Search to RefSeqBP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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= 20110601C-013478
(1028 letters)
Database: RefSeq49_BP.fasta
33,088 sequences; 17,681,374 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001015582.1| transcription factor IIIB 50 kDa subunit [Bo... 597 e-171
Alignment gi|NP_001039607.1| transcription initiation factor IIB [Bos tau... 58 2e-08
>ref|NP_001015582.1| transcription factor IIIB 50 kDa subunit [Bos taurus].
Length = 421
Score = 597 bits (1538), Expect = e-171
Identities = 292/310 (94%), Positives = 303/310 (97%)
Frame = +2
Query: 95 MPGRGRCPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTTTFSDEGNLREVTYSRSTG 274
MPGRGRCPDCGS ELVEDSHYSQ+QLVCSDCGCVVTEGVLTTTFSDEGNLREVTYSRSTG
Sbjct: 1 MPGRGRCPDCGSAELVEDSHYSQNQLVCSDCGCVVTEGVLTTTFSDEGNLREVTYSRSTG 60
Query: 275 ENEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYQHSGIRAARLQKKEVLVGC 454
ENEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQA+Q +GIR ARLQKKEVL GC
Sbjct: 61 ENEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAHQLAGIRTARLQKKEVLAGC 120
Query: 455 CVLITCRQRNWPLTMGTICTLIYADLDVFSGTYMQMVKLLGLDVPSLCLADLVKTYCSSF 634
CVLITCRQRNWPLTMGTICTL+YADLDVFSGTYMQ+VKLLGLDVPSLCL DLVKTYCSSF
Sbjct: 121 CVLITCRQRNWPLTMGTICTLLYADLDVFSGTYMQIVKLLGLDVPSLCLVDLVKTYCSSF 180
Query: 635 KLFQASPSVPAKYVEDKEKMLSRTLQLVELADETWLVTGRHPLPVVTAATFLAWQSLQPS 814
KLF+ASPSVPAKYVEDKEKMLSRTLQLVELADETWLVTGRHPLPV+TAATFLAWQSL+PS
Sbjct: 181 KLFEASPSVPAKYVEDKEKMLSRTLQLVELADETWLVTGRHPLPVITAATFLAWQSLRPS 240
Query: 815 DRLSCSLARFCKLANVDLPYPAASRLQELLAVLLRMAGQLAWLQVLKLDKRSVVKHIGDL 994
DRL+CSLARFCKLANVDLPYPA+SRLQELLAVLLRMA QLAWLQVLKLDKRSVVKHIGDL
Sbjct: 241 DRLTCSLARFCKLANVDLPYPASSRLQELLAVLLRMAEQLAWLQVLKLDKRSVVKHIGDL 300
Query: 995 LQHRHTLVRR 1024
LQHRH LVR+
Sbjct: 301 LQHRHMLVRK 310
>ref|NP_001039607.1| transcription initiation factor IIB [Bos taurus].
Length = 316
Score = 57.8 bits (138), Expect = 2e-08
Identities = 56/272 (20%), Positives = 100/272 (36%), Gaps = 39/272 (14%)
Frame = +2
Query: 104 RGRCPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTT-----TFSDEGNLREVT---- 256
R CP+ LVED Y ++C +CG VV + V+ TFS++ ++ +
Sbjct: 12 RVTCPNHPDAILVED--YRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGD 69
Query: 257 --------------------------YSRSTGENEQVSRSQQRGL----RRVRDLCRVLQ 346
+ S +N + S R + + + + +
Sbjct: 70 SQNPLLSDGDLSTMIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRIN 129
Query: 347 LPPTFEDTAVAYYQQAYQHSGIRAARLQKKEVLVGCCVLITCRQRNWPLTMGTICTLIYA 526
LP D ++Q Y+ ++ + + + C+ I CRQ P T IC +
Sbjct: 130 LPRNIVDRTNNLFKQVYEQKSLKG---RANDAIASACLYIACRQEGVPRTFKEICAVSRI 186
Query: 527 DLDVFSGTYMQMVKLLGLDVPSLCLADLVKTYCSSFKLFQASPSVPAKYVEDKEKMLSRT 706
+ ++K L V + D + +CS+ L K+ ++ T
Sbjct: 187 SKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCL-------------PKQVQMAAT 233
Query: 707 LQLVELADETWLVTGRHPLPVVTAATFLAWQS 802
+ A E LV GR P+ V AA ++A Q+
Sbjct: 234 -HIARKAVELDLVPGRSPISVAEAAIYMASQA 264
Database: RefSeq49_BP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 17,681,374
Number of sequences in database: 33,088
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 Sequences: 33088
Number of Hits to DB: 38,583,544
Number of extensions: 1045512
Number of successful extensions: 3505
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 3501
Number of HSP's successfully gapped: 2
Length of query: 342
Length of database: 17,681,374
Length adjustment: 103
Effective length of query: 239
Effective length of database: 14,273,310
Effective search space: 3411321090
Effective search space used: 3411321090
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqCP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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= 20110601C-013478
(1028 letters)
Database: RefSeq49_CP.fasta
33,336 sequences; 18,874,504 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_850010.1| PREDICTED: similar to RNA polymerase III transc... 595 e-170
Alignment gi|XP_537085.1| PREDICTED: similar to Transcription initiation ... 58 1e-08
Alignment gi|XP_867247.1| PREDICTED: similar to general transcription fac... 58 1e-08
>ref|XP_850010.1| PREDICTED: similar to RNA polymerase III transcription initiation
factor BRF2 [Canis familiaris].
Length = 421
Score = 595 bits (1533), Expect = e-170
Identities = 292/310 (94%), Positives = 303/310 (97%)
Frame = +2
Query: 95 MPGRGRCPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTTTFSDEGNLREVTYSRSTG 274
MPG GRCPDCGS ELV+DSHYSQSQLVCSDCGCVVTEGVLTTTFSDEGNLREVTYSRSTG
Sbjct: 1 MPGGGRCPDCGSAELVDDSHYSQSQLVCSDCGCVVTEGVLTTTFSDEGNLREVTYSRSTG 60
Query: 275 ENEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYQHSGIRAARLQKKEVLVGC 454
ENEQVSRSQQRGLRRVRDLCRVLQLP TFEDTAVAYYQQAY+HSGIRAARLQKKEVLVGC
Sbjct: 61 ENEQVSRSQQRGLRRVRDLCRVLQLPSTFEDTAVAYYQQAYRHSGIRAARLQKKEVLVGC 120
Query: 455 CVLITCRQRNWPLTMGTICTLIYADLDVFSGTYMQMVKLLGLDVPSLCLADLVKTYCSSF 634
CVLITCRQ NWPLTMGTIC L+YADL+VFSGTYMQ+VKLLGLDVPSLCLADLVKTYCSSF
Sbjct: 121 CVLITCRQHNWPLTMGTICALLYADLEVFSGTYMQIVKLLGLDVPSLCLADLVKTYCSSF 180
Query: 635 KLFQASPSVPAKYVEDKEKMLSRTLQLVELADETWLVTGRHPLPVVTAATFLAWQSLQPS 814
KLFQASPSVPAKYVEDKEKMLSRTLQLVELADETWLVTGRHPLPV+TAATFLAWQSLQPS
Sbjct: 181 KLFQASPSVPAKYVEDKEKMLSRTLQLVELADETWLVTGRHPLPVITAATFLAWQSLQPS 240
Query: 815 DRLSCSLARFCKLANVDLPYPAASRLQELLAVLLRMAGQLAWLQVLKLDKRSVVKHIGDL 994
+RL+CSLARFCKLANVDLP PA+SRLQELLAVLLRMA QLAWLQVL+LDKRSVVKHIGDL
Sbjct: 241 ERLTCSLARFCKLANVDLPCPASSRLQELLAVLLRMAEQLAWLQVLRLDKRSVVKHIGDL 300
Query: 995 LQHRHTLVRR 1024
LQHRHTLVR+
Sbjct: 301 LQHRHTLVRK 310
>ref|XP_537085.1| PREDICTED: similar to Transcription initiation factor IIB (General
transcription factor TFIIB) (S300-II) isoform 1 [Canis
familiaris].
Length = 316
Score = 58.2 bits (139), Expect = 1e-08
Identities = 56/272 (20%), Positives = 100/272 (36%), Gaps = 39/272 (14%)
Frame = +2
Query: 104 RGRCPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTT-----TFSDEGNLREVT---- 256
R CP+ LVED Y ++C +CG VV + V+ TFS++ ++ +
Sbjct: 12 RVTCPNHPDAILVED--YRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGD 69
Query: 257 --------------------------YSRSTGENEQVSRSQQRGL----RRVRDLCRVLQ 346
+ S +N + S R + + + + +
Sbjct: 70 SQNPLLSDGDLSTMIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRIN 129
Query: 347 LPPTFEDTAVAYYQQAYQHSGIRAARLQKKEVLVGCCVLITCRQRNWPLTMGTICTLIYA 526
LP D ++Q Y+ ++ + + + C+ I CRQ P T IC +
Sbjct: 130 LPRNIVDRTNNLFKQVYEQKSLKG---RANDAIASACLYIACRQEGVPRTFKEICAVSRI 186
Query: 527 DLDVFSGTYMQMVKLLGLDVPSLCLADLVKTYCSSFKLFQASPSVPAKYVEDKEKMLSRT 706
+ ++K L V + D + +CS+ L K+ ++ T
Sbjct: 187 SKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCL-------------PKQVQMAAT 233
Query: 707 LQLVELADETWLVTGRHPLPVVTAATFLAWQS 802
+ A E LV GR P+ V AA ++A Q+
Sbjct: 234 -HIARKAVELDLVPGRSPISVAAAAIYMASQA 264
>ref|XP_867247.1| PREDICTED: similar to general transcription factor IIB isoform 2
[Canis familiaris].
Length = 273
Score = 58.2 bits (139), Expect = 1e-08
Identities = 56/272 (20%), Positives = 100/272 (36%), Gaps = 39/272 (14%)
Frame = +2
Query: 104 RGRCPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTT-----TFSDEGNLREVT---- 256
R CP+ LVED Y ++C +CG VV + V+ TFS++ ++ +
Sbjct: 12 RVTCPNHPDAILVED--YRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGD 69
Query: 257 --------------------------YSRSTGENEQVSRSQQRGL----RRVRDLCRVLQ 346
+ S +N + S R + + + + +
Sbjct: 70 SQNPLLSDGDLSTMIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRIN 129
Query: 347 LPPTFEDTAVAYYQQAYQHSGIRAARLQKKEVLVGCCVLITCRQRNWPLTMGTICTLIYA 526
LP D ++Q Y+ ++ + + + C+ I CRQ P T IC +
Sbjct: 130 LPRNIVDRTNNLFKQVYEQKSLKG---RANDAIASACLYIACRQEGVPRTFKEICAVSRI 186
Query: 527 DLDVFSGTYMQMVKLLGLDVPSLCLADLVKTYCSSFKLFQASPSVPAKYVEDKEKMLSRT 706
+ ++K L V + D + +CS+ L K+ ++ T
Sbjct: 187 SKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCL-------------PKQVQMAAT 233
Query: 707 LQLVELADETWLVTGRHPLPVVTAATFLAWQS 802
+ A E LV GR P+ V AA ++A Q+
Sbjct: 234 -HIARKAVELDLVPGRSPISVAAAAIYMASQA 264
Database: RefSeq49_CP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,874,504
Number of sequences in database: 33,336
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 Sequences: 33336
Number of Hits to DB: 40,027,522
Number of extensions: 1063329
Number of successful extensions: 3460
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 3454
Number of HSP's successfully gapped: 3
Length of query: 342
Length of database: 18,874,504
Length adjustment: 103
Effective length of query: 239
Effective length of database: 15,440,896
Effective search space: 3690374144
Effective search space used: 3690374144
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)
Search to RefSeqSP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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= 20110601C-013478
(1028 letters)
Database: RefSeq49_SP.fasta
24,897 sequences; 11,343,932 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_003133415.2| PREDICTED: transcription factor IIIB 50 kDa ... 500 e-142
Alignment gi|XP_001929441.3| PREDICTED: transcription initiation factor I... 58 7e-09
>ref|XP_003133415.2| PREDICTED: transcription factor IIIB 50 kDa subunit [Sus scrofa].
Length = 359
Score = 500 bits (1288), Expect = e-142
Identities = 249/251 (99%), Positives = 251/251 (100%)
Frame = +2
Query: 272 GENEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYQHSGIRAARLQKKEVLVG 451
GENEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYQHSGIRAARLQKKEVLVG
Sbjct: 2 GENEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYQHSGIRAARLQKKEVLVG 61
Query: 452 CCVLITCRQRNWPLTMGTICTLIYADLDVFSGTYMQMVKLLGLDVPSLCLADLVKTYCSS 631
CCVLITCRQRNWPLTMGTICTLIYADLDVFSGTYMQMVKLLGLDVPSLCLADLVKTYCSS
Sbjct: 62 CCVLITCRQRNWPLTMGTICTLIYADLDVFSGTYMQMVKLLGLDVPSLCLADLVKTYCSS 121
Query: 632 FKLFQASPSVPAKYVEDKEKMLSRTLQLVELADETWLVTGRHPLPVVTAATFLAWQSLQP 811
FKLFQASPSVPAKYVEDKEKMLSRTLQLVELADETWLVTGRHPLPVVTAATFLAWQSLQP
Sbjct: 122 FKLFQASPSVPAKYVEDKEKMLSRTLQLVELADETWLVTGRHPLPVVTAATFLAWQSLQP 181
Query: 812 SDRLSCSLARFCKLANVDLPYPAASRLQELLAVLLRMAGQLAWLQVLKLDKRSVVKHIGD 991
SDRL+CSLARFCKLANVDLPYPAASRLQELLAVLLRMAGQLAWLQVLKLDKRSVVKHIGD
Sbjct: 182 SDRLTCSLARFCKLANVDLPYPAASRLQELLAVLLRMAGQLAWLQVLKLDKRSVVKHIGD 241
Query: 992 LLQHRHTLVRR 1024
LLQHRHTLVR+
Sbjct: 242 LLQHRHTLVRK 252
>ref|XP_001929441.3| PREDICTED: transcription initiation factor IIB [Sus scrofa].
Length = 316
Score = 58.2 bits (139), Expect = 7e-09
Identities = 56/272 (20%), Positives = 100/272 (36%), Gaps = 39/272 (14%)
Frame = +2
Query: 104 RGRCPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTT-----TFSDEGNLREVT---- 256
R CP+ LVED Y ++C +CG VV + V+ TFS++ ++ +
Sbjct: 12 RVTCPNHPDAILVED--YRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGD 69
Query: 257 --------------------------YSRSTGENEQVSRSQQRGL----RRVRDLCRVLQ 346
+ S +N + S R + + + + +
Sbjct: 70 SQNPLLSDGDLSTMIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRIN 129
Query: 347 LPPTFEDTAVAYYQQAYQHSGIRAARLQKKEVLVGCCVLITCRQRNWPLTMGTICTLIYA 526
LP D ++Q Y+ ++ + + + C+ I CRQ P T IC +
Sbjct: 130 LPRNIVDRTNNLFKQVYEQKSLKG---RANDAIASACLYIACRQEGVPRTFKEICAVSRI 186
Query: 527 DLDVFSGTYMQMVKLLGLDVPSLCLADLVKTYCSSFKLFQASPSVPAKYVEDKEKMLSRT 706
+ ++K L V + D + +CS+ L K+ ++ T
Sbjct: 187 SKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCL-------------PKQVQMAAT 233
Query: 707 LQLVELADETWLVTGRHPLPVVTAATFLAWQS 802
+ A E LV GR P+ V AA ++A Q+
Sbjct: 234 -HIARKAVELDLVPGRSPISVAAAAIYMASQA 264
Database: RefSeq49_SP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 11,343,932
Number of sequences in database: 24,897
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 Sequences: 24897
Number of Hits to DB: 24,866,584
Number of extensions: 669912
Number of successful extensions: 2422
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 2419
Number of HSP's successfully gapped: 2
Length of query: 342
Length of database: 11,343,932
Length adjustment: 100
Effective length of query: 242
Effective length of database: 8,854,232
Effective search space: 2142724144
Effective search space used: 2142724144
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqMP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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= 20110601C-013478
(1028 letters)
Database: RefSeq49_MP.fasta
30,036 sequences; 15,617,559 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_079962.1| transcription factor IIIB 50 kDa subunit [Mus m... 576 e-164
Alignment gi|NP_663521.1| transcription initiation factor IIB [Mus muscul... 58 1e-08
>ref|NP_079962.1| transcription factor IIIB 50 kDa subunit [Mus musculus].
Length = 420
Score = 576 bits (1484), Expect = e-164
Identities = 281/309 (90%), Positives = 298/309 (96%)
Frame = +2
Query: 95 MPGRGRCPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTTTFSDEGNLREVTYSRSTG 274
MP RCPDCGS+ELVEDSHYSQSQLVCSDCGCVVTEGVLTTTFSDEGN REVTYSRSTG
Sbjct: 1 MPNGSRCPDCGSSELVEDSHYSQSQLVCSDCGCVVTEGVLTTTFSDEGNFREVTYSRSTG 60
Query: 275 ENEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYQHSGIRAARLQKKEVLVGC 454
ENEQVSR QQR LRRVRDLCR+L+LP TFEDTA++YYQ+AYQ SGIRAARLQKKEVLVGC
Sbjct: 61 ENEQVSRCQQRDLRRVRDLCRILKLPLTFEDTAISYYQKAYQLSGIRAARLQKKEVLVGC 120
Query: 455 CVLITCRQRNWPLTMGTICTLIYADLDVFSGTYMQMVKLLGLDVPSLCLADLVKTYCSSF 634
CVLITCRQ NWPLTMGTICTL+YADLD+FSGTYMQMVKLLGLDVPSLCLADLVK+YCSSF
Sbjct: 121 CVLITCRQHNWPLTMGTICTLLYADLDLFSGTYMQMVKLLGLDVPSLCLADLVKSYCSSF 180
Query: 635 KLFQASPSVPAKYVEDKEKMLSRTLQLVELADETWLVTGRHPLPVVTAATFLAWQSLQPS 814
KLFQASPSVPAKYVEDK+KMLSRTL LVELADETWLVTGRHPLP++TAATFLAWQSL+PS
Sbjct: 181 KLFQASPSVPAKYVEDKDKMLSRTLLLVELADETWLVTGRHPLPIITAATFLAWQSLRPS 240
Query: 815 DRLSCSLARFCKLANVDLPYPAASRLQELLAVLLRMAGQLAWLQVLKLDKRSVVKHIGDL 994
DRL+CSLA+FCKLANVDLPYPAASRLQELLAVLL+MAGQLAWLQVLKL+KRSVVKHIGDL
Sbjct: 241 DRLTCSLAQFCKLANVDLPYPAASRLQELLAVLLQMAGQLAWLQVLKLNKRSVVKHIGDL 300
Query: 995 LQHRHTLVR 1021
LQHRH LVR
Sbjct: 301 LQHRHMLVR 309
>ref|NP_663521.1| transcription initiation factor IIB [Mus musculus].
Length = 316
Score = 58.2 bits (139), Expect = 1e-08
Identities = 56/272 (20%), Positives = 100/272 (36%), Gaps = 39/272 (14%)
Frame = +2
Query: 104 RGRCPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTT-----TFSDEGNLREVT---- 256
R CP+ LVED Y ++C +CG VV + V+ TFS++ ++ +
Sbjct: 12 RVTCPNHPDAILVED--YRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGD 69
Query: 257 --------------------------YSRSTGENEQVSRSQQRGL----RRVRDLCRVLQ 346
+ S +N + S R + + + + +
Sbjct: 70 SQNPLLSDGDLSTMIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRIN 129
Query: 347 LPPTFEDTAVAYYQQAYQHSGIRAARLQKKEVLVGCCVLITCRQRNWPLTMGTICTLIYA 526
LP D ++Q Y+ ++ + + + C+ I CRQ P T IC +
Sbjct: 130 LPRNIVDRTNNLFKQVYEQKSLKG---RANDAIASACLYIACRQEGVPRTFKEICAVSRI 186
Query: 527 DLDVFSGTYMQMVKLLGLDVPSLCLADLVKTYCSSFKLFQASPSVPAKYVEDKEKMLSRT 706
+ ++K L V + D + +CS+ L K+ ++ T
Sbjct: 187 SKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCL-------------PKQVQMAAT 233
Query: 707 LQLVELADETWLVTGRHPLPVVTAATFLAWQS 802
+ A E LV GR P+ V AA ++A Q+
Sbjct: 234 -HIARKAVELDLVPGRSPISVAAAAIYMASQA 264
Database: RefSeq49_MP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 15,617,559
Number of sequences in database: 30,036
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 Sequences: 30036
Number of Hits to DB: 33,433,537
Number of extensions: 885465
Number of successful extensions: 3004
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 2998
Number of HSP's successfully gapped: 2
Length of query: 342
Length of database: 15,617,559
Length adjustment: 102
Effective length of query: 240
Effective length of database: 12,553,887
Effective search space: 3012932880
Effective search space used: 3012932880
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqHP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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= 20110601C-013478
(1028 letters)
Database: RefSeq49_HP.fasta
32,964 sequences; 18,297,164 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_060780.2| transcription factor IIIB 50 kDa subunit [Homo ... 597 e-171
Alignment gi|NP_001505.1| transcription initiation factor IIB [Homo sapie... 58 1e-08
Alignment gi|NP_001229717.1| transcription factor IIIB 90 kDa subunit iso... 55 1e-07
>ref|NP_060780.2| transcription factor IIIB 50 kDa subunit [Homo sapiens].
Length = 419
Score = 597 bits (1538), Expect = e-171
Identities = 292/309 (94%), Positives = 304/309 (98%)
Frame = +2
Query: 95 MPGRGRCPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTTTFSDEGNLREVTYSRSTG 274
MPGRGRCPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTTTFSDEGNLREVTYSRSTG
Sbjct: 1 MPGRGRCPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTTTFSDEGNLREVTYSRSTG 60
Query: 275 ENEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYQHSGIRAARLQKKEVLVGC 454
ENEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAY+HSGIRAARLQKKEVLVGC
Sbjct: 61 ENEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYRHSGIRAARLQKKEVLVGC 120
Query: 455 CVLITCRQRNWPLTMGTICTLIYADLDVFSGTYMQMVKLLGLDVPSLCLADLVKTYCSSF 634
CVLITCRQ NWPLTMG ICTL+YADLDVFS TYMQ+VKLLGLDVPSLCLA+LVKTYCSSF
Sbjct: 121 CVLITCRQHNWPLTMGAICTLLYADLDVFSSTYMQIVKLLGLDVPSLCLAELVKTYCSSF 180
Query: 635 KLFQASPSVPAKYVEDKEKMLSRTLQLVELADETWLVTGRHPLPVVTAATFLAWQSLQPS 814
KLFQASPSVPAKYVEDKEKMLSRT+QLVELA+ETWLVTGRHPLPV+TAATFLAWQSLQP+
Sbjct: 181 KLFQASPSVPAKYVEDKEKMLSRTMQLVELANETWLVTGRHPLPVITAATFLAWQSLQPA 240
Query: 815 DRLSCSLARFCKLANVDLPYPAASRLQELLAVLLRMAGQLAWLQVLKLDKRSVVKHIGDL 994
DRLSCSLARFCKLANVDLPYPA+SRLQELLAVLLRMA QLAWL+VL+LDKRSVVKHIGDL
Sbjct: 241 DRLSCSLARFCKLANVDLPYPASSRLQELLAVLLRMAEQLAWLRVLRLDKRSVVKHIGDL 300
Query: 995 LQHRHTLVR 1021
LQHR +LVR
Sbjct: 301 LQHRQSLVR 309
>ref|NP_001505.1| transcription initiation factor IIB [Homo sapiens].
Length = 316
Score = 58.2 bits (139), Expect = 1e-08
Identities = 56/272 (20%), Positives = 100/272 (36%), Gaps = 39/272 (14%)
Frame = +2
Query: 104 RGRCPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTT-----TFSDEGNLREVT---- 256
R CP+ LVED Y ++C +CG VV + V+ TFS++ ++ +
Sbjct: 12 RVTCPNHPDAILVED--YRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGD 69
Query: 257 --------------------------YSRSTGENEQVSRSQQRGL----RRVRDLCRVLQ 346
+ S +N + S R + + + + +
Sbjct: 70 SQNPLLSDGDLSTMIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRIN 129
Query: 347 LPPTFEDTAVAYYQQAYQHSGIRAARLQKKEVLVGCCVLITCRQRNWPLTMGTICTLIYA 526
LP D ++Q Y+ ++ + + + C+ I CRQ P T IC +
Sbjct: 130 LPRNIVDRTNNLFKQVYEQKSLKG---RANDAIASACLYIACRQEGVPRTFKEICAVSRI 186
Query: 527 DLDVFSGTYMQMVKLLGLDVPSLCLADLVKTYCSSFKLFQASPSVPAKYVEDKEKMLSRT 706
+ ++K L V + D + +CS+ L K+ ++ T
Sbjct: 187 SKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCL-------------PKQVQMAAT 233
Query: 707 LQLVELADETWLVTGRHPLPVVTAATFLAWQS 802
+ A E LV GR P+ V AA ++A Q+
Sbjct: 234 -HIARKAVELDLVPGRSPISVAAAAIYMASQA 264
>ref|NP_001229717.1| transcription factor IIIB 90 kDa subunit isoform 6 [Homo sapiens].
Length = 650
Score = 55.1 bits (131), Expect = 1e-07
Identities = 50/231 (21%), Positives = 95/231 (41%), Gaps = 4/231 (1%)
Frame = +2
Query: 113 CPDCGSTELVEDSHYSQSQLVCSDCGCVVTEGVLTTTFSDEGNLREVTYSRSTGENEQVS 292
C CG T++ D+ ++ VC+ CG V+ + ++ + EV + S+G
Sbjct: 6 CRGCGGTDIELDA--ARGDAVCTACGSVLEDNIIVS---------EVQFVESSGGGSSAV 54
Query: 293 RS--QQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYQHSGIRAARLQKKEVLVGCCVLI 466
G R + L LQL DTA +++ A R +K ++ C+ +
Sbjct: 55 GQFVSLDGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSR---HLTRGRKMAHVIAACLYL 111
Query: 467 TCRQRNWPLTMGTICTLIYADLDVFSGTYMQMVKLLGLDVPSL--CLADLVKTYCSSFKL 640
CR P + + L+ ++ V T++ + + L ++ P++ CL Y F
Sbjct: 112 VCRTEGTPHMLLDLSDLLQVNVYVLGKTFLLLARELCINAPAIDPCL------YIPRFAH 165
Query: 641 FQASPSVPAKYVEDKEKMLSRTLQLVELADETWLVTGRHPLPVVTAATFLA 793
++ E ++ L+L++ W+ TGR P + AA +A
Sbjct: 166 L-------LEFGEKNHEVSMTALRLLQRMKRDWMHTGRRPSGLCGAALLVA 209
Database: RefSeq49_HP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,297,164
Number of sequences in database: 32,964
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 Sequences: 32964
Number of Hits to DB: 39,406,114
Number of extensions: 1050872
Number of successful extensions: 3556
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 3550
Number of HSP's successfully gapped: 3
Length of query: 342
Length of database: 18,297,164
Length adjustment: 103
Effective length of query: 239
Effective length of database: 14,901,872
Effective search space: 3561547408
Effective search space used: 3561547408
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to Sscrofa10_2
BLASTN 2.2.24 [Aug-08-2010]
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= 20110601C-013478
(1028 letters)
Database: Sscrofa_10.2.fasta
4582 sequences; 2,808,509,378 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Sscrofa_Chr15 775 0.0
>Sscrofa_Chr15
|| Length = 157681621
Score = 775 bits (391), Expect = 0.0
Identities = 394/395 (99%)
Strand = Plus / Plus
Query: 628 cagcttcaaactttttcaagcctccccgtctgtgccagccaagtacgtggaagacaagga 687
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55688170 cagcttcaaactttttcaagcctccccgtctgtgccagccaagtacgtggaagacaagga 55688229
Query: 688 gaagatgctgtctcgaacactgcagctggtggagctggcggatgagacgtggctggtgac 747
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55688230 gaagatgctgtctcgaacactgcagctggtggagctggcggatgagacgtggctggtgac 55688289
Query: 748 tgggcggcatcccctacctgtcgttactgctgccactttcctggcctggcagtcgctgca 807
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55688290 tgggcggcatcccctacctgtcgttactgctgccactttcctggcctggcagtcgctgca 55688349
Query: 808 gccttctgatcggctgagttgttccctggcccgattttgtaaattggcaaacgtggacct 867
||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55688350 gccttctgatcggctgacttgttccctggcccgattttgtaaattggcaaacgtggacct 55688409
Query: 868 tccctaccctgctgcctcccgcctgcaggagctgttggccgtgctgctgcggatggccgg 927
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55688410 tccctaccctgctgcctcccgcctgcaggagctgttggccgtgctgctgcggatggccgg 55688469
Query: 928 gcagctggcctggttgcaggttctgaagcttgacaagcggtctgtggtgaagcacatcgg 987
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55688470 gcagctggcctggttgcaggttctgaagcttgacaagcggtctgtggtgaagcacatcgg 55688529
Query: 988 tgacctcctccagcaccgccacacgctagtccgca 1022
|||||||||||||||||||||||||||||||||||
Sbjct: 55688530 tgacctcctccagcaccgccacacgctagtccgca 55688564
Score = 642 bits (324), Expect = 0.0
Identities = 324/324 (100%)
Strand = Plus / Plus
Query: 307 aggtctccgccgagtgagagacctctgtcgagttctgcagctaccaccaacatttgagga 366
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55687038 aggtctccgccgagtgagagacctctgtcgagttctgcagctaccaccaacatttgagga 55687097
Query: 367 cacggcagttgcctactaccaacaggcataccagcactctggcatccgtgctgccaggct 426
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55687098 cacggcagttgcctactaccaacaggcataccagcactctggcatccgtgctgccaggct 55687157
Query: 427 gcaaaagaaggaggtgttggtcgggtgctgtgtcttaattacctgccggcagcgtaactg 486
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55687158 gcaaaagaaggaggtgttggtcgggtgctgtgtcttaattacctgccggcagcgtaactg 55687217
Query: 487 gcccctgaccatgggaaccatctgcaccctaatctatgcagatttggatgtgttttctgg 546
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55687218 gcccctgaccatgggaaccatctgcaccctaatctatgcagatttggatgtgttttctgg 55687277
Query: 547 cacctacatgcagatggtgaagctcctggggctagacgtgccgtctctgtgcttggcaga 606
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55687278 cacctacatgcagatggtgaagctcctggggctagacgtgccgtctctgtgcttggcaga 55687337
Query: 607 cctggtgaagacttactgtagcag 630
||||||||||||||||||||||||
Sbjct: 55687338 cctggtgaagacttactgtagcag 55687361
Score = 492 bits (248), Expect = e-136
Identities = 248/248 (100%)
Strand = Plus / Plus
Query: 1 gctccgctcctacttcctgtttgcaacactgttgctgttgtcgacgttaggggcggttac 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55684689 gctccgctcctacttcctgtttgcaacactgttgctgttgtcgacgttaggggcggttac 55684748
Query: 61 ccgaaggcttcctcggctctggacgggttgtaagatgccgggaagaggccgctgccccga 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55684749 ccgaaggcttcctcggctctggacgggttgtaagatgccgggaagaggccgctgccccga 55684808
Query: 121 ttgcggctccactgagctggtggaagactcacactattcgcagagccagctggtgtgctc 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55684809 ttgcggctccactgagctggtggaagactcacactattcgcagagccagctggtgtgctc 55684868
Query: 181 cgactgcggctgtgtggtcaccgagggagtccttacgaccaccttcagtgatgagggcaa 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55684869 cgactgcggctgtgtggtcaccgagggagtccttacgaccaccttcagtgatgagggcaa 55684928
Query: 241 cctccgag 248
||||||||
Sbjct: 55684929 cctccgag 55684936
Score = 127 bits (64), Expect = 1e-26
Identities = 64/64 (100%)
Strand = Plus / Plus
Query: 247 agaagtaacatattcccgaagcacaggggaaaatgaacaagttagtcgcagccagcaacg 306
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55685607 agaagtaacatattcccgaagcacaggggaaaatgaacaagttagtcgcagccagcaacg 55685666
Query: 307 aggt 310
||||
Sbjct: 55685667 aggt 55685670
Database: Sscrofa_10.2.fasta
Posted date: Nov 16, 2011 10:34 AM
Number of letters in database: 2,808,509,378
Number of sequences in database: 4582
Lambda K H
1.37 0.711 1.31
Gapped
Lambda K H
1.37 0.711 1.31
Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 4582
Number of Hits to DB: 26,403,144
Number of extensions: 124
Number of successful extensions: 124
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 124
Number of HSP's successfully gapped: 4
Length of query: 1028
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1007
Effective length of database: 2,808,413,156
Effective search space: 2828072048092
Effective search space used: 2828072048092
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 50 (99.1 bits)
S1: 18 (36.2 bits)
S2: 29 (58.0 bits)