Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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= Dr_sW_008_A04
(708 letters)
Database: Non-redundant SwissProt sequences
184,735 sequences; 68,354,980 total letters
Score E
Sequences producing significant alignments: (bits) Value
sp|Q8VD76|TF2H3_MOUSE TFIIH basal transcription factor comp... 122 9e-28
sp|Q13889|TF2H3_HUMAN TFIIH basal transcription factor comp... 120 3e-27
sp|O74366|TFB4_SCHPO RNA polymerase II transcription factor... 89 1e-17
sp|Q6CD24|TFB4_YARLI RNA polymerase II transcription factor... 78 2e-14
sp|Q6CVX9|TFB4_KLULA RNA polymerase II transcription factor... 77 6e-14
sp|Q75B93|TFB4_ASHGO RNA polymerase II transcription factor... 73 6e-13
sp|Q6BL86|TFB4_DEBHA RNA polymerase II transcription factor... 72 1e-12
sp|Q12004|TFB4_YEAST RNA polymerase II transcription factor... 70 4e-12
sp|Q6FWA7|TFB4_CANGA RNA polymerase II transcription factor... 70 4e-12
sp|Q04673|SSL1_YEAST Suppressor of stem-loop protein 1 36 0.11
>sp|Q8VD76|TF2H3_MOUSE TFIIH basal transcription factor complex p34 subunit (Basic
transcription factor 2 34 kDa subunit) (BTF2-p34)
(General transcription factor IIH polypeptide 3)
Length = 309
Score = 122 bits (306), Expect = 9e-28
Identities = 61/176 (34%), Positives = 101/176 (57%)
Frame = +1
Query: 22 SFIKSLCYYKRILKIHKTHNNQLGFCGRFIVVRTGLPDSSASFMSMMNGVFTAQKHDICI 201
S K+LCY R+ K K + R +V++ DS+ +M+ MN +F AQK +I I
Sbjct: 137 SLAKALCYIHRVNKAVKDNQEMKS---RILVIKAA-EDSALQYMNFMNVIFAAQKQNILI 192
Query: 202 DVCILNPDEAIMHNNLHSNEFDKANILRQSVDMTNGIYLTINKIRDLLQYFITLYLTDVA 381
D C+L+ D + +L+Q+ D+T G+YL + ++ LLQY + ++L D
Sbjct: 193 DACVLDSD---------------SGLLQQACDITGGLYLKVPQMPSLLQYLLWVFLPDQD 237
Query: 382 DRQFMTMINNSNVDIDFRASCFCHGTLVSVGYVCSLCLAVFCHYSSLCACCYAVFQ 549
R +I + +D+RA+CFCH +L+ +GYVCS+CL++FC++S +C C F+
Sbjct: 238 QRS--QLILPPPIHVDYRAACFCHRSLIEIGYVCSVCLSIFCNFSPICTTCETAFK 291
>sp|Q13889|TF2H3_HUMAN TFIIH basal transcription factor complex p34 subunit (Basic
transcription factor 2 34 kDa subunit) (BTF2-p34)
(General transcription factor IIH polypeptide 3)
Length = 308
Score = 120 bits (302), Expect = 3e-27
Identities = 62/176 (35%), Positives = 100/176 (56%)
Frame = +1
Query: 22 SFIKSLCYYKRILKIHKTHNNQLGFCGRFIVVRTGLPDSSASFMSMMNGVFTAQKHDICI 201
S K+LCY R+ K K + R +V++ DS+ +M+ MN +F AQK +I I
Sbjct: 136 SLAKALCYIHRMNKEVKDNQEMKS---RILVIKAA-EDSALQYMNFMNVIFAAQKQNILI 191
Query: 202 DVCILNPDEAIMHNNLHSNEFDKANILRQSVDMTNGIYLTINKIRDLLQYFITLYLTDVA 381
D C+L+ D + +L+Q+ D+T G+YL + ++ LLQY + ++L D
Sbjct: 192 DACVLDSD---------------SGLLQQACDITGGLYLKVPQMPSLLQYLLWVFLPDQD 236
Query: 382 DRQFMTMINNSNVDIDFRASCFCHGTLVSVGYVCSLCLAVFCHYSSLCACCYAVFQ 549
R +I V +D+RA+CFCH L+ +GYVCS+CL++FC++S +C C F+
Sbjct: 237 QRS--QLILPPPVHVDYRAACFCHRNLIEIGYVCSVCLSIFCNFSPICTTCETAFK 290
>sp|O74366|TFB4_SCHPO RNA polymerase II transcription factor B subunit 4 (RNA polymerase
II transcription factor B p34 subunit) (RNA polymerase
II transcription factor B 34 kDa subunit)
Length = 297
Score = 88.6 bits (218), Expect = 1e-17
Identities = 48/138 (34%), Positives = 73/138 (52%)
Frame = +1
Query: 133 DSSASFMSMMNGVFTAQKHDICIDVCILNPDEAIMHNNLHSNEFDKANILRQSVDMTNGI 312
D + ++ MN +F AQK +I I+VC N+ L Q+ D T GI
Sbjct: 166 DVALQYIPTMNCIFCAQKKNIPINVC-----------NIEGGTL----FLEQAADATGGI 210
Query: 313 YLTINKIRDLLQYFITLYLTDVADRQFMTMINNSNVDIDFRASCFCHGTLVSVGYVCSLC 492
YL ++ + LLQY + D R+ + N +NVD FRA+CFCH ++ +G+VCS+C
Sbjct: 211 YLKVDNPKGLLQYLMMSLFPDQNLRKHLNTPNQANVD--FRATCFCHKKVLDIGFVCSVC 268
Query: 493 LAVFCHYSSLCACCYAVF 546
L++FC C+ C+ F
Sbjct: 269 LSIFCEPRVHCSTCHTKF 286
>sp|Q6CD24|TFB4_YARLI RNA polymerase II transcription factor B subunit 4 (RNA polymerase
II transcription factor B p34 subunit) (RNA polymerase
II transcription factor B 34 kDa subunit)
Length = 340
Score = 78.2 bits (191), Expect = 2e-14
Identities = 48/158 (30%), Positives = 81/158 (51%), Gaps = 7/158 (4%)
Frame = +1
Query: 103 RFIVVRTGLPDSSASFMSMMNGVFTAQKHDICIDVCILNPDEAIMHNNLHSNEFDKANIL 282
R +++ G + + ++ MN +F AQK I +DVC L P + L
Sbjct: 178 RILLLTVGHKNETIQYIPTMNCIFAAQKLKIPVDVCKLGPGSDQV-------------FL 224
Query: 283 RQSVDMTNGIYLTINKI-----RDLLQYFITLYLTDVADRQFMTMINNSNVDIDFRASCF 447
+Q+ D T+GIY+ I++ + L+QY ++ +++D + R + + SNVD FRA+CF
Sbjct: 225 QQACDSTHGIYMDISEKNSKTPKGLVQYLLSGFISDPSLRPHIVLPTQSNVD--FRAACF 282
Query: 448 CHGTLVSVGYVCSLCLAVFCHYSS--LCACCYAVFQDK 555
+V +GYVCS+CL + S C C + +K
Sbjct: 283 LTKQVVDIGYVCSVCLCIMSQIPSNRRCPTCDTTYSEK 320
>sp|Q6CVX9|TFB4_KLULA RNA polymerase II transcription factor B subunit 4 (RNA polymerase
II transcription factor B p34 subunit) (RNA polymerase
II transcription factor B 34 kDa subunit)
Length = 337
Score = 76.6 bits (187), Expect = 6e-14
Identities = 55/179 (30%), Positives = 80/179 (44%), Gaps = 5/179 (2%)
Frame = +1
Query: 34 SLCYYKRILKIHKTHNNQLGFCGRFIVVRTGLP---DSSASFMSMMNGVFTAQKHDICID 204
+L Y RILK N R +V+ G D ++ +MN +F+A K ID
Sbjct: 154 ALTYVNRILK----ENENTSLRSRLLVITCGTSQGKDEIFQYIPIMNCIFSATKMKCSID 209
Query: 205 VCILNPDEAIMHNNLHSNEFDKANILRQSVDMTNGIYLTINKIRDLLQYFITLYLTDVAD 384
V + ++ L+Q+ D T+G+YL + R L+QY T D +
Sbjct: 210 VVKIGGGI-------------ESTFLQQATDATSGVYLHVENTRGLIQYLSTAMFIDPSL 256
Query: 385 RQFMTMINNSNVDIDFRASCFCHGTLVSVGYVCSLCLAVFCHY--SSLCACCYAVFQDK 555
R + N +VD FR SCF G +V+VG+VCS+CL V C C + F K
Sbjct: 257 RNVIIKPNQGSVD--FRTSCFLTGKVVAVGFVCSVCLCVLSVIPPGQKCPACDSPFDSK 313
>sp|Q75B93|TFB4_ASHGO RNA polymerase II transcription factor B subunit 4 (RNA polymerase
II transcription factor B p34 subunit) (RNA polymerase
II transcription factor B 34 kDa subunit)
Length = 341
Score = 73.2 bits (178), Expect = 6e-13
Identities = 56/180 (31%), Positives = 84/180 (46%), Gaps = 5/180 (2%)
Frame = +1
Query: 37 LCYYKRILKIHKTHNNQLGFCGRFIVVRTGLP---DSSASFMSMMNGVFTAQKHDICIDV 207
L Y RI H+T L R +V+ G D ++ +MN +F+A K IDV
Sbjct: 158 LTYINRIT--HETEGVSLK--SRLLVITCGSSASKDEVFQYIPIMNCIFSATKMKCPIDV 213
Query: 208 CILNPDEAIMHNNLHSNEFDKANILRQSVDMTNGIYLTINKIRDLLQYFITLYLTDVADR 387
+ ++ L+Q+ D TNG YL + L+QY T D + R
Sbjct: 214 -------------VKVGGVKESTFLQQATDATNGNYLHVANTDGLIQYLSTAMFIDPSLR 260
Query: 388 QFMTMINNSNVDIDFRASCFCHGTLVSVGYVCSLCLAVFCHY--SSLCACCYAVFQDKKV 561
Q++ N S+VD FR SC+ G +V++G+VCS+CL V + C C + F +K V
Sbjct: 261 QWVVKPNQSSVD--FRTSCYLTGKVVAIGFVCSVCLCVLSIIPPGNKCPACDSEFDEKVV 318
>sp|Q6BL86|TFB4_DEBHA RNA polymerase II transcription factor B subunit 4 (RNA polymerase
II transcription factor B p34 subunit) (RNA polymerase
II transcription factor B 34 kDa subunit)
Length = 387
Score = 72.0 bits (175), Expect = 1e-12
Identities = 46/151 (30%), Positives = 75/151 (49%), Gaps = 2/151 (1%)
Frame = +1
Query: 109 IVVRTGLPDSSASFMSMMNGVFTAQKHDICIDVCILNPDEAIMHNNLHSNEFDKANILRQ 288
I++ + D+ ++ +MN F AQK + IDV L ++ + L+Q
Sbjct: 219 ILIVSSNDDNDIKYIPIMNTTFAAQKMKVPIDVAKLGERDS--------------SYLQQ 264
Query: 289 SVDMTNGIYLTINKIRDLLQYFITLYLTDVADRQFMTMINNSNVDIDFRASCFCHGTLVS 468
+ D TNG+YL I L+Q T + + + R + + NSNV+ +RASCF G V+
Sbjct: 265 ASDATNGVYLHIANPEGLIQTLSTAFFIEPSIRLLIILPTNSNVN--YRASCFITGKSVN 322
Query: 469 VGYVCSLCLAV--FCHYSSLCACCYAVFQDK 555
+G+VCS+CL + C C + F +K
Sbjct: 323 LGFVCSVCLCIMSIIPKEGKCPTCGSKFDEK 353
>sp|Q12004|TFB4_YEAST RNA polymerase II transcription factor B subunit 4 (RNA polymerase
II transcription factor B p34 subunit) (RNA polymerase
II transcription factor B 34 kDa subunit)
Length = 338
Score = 70.5 bits (171), Expect = 4e-12
Identities = 51/177 (28%), Positives = 82/177 (46%), Gaps = 5/177 (2%)
Frame = +1
Query: 37 LCYYKRILKIHKTHNNQLGFCGRFIVVRTGL---PDSSASFMSMMNGVFTAQKHDICIDV 207
L Y RI K T + + R +V+ G D ++ +MN +F+A K IDV
Sbjct: 157 LTYVNRISKESVTTSLK----SRLLVLTCGSGSSKDEIFQYIPIMNCIFSATKMKCPIDV 212
Query: 208 CILNPDEAIMHNNLHSNEFDKANILRQSVDMTNGIYLTINKIRDLLQYFITLYLTDVADR 387
+ + ++ L+Q+ D TNG+YL + L+QY T D + R
Sbjct: 213 VKIGGSK-------------ESTFLQQTTDATNGVYLHVESTEGLIQYLATAMFIDPSLR 259
Query: 388 QFMTMINNSNVDIDFRASCFCHGTLVSVGYVCSLCLAVFCHY--SSLCACCYAVFQD 552
+ N+ +VD FR SC+ G +V+VG++CS+CL V + C C + F +
Sbjct: 260 PIIVKPNHGSVD--FRTSCYLTGRVVAVGFICSVCLCVLSIIPPGNKCPACDSQFDE 314
>sp|Q6FWA7|TFB4_CANGA RNA polymerase II transcription factor B subunit 4 (RNA polymerase
II transcription factor B p34 subunit) (RNA polymerase
II transcription factor B 34 kDa subunit)
Length = 335
Score = 70.5 bits (171), Expect = 4e-12
Identities = 46/181 (25%), Positives = 86/181 (47%), Gaps = 5/181 (2%)
Frame = +1
Query: 34 SLCYYKRILKIHKTHNNQLGFCGRFIVVRTGLP---DSSASFMSMMNGVFTAQKHDICID 204
+L Y R+ K ++ + R +V+ G D ++ +MN +F+A K ID
Sbjct: 153 ALTYTNRLTKEFES----ISLRSRLLVITCGSSREKDEIFQYIPIMNCIFSATKLKCPID 208
Query: 205 VCILNPDEAIMHNNLHSNEFDKANILRQSVDMTNGIYLTINKIRDLLQYFITLYLTDVAD 384
V + ++ ++ L+Q+ D TNG+Y+ + ++QY T D +
Sbjct: 209 VIKIGGNK-------------QSTFLQQTTDATNGVYIHLESTNGIIQYLSTAMSIDPSL 255
Query: 385 RQFMTMINNSNVDIDFRASCFCHGTLVSVGYVCSLCLAVFCHY--SSLCACCYAVFQDKK 558
RQ + + + +DFR SC+ G +V++GY+CS+CL V + C C + F ++
Sbjct: 256 RQII--VRPTQGSVDFRTSCYLTGKVVAIGYICSVCLCVLSIIPPGNKCPACDSQFDERV 313
Query: 559 V 561
+
Sbjct: 314 I 314
>sp|Q04673|SSL1_YEAST Suppressor of stem-loop protein 1
Length = 461
Score = 35.8 bits (81), Expect = 0.11
Identities = 13/31 (41%), Positives = 16/31 (51%)
Frame = +1
Query: 442 CFCHGTLVSVGYVCSLCLAVFCHYSSLCACC 534
C CH LV GY C C + C ++C CC
Sbjct: 336 CSCHSKLVYGGYFCPNCHSKVCSLPTVCPCC 366
Database: Non-redundant SwissProt sequences
Posted date: Dec 6, 2005 7:40 AM
Number of letters in database: 68,354,980
Number of sequences in database: 184,735
Database: swissprot.01
Posted date: Dec 6, 2005 8:18 AM
Number of letters in database: 66,202,850
Number of sequences in database: 184,431
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 74,606,407
Number of Sequences: 369166
Number of extensions: 1439162
Number of successful extensions: 3644
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 3528
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 3626
length of database: 68,354,980
effective HSP length: 107
effective length of database: 48,588,335
effective search space used: 6219306880
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)