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_003_B16
(727 letters)
Database: Non-redundant SwissProt sequences
184,735 sequences; 68,354,980 total letters
Score E
Sequences producing significant alignments: (bits) Value
sp|Q07381|TSR1_YEAST Ribosome biogenesis protein TSR1 (20S ... 105 2e-22
sp|O94653|BMS1_SCHPO Ribosome biogenesis protein BMS1 homolog 72 2e-12
sp|Q14692|BMS1_HUMAN Ribosome biogenesis protein BMS1 homolog 64 5e-10
sp|Q08965|BMS1_YEAST Ribosome biogenesis protein BMS1 58 3e-08
sp|Q8RA32|DPO3_THETN DNA polymerase III polC-type (PolIII) 33 0.78
sp|P09133|NIFA_AZOCA Nif-specific regulatory protein 31 3.9
sp|Q59191|RPOB_BORBU DNA-directed RNA polymerase beta chain... 30 8.6
>sp|Q07381|TSR1_YEAST Ribosome biogenesis protein TSR1 (20S rRNA accumulation protein 1)
Length = 788
Score = 105 bits (261), Expect = 2e-22
Identities = 63/188 (33%), Positives = 100/188 (53%)
Frame = +2
Query: 50 EPVESKETMLFQVGFRRFSSTPIYSEFTATSDESGDKGKSRLCKFMELKKNVVATVYGPV 229
+PV S+E ++ Q G RR++ P++S+ + + +F+ VAT PV
Sbjct: 606 KPVPSQEPIVVQYGVRRYTIQPLFSQ-----GSNSPNNVHKYERFLHPDTVSVATCIAPV 660
Query: 230 TYGPTSVLQFRIRQNDLGMGELGRPYVAELVATGSLLSIDPSKPIIKRILLTGQVYKVNK 409
+ + + F+ D EL+ G+ L+ D S+ + KR +LTG ++ +K
Sbjct: 661 DFTQSPAIFFKPSPTDAKN--------IELIGHGTFLNADHSRILAKRAILTGHPFRFHK 712
Query: 410 RSVMIRYMFFNTKDIEHFKVVPLHTKGSNISGRIVSPHGSHGYMKCRFERPISQDEVVCM 589
V +RYMFF +D+E FK +PL TK S SG I G+HGY K F+ +S +VV M
Sbjct: 713 TVVTVRYMFFRPEDVEWFKSIPLFTK-SGRSGFIKESLGTHGYFKATFDGKLSAQDVVAM 771
Query: 590 ALYKRVFP 613
+LYKR++P
Sbjct: 772 SLYKRMWP 779
>sp|O94653|BMS1_SCHPO Ribosome biogenesis protein BMS1 homolog
Length = 1121
Score = 71.6 bits (174), Expect = 2e-12
Identities = 48/177 (27%), Positives = 86/177 (48%), Gaps = 1/177 (0%)
Frame = +2
Query: 56 VESKETMLFQVGFRRFSSTPIYSEFTATSDESGDKGKSRLCKFMELKKNVVATVYGPVTY 235
+++ + ++F +G+RRF S P+YS S + ++R+ K+ + T YGP
Sbjct: 776 LKTNDPLIFSMGWRRFQSIPVYSI-------SDSRTRNRMLKYTPEHMHCFGTFYGPFVA 828
Query: 236 GPTSVLQFRIRQNDLGMGELGRPYVAELVATGSLLSIDPSKPIIKRILLTGQVYKVNKRS 415
+ + N R + ATGS+L+ID S I+K++ LTG YK+ K +
Sbjct: 829 PNSGFCAVQSVANSFAKAGSFR-----IAATGSVLNIDQSTDIVKKLKLTGVPYKIFKNT 883
Query: 416 VMIRYMFFNTKDIEHFKVVPLHTKGSNISGRI-VSPHGSHGYMKCRFERPISQDEVV 583
I+ MF + ++ F+ + T S I G++ + HG+ + FE I ++V
Sbjct: 884 AFIKKMFSSPLEVAKFEGANIRTV-SGIRGQVKKAVDQEHGHFRATFEDKILMSDIV 939
>sp|Q14692|BMS1_HUMAN Ribosome biogenesis protein BMS1 homolog
Length = 1282
Score = 63.5 bits (153), Expect = 5e-10
Identities = 54/200 (27%), Positives = 93/200 (46%), Gaps = 1/200 (0%)
Frame = +2
Query: 56 VESKETMLFQVGFRRFSSTPIYSEFTATSDESGDKGKSRLCKFMELKKNVVATVYGPVTY 235
++S++ ++F VG+RRF + P+Y G+ RL K+ + A +GP+T
Sbjct: 936 LKSRDPIIFSVGWRRFQTIPLYYI-------EDHNGRQRLLKYTPQHMHCGAAFWGPITP 988
Query: 236 GPTSVLQFRIRQNDLGMGELGRPYVAELVATGSLLSIDPSKPIIKRILLTGQVYKVNKRS 415
T L Q+ G+ R + ATG +L +D S I+K++ LTG YK+ K +
Sbjct: 989 QGTGFLAI---QSVSGIMPDFR-----IAATGVVLDLDKSIKIVKKLKLTGFPYKIFKNT 1040
Query: 416 VMIRYMFFNTKDIEHFKVVPLHTKGSNISGRIVSP-HGSHGYMKCRFERPISQDEVVCMA 592
I+ MF + ++ F+ + T S I G+I G + FE + ++V M
Sbjct: 1041 SFIKGMFNSALEVAKFEGAVIRTV-SGIRGQIKKALRAPEGAFRASFEDKLLMSDIVFM- 1098
Query: 593 LYKRVFPKYTVENMYNHLPS 652
R + ++ YN + S
Sbjct: 1099 ---RTWYPVSIPAFYNPVTS 1115
>sp|Q08965|BMS1_YEAST Ribosome biogenesis protein BMS1
Length = 1183
Score = 57.8 bits (138), Expect = 3e-08
Identities = 52/201 (25%), Positives = 92/201 (45%), Gaps = 2/201 (0%)
Frame = +2
Query: 56 VESKETMLFQVGFRRFSSTPIYSEFTATSDESGDKGKSRLCKFMELKKNVVATVYGPVTY 235
+++ + ++ +G+RRF + PIY+ T+D + ++R+ K+ A YGP+
Sbjct: 839 LKTNDPLVLSLGWRRFQTLPIYT----TTDS---RTRTRMLKYTPEHTYCNAAFYGPLCS 891
Query: 236 GPTSVLQFRIRQN-DLGMGELGRPYVAELVATGSLLSIDPSKPIIKRILLTGQVYKVNKR 412
T +I N D G G + ATG + ID + I+K++ L G YK+ K
Sbjct: 892 PNTPFCGVQIVANSDTGNG-------FRIAATGIVEEIDVNIEIVKKLKLVGFPYKIFKN 944
Query: 413 SVMIRYMFFNTKDIEHFKVVPLHTKGSNISGRIVSPHGS-HGYMKCRFERPISQDEVVCM 589
+ I+ MF + ++ F+ + T S I G I G+ + FE I ++V +
Sbjct: 945 TAFIKDMFSSAMEVARFEGAQIKTV-SGIRGEIKRALSKPEGHYRAAFEDKILMSDIVIL 1003
Query: 590 ALYKRVFPKYTVENMYNHLPS 652
R + V+ YN + S
Sbjct: 1004 ----RSWYPVRVKKFYNPVTS 1020
>sp|Q8RA32|DPO3_THETN DNA polymerase III polC-type (PolIII)
Length = 1401
Score = 33.1 bits (74), Expect = 0.78
Identities = 15/37 (40%), Positives = 24/37 (64%)
Frame = +2
Query: 290 ELGRPYVAELVATGSLLSIDPSKPIIKRILLTGQVYK 400
ELG+ Y +VATG + +DP + ++IL+ G+ YK
Sbjct: 689 ELGKKYNKLVVATGDVHFLDPWDDVYRKILMAGKGYK 725
>sp|P09133|NIFA_AZOCA Nif-specific regulatory protein
Length = 615
Score = 30.8 bits (68), Expect = 3.9
Identities = 16/42 (38%), Positives = 25/42 (59%)
Frame = +2
Query: 302 PYVAELVATGSLLSIDPSKPIIKRILLTGQVYKVNKRSVMIR 427
P VAE A GS + I P++KR++ T QV + +V++R
Sbjct: 243 PEVAE-AANGSAMGIVGDSPLVKRLIATAQVVARSNSTVLLR 283
>sp|Q59191|RPOB_BORBU DNA-directed RNA polymerase beta chain (RNAP beta subunit)
(Transcriptase beta chain) (RNA polymerase beta subunit)
Length = 1155
Score = 29.6 bits (65), Expect = 8.6
Identities = 12/22 (54%), Positives = 17/22 (77%)
Frame = +3
Query: 558 DRLVKMKLYAWLYIKEFSLNIR 623
DR+VK LY ++IKEFS+ +R
Sbjct: 769 DRIVKEDLYTSIHIKEFSIEVR 790
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: 92,519,548
Number of Sequences: 369166
Number of extensions: 2012415
Number of successful extensions: 4821
Number of sequences better than 10.0: 7
Number of HSP's better than 10.0 without gapping: 4692
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): 4814
length of database: 68,354,980
effective HSP length: 107
effective length of database: 48,588,335
effective search space used: 6510836890
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)