BLASTP 2.2.26 [Sep-21-2011]
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.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 002404
(927 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QIZ|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 202 bits (513), Expect = 9e-52, Method: Compositional matrix adjust.
Identities = 166/610 (27%), Positives = 283/610 (46%), Gaps = 84/610 (13%)
Query: 333 DTRENVLEYLAEVINRNSSRAHIQVEPLSCASSGMFVNLSAVMLRLCDPFLDANLTKRDK 392
++R +++ Y A + N+N R +S+G N++ +++R PFLD + K DK
Sbjct: 298 NSRTDMISYFAHIANKNHLRRADHPPFKELSSNGFMSNITLLLVRFSQPFLDISYKKIDK 357
Query: 393 IDPKYVFYSSR-LDLRSLTALHASSEEVSEWINKGNPAKADGSKHFSDGENQLLQSQEAT 451
ID Y S +DL T L++ +E + +K N AD
Sbjct: 358 IDANYFNNPSLFIDLSGETRLNSDFKEADAFYDK-NRKTAD------------------- 397
Query: 452 SSSGGASEPSLPAGRPASIGGGKSKYPFICECFFMTARVLNLGL-------------LKA 498
SK FI +CFF+T L+ GL +KA
Sbjct: 398 -----------------------SKPNFISDCFFLTLTYLHYGLGGTLSFEEKMGSEIKA 434
Query: 499 FSDFKHLVQDISRAEDTLATLKATQ--------GQTPSSQLNLEITRIEKEIELSSQEKL 550
+ V+ I+ D A Q T S + L+ + ++L + +
Sbjct: 435 LKEEIEKVKKIAANHDVFARFITAQLSKMEKALKTTESLRFALQGFFAHRSLQLEVFDFI 494
Query: 551 CYEAQILRDGDLIQHALSFYRLMIVWLVDLVGGFKMPLPD----TCPMEFACMPEHFVED 606
C + L +H F ++ + + D +G + D P+ F PE VE
Sbjct: 495 CGASTFLIRVVDPEHEFPFKQIKLPLIPDQIGVENVDNADFLRAHAPVPFKYYPEFVVEG 554
Query: 607 AMELLIFASRIPKA--LDGVLLDDFMNFIIMFMASPKYIRNPYLRSKMVEVLNCW-MPRR 663
+ ++ S+ + L F+ F M + P+ + NP+L+ K+V++L+ MP
Sbjct: 555 PVNYSLYISKYQTSPIFRNPRLGSFVEFTTMVLRCPELVSNPHLKGKLVQLLSVGAMPLT 614
Query: 664 SGSSSATATLFEGHQMSLEYLVRNLLKLYVDIEFTGSHTQFYDKFNIRHNIAELLEYLW- 722
S +FE ++ + L+ LL YV +E TGS +QFYDKFN R++I+ +LE L+
Sbjct: 615 DNSPGFMMDIFEHDELVNKNLLYALLDFYVIVEKTGSSSQFYDKFNSRYSISIILEELYY 674
Query: 723 QVPSHRNA--WRQIAKEEEKGVYLNFLNFLINDSIYLLDESLNKILELKVIEAEMSNTAE 780
++PS++N W+ + ++ F+ ++ND +LLDE L+ + E+ I+ E+ N A
Sbjct: 675 KIPSYKNQLIWQS---QNNADFFVRFVARMLNDLTFLLDEGLSNLAEVHNIQNELDNRAR 731
Query: 781 WE--RRPAQERQERTRLFHSQENIIRIDMKLANEDVSMLAFTSEQIVAPFLLPEMIERVA 838
R ++++ +TRL S + LA++ + + S+ I A F+ PE++ R+A
Sbjct: 732 GAPPTREEEDKELQTRL-ASASRQAKSSCGLADKSMKLFEIYSKDIPAAFVTPEIVYRLA 790
Query: 839 SMLNYFLLQLVGPQRKSLTLKDPEKYEFRPKQLLKQIVCIYVHLARGDTQNLFPAAISSD 898
SMLNY L LVGP+ L +KDP+ Y F PK LLK + +Y++L+ Q+ F +A++ D
Sbjct: 791 SMLNYNLESLVGPKCGELKVKDPQSYSFNPKDLLKALTTVYINLSE---QSEFISAVAKD 847
Query: 899 GRSYNEQVSV 908
RS+N + V
Sbjct: 848 ERSFNRNLFV 857
Score = 32.3 bits (72), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 59/126 (46%), Gaps = 17/126 (13%)
Query: 8 RSPEEIEDIILRKIFLVTLNEATTDADPRIAYLELTAAELLSEGKDMRLSRDLMERVLVD 67
RS IEDI+ + TTD Y L +E + +G L D ++ +L+
Sbjct: 20 RSMTAIEDIL----------QITTDPSDTRGY-SLLKSEEVPQGS--TLGVDFIDTLLLY 66
Query: 68 RLSGNFPAAEPPFLYLINCYRRAHDELKKIGNMKDKNLRSELEAVVKQAKKMIVSYCRIH 127
+L+ N + PF YL +C+RR + K+I K+K L + ++ ++++ Y +
Sbjct: 67 QLTEN-EKLDKPFEYLNDCFRRNQQQ-KRI--TKNKPNAESLHSTFQEIDRLVIGYGVVA 122
Query: 128 LANPDF 133
L +F
Sbjct: 123 LQIENF 128
>pdb|3M62|A Chain A, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Rad23
pdb|3M63|A Chain A, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Dsk2
Length = 968
Score = 202 bits (513), Expect = 1e-51, Method: Compositional matrix adjust.
Identities = 166/610 (27%), Positives = 283/610 (46%), Gaps = 84/610 (13%)
Query: 333 DTRENVLEYLAEVINRNSSRAHIQVEPLSCASSGMFVNLSAVMLRLCDPFLDANLTKRDK 392
++R +++ Y A + N+N R +S+G N++ +++R PFLD + K DK
Sbjct: 284 NSRTDMISYFAHIANKNHLRRADHPPFKELSSNGFMSNITLLLVRFSQPFLDISYKKIDK 343
Query: 393 IDPKYVFYSSR-LDLRSLTALHASSEEVSEWINKGNPAKADGSKHFSDGENQLLQSQEAT 451
ID Y S +DL T L++ +E + +K N AD
Sbjct: 344 IDANYFNNPSLFIDLSGETRLNSDFKEADAFYDK-NRKTAD------------------- 383
Query: 452 SSSGGASEPSLPAGRPASIGGGKSKYPFICECFFMTARVLNLGL-------------LKA 498
SK FI +CFF+T L+ GL +KA
Sbjct: 384 -----------------------SKPNFISDCFFLTLTYLHYGLGGTLSFEEKMGSEIKA 420
Query: 499 FSDFKHLVQDISRAEDTLATLKATQ--------GQTPSSQLNLEITRIEKEIELSSQEKL 550
+ V+ I+ D A Q T S + L+ + ++L + +
Sbjct: 421 LKEEIEKVKKIAANHDVFARFITAQLSKMEKALKTTESLRFALQGFFAHRSLQLEVFDFI 480
Query: 551 CYEAQILRDGDLIQHALSFYRLMIVWLVDLVGGFKMPLPD----TCPMEFACMPEHFVED 606
C + L +H F ++ + + D +G + D P+ F PE VE
Sbjct: 481 CGASTFLIRVVDPEHEFPFKQIKLPLIPDQIGVENVDNADFLRAHAPVPFKYYPEFVVEG 540
Query: 607 AMELLIFASRIPKA--LDGVLLDDFMNFIIMFMASPKYIRNPYLRSKMVEVLNCW-MPRR 663
+ ++ S+ + L F+ F M + P+ + NP+L+ K+V++L+ MP
Sbjct: 541 PVNYSLYISKYQTSPIFRNPRLGSFVEFTTMVLRCPELVSNPHLKGKLVQLLSVGAMPLT 600
Query: 664 SGSSSATATLFEGHQMSLEYLVRNLLKLYVDIEFTGSHTQFYDKFNIRHNIAELLEYLW- 722
S +FE ++ + L+ LL YV +E TGS +QFYDKFN R++I+ +LE L+
Sbjct: 601 DNSPGFMMDIFEHDELVNKNLLYALLDFYVIVEKTGSSSQFYDKFNSRYSISIILEELYY 660
Query: 723 QVPSHRNA--WRQIAKEEEKGVYLNFLNFLINDSIYLLDESLNKILELKVIEAEMSNTAE 780
++PS++N W+ + ++ F+ ++ND +LLDE L+ + E+ I+ E+ N A
Sbjct: 661 KIPSYKNQLIWQS---QNNADFFVRFVARMLNDLTFLLDEGLSNLAEVHNIQNELDNRAR 717
Query: 781 WE--RRPAQERQERTRLFHSQENIIRIDMKLANEDVSMLAFTSEQIVAPFLLPEMIERVA 838
R ++++ +TRL S + LA++ + + S+ I A F+ PE++ R+A
Sbjct: 718 GAPPTREEEDKELQTRL-ASASRQAKSSCGLADKSMKLFEIYSKDIPAAFVTPEIVYRLA 776
Query: 839 SMLNYFLLQLVGPQRKSLTLKDPEKYEFRPKQLLKQIVCIYVHLARGDTQNLFPAAISSD 898
SMLNY L LVGP+ L +KDP+ Y F PK LLK + +Y++L+ Q+ F +A++ D
Sbjct: 777 SMLNYNLESLVGPKCGELKVKDPQSYSFNPKDLLKALTTVYINLSE---QSEFISAVAKD 833
Query: 899 GRSYNEQVSV 908
RS+N + V
Sbjct: 834 ERSFNRNLFV 843
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 59/126 (46%), Gaps = 17/126 (13%)
Query: 8 RSPEEIEDIILRKIFLVTLNEATTDADPRIAYLELTAAELLSEGKDMRLSRDLMERVLVD 67
RS IEDI+ + TTD Y L +E + +G L D ++ +L+
Sbjct: 6 RSMTAIEDIL----------QITTDPSDTRGY-SLLKSEEVPQGS--TLGVDFIDTLLLY 52
Query: 68 RLSGNFPAAEPPFLYLINCYRRAHDELKKIGNMKDKNLRSELEAVVKQAKKMIVSYCRIH 127
+L+ N + PF YL +C+RR + K+I K+K L + ++ ++++ Y +
Sbjct: 53 QLTEN-EKLDKPFEYLNDCFRRNQQQ-KRI--TKNKPNAESLHSTFQEIDRLVIGYGVVA 108
Query: 128 LANPDF 133
L +F
Sbjct: 109 LQIENF 114
>pdb|2QJ0|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 192 bits (489), Expect = 6e-49, Method: Compositional matrix adjust.
Identities = 163/610 (26%), Positives = 277/610 (45%), Gaps = 84/610 (13%)
Query: 333 DTRENVLEYLAEVINRNSSRAHIQVEPLSCASSGMFVNLSAVMLRLCDPFLDANLTKRDK 392
++R + + Y A + N+N R +S+G N++ +++R PFLD + K DK
Sbjct: 298 NSRTDXISYFAHIANKNHLRRADHPPFKELSSNGFXSNITLLLVRFSQPFLDISYKKIDK 357
Query: 393 IDPKYVFYSSR-LDLRSLTALHASSEEVSEWINKGNPAKADGSKHFSDGENQLLQSQEAT 451
ID Y S +DL T L++ +E + +K N AD
Sbjct: 358 IDANYFNNPSLFIDLSGETRLNSDFKEADAFYDK-NRKTAD------------------- 397
Query: 452 SSSGGASEPSLPAGRPASIGGGKSKYPFICECFFMTARVLNLGL-------------LKA 498
SK FI +CFF+T L+ GL +KA
Sbjct: 398 -----------------------SKPNFISDCFFLTLTYLHYGLGGTLSFEEKXGSEIKA 434
Query: 499 FSDFKHLVQDISRAEDTLATLKATQ--------GQTPSSQLNLEITRIEKEIELSSQEKL 550
+ V+ I+ D A Q T S + L+ + ++L + +
Sbjct: 435 LKEEIEKVKKIAANHDVFARFITAQLSKXEKALKTTESLRFALQGFFAHRSLQLEVFDFI 494
Query: 551 CYEAQILRDGDLIQHALSFYRLMIVWLVDLVGGFKMPLPD----TCPMEFACMPEHFVED 606
C + L +H F ++ + + D +G + D P+ F PE VE
Sbjct: 495 CGASTFLIRVVDPEHEFPFKQIKLPLIPDQIGVENVDNADFLRAHAPVPFKYYPEFVVEG 554
Query: 607 AMELLIFASRIPKA--LDGVLLDDFMNFIIMFMASPKYIRNPYLRSKMVEVLNCW-MPRR 663
+ ++ S+ + L F+ F + P+ + NP+L+ K+V++L+ P
Sbjct: 555 PVNYSLYISKYQTSPIFRNPRLGSFVEFTTXVLRCPELVSNPHLKGKLVQLLSVGAXPLT 614
Query: 664 SGSSSATATLFEGHQMSLEYLVRNLLKLYVDIEFTGSHTQFYDKFNIRHNIAELLEYLW- 722
S +FE ++ + L+ LL YV +E TGS +QFYDKFN R++I+ +LE L+
Sbjct: 615 DNSPGFXXDIFEHDELVNKNLLYALLDFYVIVEKTGSSSQFYDKFNSRYSISIILEELYY 674
Query: 723 QVPSHRNA--WRQIAKEEEKGVYLNFLNFLINDSIYLLDESLNKILELKVIEAEMSNTAE 780
++PS++N W+ + ++ F+ +ND +LLDE L+ + E+ I+ E+ N A
Sbjct: 675 KIPSYKNQLIWQS---QNNADFFVRFVARXLNDLTFLLDEGLSNLAEVHNIQNELDNRAR 731
Query: 781 WE--RRPAQERQERTRLFHSQENIIRIDMKLANEDVSMLAFTSEQIVAPFLLPEMIERVA 838
R ++++ +TRL S + LA++ + S+ I A F+ PE++ R+A
Sbjct: 732 GAPPTREEEDKELQTRL-ASASRQAKSSCGLADKSXKLFEIYSKDIPAAFVTPEIVYRLA 790
Query: 839 SMLNYFLLQLVGPQRKSLTLKDPEKYEFRPKQLLKQIVCIYVHLARGDTQNLFPAAISSD 898
S LNY L LVGP+ L +KDP+ Y F PK LLK + +Y++L+ Q+ F +A++ D
Sbjct: 791 SXLNYNLESLVGPKCGELKVKDPQSYSFNPKDLLKALTTVYINLSE---QSEFISAVAKD 847
Query: 899 GRSYNEQVSV 908
RS+N + V
Sbjct: 848 ERSFNRNLFV 857
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 59/126 (46%), Gaps = 17/126 (13%)
Query: 8 RSPEEIEDIILRKIFLVTLNEATTDADPRIAYLELTAAELLSEGKDMRLSRDLMERVLVD 67
RS IEDI+ + TTD Y L +E + +G L D ++ +L+
Sbjct: 20 RSXTAIEDIL----------QITTDPSDTRGY-SLLKSEEVPQGS--TLGVDFIDTLLLY 66
Query: 68 RLSGNFPAAEPPFLYLINCYRRAHDELKKIGNMKDKNLRSELEAVVKQAKKMIVSYCRIH 127
+L+ N + PF YL +C+RR + K+I K+K L + ++ ++++ Y +
Sbjct: 67 QLTEN-EKLDKPFEYLNDCFRRNQQQ-KRI--TKNKPNAESLHSTFQEIDRLVIGYGVVA 122
Query: 128 LANPDF 133
L +F
Sbjct: 123 LQIENF 128
>pdb|3FLE|A Chain A, Se_1780 Protein Of Unknown Function From Staphylococcus
Epidermidis.
pdb|3FLE|B Chain B, Se_1780 Protein Of Unknown Function From Staphylococcus
Epidermidis
Length = 249
Score = 35.8 bits (81), Expect = 0.099, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 651 KMVEVLNCWMPRRSGSSSATATLFEGHQMSLEYLVRNLLKLYVDIEFTGS---HTQFYDK 707
K +EVLN + GS S + SL+YL+R K Y + +F G+ H+Q ++
Sbjct: 178 KEIEVLNIYGDLEDGSHS-DGRVSNSSSQSLQYLLRGSTKSYQEXKFKGAKAQHSQLHEN 236
Query: 708 FNIRHNIAELLEYLWQ 723
++ + E++++LW+
Sbjct: 237 KDVAN---EIIQFLWE 249
>pdb|3HOA|A Chain A, Crystal Structure Of The Thermus Thermophilus M32
Carboxypeptidase
pdb|3HOA|B Chain B, Crystal Structure Of The Thermus Thermophilus M32
Carboxypeptidase
Length = 509
Score = 31.6 bits (70), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 12/60 (20%)
Query: 34 DPRIA------YLELTAAELLSEGKDMRLSRDLMERVLVDRLSGNFPAAEPPFLYLINCY 87
+PR A +L+ T A + +EG R RVLV+R++G P+A P YL Y
Sbjct: 452 EPRFARGEFQPFLDWTRARIHAEGSRFR------PRVLVERVTGEAPSARPFLAYLEKKY 505
>pdb|1WGZ|A Chain A, Crystal Structure Of Carboxypeptidase 1 From Thermus
Thermophilus
pdb|1WGZ|B Chain B, Crystal Structure Of Carboxypeptidase 1 From Thermus
Thermophilus
pdb|1WGZ|C Chain C, Crystal Structure Of Carboxypeptidase 1 From Thermus
Thermophilus
Length = 510
Score = 31.6 bits (70), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 12/60 (20%)
Query: 34 DPRIA------YLELTAAELLSEGKDMRLSRDLMERVLVDRLSGNFPAAEPPFLYLINCY 87
+PR A +L+ T A + +EG R RVLV+R++G P+A P YL Y
Sbjct: 452 EPRFARGEFQPFLDWTRARIHAEGSRFR------PRVLVERVTGEAPSARPFLAYLEKKY 505
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 30.4 bits (67), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 29/65 (44%)
Query: 202 LKGLYENLRGSVLNVSALGNFQQPLRALLYLVSFPVGVKSLVNHQWWIPKSVYLNGRVIE 261
++GL GS++ NF++ L L Y +S K L + S YL R+++
Sbjct: 743 MRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVD 802
Query: 262 MTSIL 266
+ L
Sbjct: 803 VAQDL 807
>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|4IGC|D Chain D, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|I Chain I, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1407
Score = 30.4 bits (67), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 29/65 (44%)
Query: 202 LKGLYENLRGSVLNVSALGNFQQPLRALLYLVSFPVGVKSLVNHQWWIPKSVYLNGRVIE 261
++GL GS++ NF++ L L Y +S K L + S YL R+++
Sbjct: 743 MRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVD 802
Query: 262 MTSIL 266
+ L
Sbjct: 803 VAQDL 807
>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2V1X|B Chain B, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2WWY|A Chain A, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
pdb|2WWY|B Chain B, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
Length = 591
Score = 29.3 bits (64), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 319 KDLGDVLLALLKNTDTRENVLEYLAEVINRNSSRAHIQVEPLSCASSGMFVN 370
K LG + +L + ++E+V AE++N+NS I V P A S MF++
Sbjct: 105 KQLG-ISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMS 155
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.136 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,717,391
Number of Sequences: 62578
Number of extensions: 1034034
Number of successful extensions: 2507
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2483
Number of HSP's gapped (non-prelim): 15
length of query: 927
length of database: 14,973,337
effective HSP length: 108
effective length of query: 819
effective length of database: 8,214,913
effective search space: 6728013747
effective search space used: 6728013747
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)