQGY F ++T + + + Y +
Sbjct: 575 YFYSLVSKDTDEMFYSSKRQQFLIDQGYTFTILTDIPEVHENEHCVYKTKGQQRELLAGV 634
Query: 778 XXKNEEAAGIEAGEDNDSYIWKNGGNKRPRNKSKAVKSEGSLAGLAGGEDMAYLEYSSNK 837
+E+ E ED++ ++ S L L+GG++MAY+E + +
Sbjct: 635 LLASEKELESEESEDSEGIVY----------------STTKLKSLSGGDEMAYIERKAPQ 678
Query: 838 NKDL 841
+ L
Sbjct: 679 GRTL 682
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 0.386
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 47,698,892
Number of Sequences: 60738
Number of extensions: 1983609
Number of successful extensions: 5020
Number of sequences better than 1.0e-05: 8
Number of HSP's better than 0.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 4977
Number of HSP's gapped (non-prelim): 13
length of query: 858
length of database: 30,389,216
effective HSP length: 115
effective length of query: 743
effective length of database: 23,404,346
effective search space: 17389429078
effective search space used: 17389429078
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)