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= 007931
(584 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KX2|B Chain B, Crystal Structure Of Prp43p In Complex With Adp
pdb|3KX2|A Chain A, Crystal Structure Of Prp43p In Complex With Adp
Length = 767
Score = 431 bits (1107), Expect = e-121, Method: Compositional matrix adjust.
Identities = 237/546 (43%), Positives = 342/546 (62%), Gaps = 33/546 (6%)
Query: 44 KQRQRLPVYKYRTAILYLVETHATTIIVGETGSGKTTQIPQY--LKEAGWADGGRVIACT 101
K R+ LPV+ R L L + + + VGETGSGKTTQIPQ+ E + +V ACT
Sbjct: 88 KIRRELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQV-ACT 146
Query: 102 QPRRLAVQAVASRXXXXXXXXXXXXXXYTIRFEDFTNKDLTAIKFLTDGVLLREMMDDPL 161
QPRR+A +VA R Y+IRFE+ T+ + T +K++TDG+LLRE M+D
Sbjct: 147 QPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFENKTS-NKTILKYMTDGMLLREAMEDHD 205
Query: 162 LTKYSVIMVDEAHERSISTDILLGLLKKIQRCRSDLRLIISSATIEAKSMSAFFHARKGR 221
L++YS I++DEAHER+++TDIL+GLLK++ + R DL++II SAT++A+ +F+
Sbjct: 206 LSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFN----- 260
Query: 222 RGLEGVELVPRLEPAILSVEGRGFNVQIHYVEEPVSDYVQAAVSTVLLIHDKEPPGDILV 281
+ +L+V GR + V+++Y E DY+ +A+ TVL IH E GDIL+
Sbjct: 261 ------------DAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILL 308
Query: 282 FLTGQDDI-DATIQLLTEEARTSKKNSSG-LIILPLYSGLSRAEQEQVFSPTP-----RG 334
FLTG+D+I DA ++ E + ++ G L + PLY L +Q+++F P P R
Sbjct: 309 FLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRP 368
Query: 335 KRKVVISTNIAETSLTLEGIVYVVDSGFSKQRFYNPISDIENLVVAPISKASXXXXXXXX 394
RKVVISTNIAETSLT++GIVYVVD GFSKQ+ YNP +E+L+V+PISKAS
Sbjct: 369 GRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRA 428
Query: 395 XXXXXXKCYRLYTEEYFVKEIPAEGIPEMQRSNLVSCVIQLKALGIDNILGFDWPASPPP 454
KC+RLYTEE F KE+ + PE+ RSNL S V++LK LGID+++ FD+ P P
Sbjct: 429 GRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKLGIDDLVHFDFMDPPAP 488
Query: 455 EAMIRALEVLYSLGVLDDDAKLTSPTGFQVAEIPLEPMISKMILSSNELGCSEEIITISA 514
E M+RALE L L LDD+ LT P G ++ PL+PM++ M++ S E CS+EI+TI A
Sbjct: 489 ETMMRALEELNYLACLDDEGNLT-PLGRLASQFPLDPMLAVMLIGSFEFQCSQEILTIVA 547
Query: 515 VLSIQSIWVSGRGAQKELDEAKLRFAAAEGDHVTFLNIYKGFLQSCKSSH----WCHKNF 570
+LS+ ++++ +K D+AK FA +GDH+T LN+Y F + WC ++
Sbjct: 548 MLSVPNVFIRPTKDKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIHKWCRDHY 607
Query: 571 INYHAM 576
+NY ++
Sbjct: 608 LNYRSL 613
>pdb|2XAU|A Chain A, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
pdb|2XAU|B Chain B, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
Length = 773
Score = 431 bits (1107), Expect = e-121, Method: Compositional matrix adjust.
Identities = 237/546 (43%), Positives = 342/546 (62%), Gaps = 33/546 (6%)
Query: 44 KQRQRLPVYKYRTAILYLVETHATTIIVGETGSGKTTQIPQY--LKEAGWADGGRVIACT 101
K R+ LPV+ R L L + + + VGETGSGKTTQIPQ+ E + +V ACT
Sbjct: 88 KIRRELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQV-ACT 146
Query: 102 QPRRLAVQAVASRXXXXXXXXXXXXXXYTIRFEDFTNKDLTAIKFLTDGVLLREMMDDPL 161
QPRR+A +VA R Y+IRFE+ T+ + T +K++TDG+LLRE M+D
Sbjct: 147 QPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFENKTS-NKTILKYMTDGMLLREAMEDHD 205
Query: 162 LTKYSVIMVDEAHERSISTDILLGLLKKIQRCRSDLRLIISSATIEAKSMSAFFHARKGR 221
L++YS I++DEAHER+++TDIL+GLLK++ + R DL++II SAT++A+ +F+
Sbjct: 206 LSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFN----- 260
Query: 222 RGLEGVELVPRLEPAILSVEGRGFNVQIHYVEEPVSDYVQAAVSTVLLIHDKEPPGDILV 281
+ +L+V GR + V+++Y E DY+ +A+ TVL IH E GDIL+
Sbjct: 261 ------------DAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILL 308
Query: 282 FLTGQDDI-DATIQLLTEEARTSKKNSSG-LIILPLYSGLSRAEQEQVFSPTP-----RG 334
FLTG+D+I DA ++ E + ++ G L + PLY L +Q+++F P P R
Sbjct: 309 FLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRP 368
Query: 335 KRKVVISTNIAETSLTLEGIVYVVDSGFSKQRFYNPISDIENLVVAPISKASXXXXXXXX 394
RKVVISTNIAETSLT++GIVYVVD GFSKQ+ YNP +E+L+V+PISKAS
Sbjct: 369 GRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRA 428
Query: 395 XXXXXXKCYRLYTEEYFVKEIPAEGIPEMQRSNLVSCVIQLKALGIDNILGFDWPASPPP 454
KC+RLYTEE F KE+ + PE+ RSNL S V++LK LGID+++ FD+ P P
Sbjct: 429 GRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKLGIDDLVHFDFMDPPAP 488
Query: 455 EAMIRALEVLYSLGVLDDDAKLTSPTGFQVAEIPLEPMISKMILSSNELGCSEEIITISA 514
E M+RALE L L LDD+ LT P G ++ PL+PM++ M++ S E CS+EI+TI A
Sbjct: 489 ETMMRALEELNYLACLDDEGNLT-PLGRLASQFPLDPMLAVMLIGSFEFQCSQEILTIVA 547
Query: 515 VLSIQSIWVSGRGAQKELDEAKLRFAAAEGDHVTFLNIYKGFLQSCKSSH----WCHKNF 570
+LS+ ++++ +K D+AK FA +GDH+T LN+Y F + WC ++
Sbjct: 548 MLSVPNVFIRPTKDKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIHKWCRDHY 607
Query: 571 INYHAM 576
+NY ++
Sbjct: 608 LNYRSL 613
>pdb|3I4U|A Chain A, Crystal Structure Analysis Of A Helicase Associated Domain
Length = 270
Score = 113 bits (283), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 54/126 (42%), Positives = 83/126 (65%), Gaps = 1/126 (0%)
Query: 453 PPEAMIRALEVLYSLGVLDDDAKLTSPTGFQVAEIPLEPMISKMILSSNELGCSEEIITI 512
P E +I A+E LY+LG LDD+ LT G ++AE PLEPM+ KM++ S LGCSEE++TI
Sbjct: 16 PMETLITAMEQLYTLGALDDEGLLTR-LGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTI 74
Query: 513 SAVLSIQSIWVSGRGAQKELDEAKLRFAAAEGDHVTFLNIYKGFLQSCKSSHWCHKNFIN 572
++LS+Q+++ + Q D+ K +F EGDH+T L +Y + + S+ WC++NFI
Sbjct: 75 VSMLSVQNVFYRPKDKQALADQKKAKFHQTEGDHLTLLAVYNSWKNNKFSNPWCYENFIQ 134
Query: 573 YHAMVR 578
++ R
Sbjct: 135 ARSLRR 140
>pdb|3LLM|A Chain A, Crystal Structure Analysis Of A Rna Helicase
pdb|3LLM|B Chain B, Crystal Structure Analysis Of A Rna Helicase
Length = 235
Score = 106 bits (265), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 60/176 (34%), Positives = 98/176 (55%), Gaps = 7/176 (3%)
Query: 44 KQRQRLPVYKYRTAILYLVETHATTIIVGETGSGKTTQIPQYLKEAGWADGGRVIAC--- 100
++R+ LPV K+ + IL + ++ II G TG GKTTQ+PQ++ + + R C
Sbjct: 55 QERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILD-DFIQNDRAAECNIV 113
Query: 101 -TQPRRLAVQAVASRXXXXXXXXXXXXXXYTIRFEDFTNKDLTAIKFLTDGVLLREMMDD 159
TQPRR++ +VA R Y++RFE + +I F T GVLLR++ +
Sbjct: 114 VTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHASIXFCTVGVLLRKL--E 171
Query: 160 PLLTKYSVIMVDEAHERSISTDILLGLLKKIQRCRSDLRLIISSATIEAKSMSAFF 215
+ S ++VDE HER I+TD LL +L+ + + ++R+++ SATI+ +F
Sbjct: 172 AGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLXSATIDTSXFCEYF 227
>pdb|3VAR|A Chain A, Crystal Structure Of Dnpep, Znzn Form
pdb|3VAT|A Chain A, Crystal Structure Of Dnpep, Znmg Form
Length = 496
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 524 SGRGAQKELDEAKLRFAAAEGDHVTFLN--IYKGFLQSCKSSHWCHKNFINYH 574
S +GAQ L E LR +A H+T I K ++ S +H H N+++ H
Sbjct: 328 SAQGAQSLLTELVLRRISASPQHLTAFEEAIPKSYMISADMAHAVHPNYLDKH 380
>pdb|4DYO|A Chain A, Crystal Structure Of Human Aspartyl Aminopeptidase (Dnpep)
In Complex With Aspartic Acid Hydroxamate
Length = 485
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 524 SGRGAQKELDEAKLRFAAAEGDHVTFLN--IYKGFLQSCKSSHWCHKNFINYH 574
S +GAQ L E LR +A H T I K F+ S +H H N+++ H
Sbjct: 317 SAQGAQSLLTELVLRRISASCQHPTAFEEAIPKSFMISADMAHAVHPNYLDKH 369
>pdb|3G77|A Chain A, Bacterial Cytosine Deaminase V152aF316CD317G MUTANT
Length = 423
Score = 30.8 bits (68), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 10/79 (12%)
Query: 283 LTGQDDIDATIQLLTEE-ART--------SKKNSSGLIILPLYSGLSRAEQEQVFSPTPR 333
L G I+ + L+T ART + NS+ LIILP +G ++ + R
Sbjct: 337 LMGYGQINDGLNLITHHSARTLNLQDYGIAAGNSANLIILPAENGFDALRRQVPVRYSVR 396
Query: 334 GKRKVVISTNIAETSLTLE 352
G KV+ ST A+T++ LE
Sbjct: 397 GG-KVIASTQPAQTTVYLE 414
>pdb|1R9Y|A Chain A, Bacterial Cytosine Deaminase D314a Mutant.
pdb|1RA5|A Chain A, Bacterial Cytosine Deaminase D314a Mutant Bound To
5-Fluoro-4-(S)- Hydroxyl-3,4-Dihydropyrimidine
Length = 430
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 10/79 (12%)
Query: 283 LTGQDDIDATIQLLTEE-ART--------SKKNSSGLIILPLYSGLSRAEQEQVFSPTPR 333
L G I+ + L+T ART + NS+ LIILP +G ++ + R
Sbjct: 344 LMGYGQINDGLNLITHHSARTLNLQDYGIAAGNSANLIILPAENGFDALRRQVPVRYSVR 403
Query: 334 GKRKVVISTNIAETSLTLE 352
G KV+ ST A+T++ LE
Sbjct: 404 GG-KVIASTQPAQTTVYLE 421
>pdb|1R9Z|A Chain A, Bacterial Cytosine Deaminase D314s Mutant.
pdb|1RAK|A Chain A, Bacterial Cytosine Deaminase D314s Mutant Bound To
5-Fluoro-4-(S)- Hydroxyl-3,4-Dihydropyrimidine
Length = 430
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 10/79 (12%)
Query: 283 LTGQDDIDATIQLLTEE-ART--------SKKNSSGLIILPLYSGLSRAEQEQVFSPTPR 333
L G I+ + L+T ART + NS+ LIILP +G ++ + R
Sbjct: 344 LMGYGQINDGLNLITHHSARTLNLQDYGIAAGNSANLIILPAENGFDALRRQVPVRYSVR 403
Query: 334 GKRKVVISTNIAETSLTLE 352
G KV+ ST A+T++ LE
Sbjct: 404 GG-KVIASTQPAQTTVYLE 421
>pdb|1R9X|A Chain A, Bacterial Cytosine Deaminase D314g Mutant.
pdb|1RA0|A Chain A, Bacterial Cytosine Deaminase D314g Mutant Bound To
5-Fluoro-4-(S)- Hydroxy-3,4-Dihydropyrimidine
Length = 430
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 10/79 (12%)
Query: 283 LTGQDDIDATIQLLTEE-ART--------SKKNSSGLIILPLYSGLSRAEQEQVFSPTPR 333
L G I+ + L+T ART + NS+ LIILP +G ++ + R
Sbjct: 344 LMGYGQINDGLNLITHHSARTLNLQDYGIAAGNSANLIILPAENGFDALRRQVPVRYSVR 403
Query: 334 GKRKVVISTNIAETSLTLE 352
G KV+ ST A+T++ LE
Sbjct: 404 GG-KVIASTQPAQTTVYLE 421
>pdb|1K6W|A Chain A, The Structure Of Escherichia Coli Cytosine Deaminase
pdb|1K70|A Chain A, The Structure Of Escherichia Coli Cytosine Deaminase Bound
To 4- Hydroxy-3,4-Dihydro-1h-Pyrimidin-2-One
Length = 426
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 10/79 (12%)
Query: 283 LTGQDDIDATIQLLTEE-ART--------SKKNSSGLIILPLYSGLSRAEQEQVFSPTPR 333
L G I+ + L+T ART + NS+ LIILP +G ++ + R
Sbjct: 340 LMGYGQINDGLNLITHHSARTLNLQDYGIAAGNSANLIILPAENGFDALRRQVPVRYSVR 399
Query: 334 GKRKVVISTNIAETSLTLE 352
G KV+ ST A+T++ LE
Sbjct: 400 GG-KVIASTQPAQTTVYLE 417
>pdb|3O7U|A Chain A, Crystal Structure Of Cytosine Deaminase From Escherichia
Coli Complexed With Zinc And Phosphono-Cytosine
pdb|3RN6|A Chain A, Crystal Structure Of Cytosine Deaminase From Escherichia
Coli Complexed With Zinc And Isoguanine
pdb|3R0D|A Chain A, Crystal Structure Of Cytosine Deaminase From Escherichia
Coli Complexed With Two Zinc Atoms In The Active Site
Length = 427
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 10/79 (12%)
Query: 283 LTGQDDIDATIQLLTEE-ART--------SKKNSSGLIILPLYSGLSRAEQEQVFSPTPR 333
L G I+ + L+T ART + NS+ LIILP +G ++ + R
Sbjct: 341 LMGYGQINDGLNLITHHSARTLNLQDYGIAAGNSANLIILPAENGFDALRRQVPVRYSVR 400
Query: 334 GKRKVVISTNIAETSLTLE 352
G KV+ ST A+T++ LE
Sbjct: 401 GG-KVIASTQPAQTTVYLE 418
>pdb|2VOZ|A Chain A, Apo Futa2 From Synechocystis Pcc6803
pdb|2VOZ|B Chain B, Apo Futa2 From Synechocystis Pcc6803
pdb|2VP1|A Chain A, Fe-Futa2 From Synechocystis Pcc6803
pdb|2VP1|B Chain B, Fe-Futa2 From Synechocystis Pcc6803
Length = 346
Score = 30.4 bits (67), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 289 IDATIQLLTEEARTSKKNSSGLIILPLYSG-LSRAEQEQVFSPTPRGKRKVVISTNI 344
I+A+ + L E ++ NS G I+ + +G L RAEQ +F P GK I N+
Sbjct: 60 IEASAEELIERIQSEGANSPGDILFTVDAGMLWRAEQAGLFQPVRSGKLNERIPENL 116
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 55 RTAILYLVETHATTIIVGETGSGKTTQIPQYLKEAGWADGGRVIACTQPRRLAVQAVASR 114
+ A+L+ + II G G+GKTT + + + +A G + C P +AV + R
Sbjct: 195 KEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQA--VKQGLKVLCCAPSNIAVDNLVER 252
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1752
Score = 29.3 bits (64), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 30/87 (34%)
Query: 214 FFHARKGRRGLEGVELVPRLEPAILSVEGRGFNVQIHYVEEPVSDYVQ----AAVSTVLL 269
FFHA GR GL ++ A+ + E + Y+Q A+ V++
Sbjct: 820 FFHAMAGREGL--------IDTAVKTAE---------------TGYIQRRLVKAMEDVMV 856
Query: 270 IHD---KEPPGDILVFLTGQDDIDATI 293
+D + GDI+ F G+D +DAT+
Sbjct: 857 RYDGTVRNAMGDIIQFAYGEDGLDATL 883
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
pdb|4B3G|B Chain B, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
Length = 646
Score = 29.3 bits (64), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 55 RTAILYLVETHATTIIVGETGSGKTTQIPQYLKEAGWADGGRVIACTQPRRLAVQAVASR 114
+ A+L+ + II G G+GKTT + + + +A G + C P +AV + R
Sbjct: 195 KEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQA--VKQGLKVLCCAPSNIAVDNLVER 252
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
0.319 0.136 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,291,191
Number of Sequences: 62578
Number of extensions: 578166
Number of successful extensions: 1653
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1631
Number of HSP's gapped (non-prelim): 25
length of query: 584
length of database: 14,973,337
effective HSP length: 104
effective length of query: 480
effective length of database: 8,465,225
effective search space: 4063308000
effective search space used: 4063308000
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)