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= 005605
(688 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 = 820 bits (2117), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 405/658 (61%), Positives = 505/658 (76%), Gaps = 23/658 (3%)
Query: 43 INRWNGKPYSQRYYEILEKRKSLPVWQQKEEFLQVLKANQVIILVGETGSGKTTQIPQFV 102
IN + G+ ++ +Y +IL+ R+ LPV Q++EFL++ + NQ+++ VGETGSGKTTQIPQFV
Sbjct: 71 INPFTGREFTPKYVDILKIRRELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFV 130
Query: 103 LEGVDIETPDRRRKMMIACTQPXXXXXXXXXXXXXEEMDVTIGEEVGYSIRFEDCSSART 162
L E P +ACTQP EEMDV +GEEVGYSIRFE+ +S +T
Sbjct: 131 LFD---EMP-HLENTQVACTQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKT 186
Query: 163 VLKYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVM 222
+LKY+TDGMLLREAM D L RY I+LDEAHERTLATD+L GLLK+V+K RPDLK+++M
Sbjct: 187 ILKYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIM 246
Query: 223 SATLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDI 282
SATL+AEKFQ YF APL+ VPGR +PVE++YT E +RDYL++AIRTV+QIH E +GDI
Sbjct: 247 SATLDAEKFQRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDI 306
Query: 283 LVFLTGEEEIEDACRKITKEITNMGDQV------GPVKVVPLYSTLPPAMQQKIFEXXXX 336
L+FLTGE+EIEDA RKI+ E GDQ+ GP+ V PLY +LPP QQ+IFE
Sbjct: 307 LLFLTGEDEIEDAVRKISLE----GDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPE 362
Query: 337 XXXXXXXXXRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKAS 396
RK+V+STNIAETSLTIDGIVYV+DPGF+KQKVYNPR+RVESLLVSPISKAS
Sbjct: 363 SHNGRPG--RKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKAS 420
Query: 397 AHQRSGRAGRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHF 456
A QR+GRAGRT+PGKCFRLYTE++F +L Q+YPEILRSNL++TVL LKKLGIDDLVHF
Sbjct: 421 AQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKLGIDDLVHF 480
Query: 457 DFMDPPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSN 516
DFMDPPAPET+MRALE LNYL LDD+GNLT +G S+FPLDP ++ ML+ S ++ CS
Sbjct: 481 DFMDPPAPETMMRALEELNYLACLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQ 540
Query: 517 EILSISAMLSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDP---- 572
EIL+I AMLSVPN F+RP + +K AD+AK F H DGDH+TLLNVYHA+K +
Sbjct: 541 EILTIVAMLSVPNVFIRPTKDKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIH 600
Query: 573 SWCYDNFVNHRALKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQV 632
WC D+++N+R+L +ADN+R QL R+M R+NL+L + D+ S Y+ NIRKA+ +G+FMQV
Sbjct: 601 KWCRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDYESPKYFDNIRKALASGFFMQV 660
Query: 633 AHLERTGQ--YLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEW 688
A +R+G Y+TVKDNQ V +HPS L H EWVIYNE+VLTS+N+IRTVT VR EW
Sbjct: 661 AK-KRSGAKGYITVKDNQDVLIHPSTVLGHDAEWVIYNEFVLTSKNYIRTVTSVRPEW 717
>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 = 820 bits (2117), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 405/658 (61%), Positives = 505/658 (76%), Gaps = 23/658 (3%)
Query: 43 INRWNGKPYSQRYYEILEKRKSLPVWQQKEEFLQVLKANQVIILVGETGSGKTTQIPQFV 102
IN + G+ ++ +Y +IL+ R+ LPV Q++EFL++ + NQ+++ VGETGSGKTTQIPQFV
Sbjct: 71 INPFTGREFTPKYVDILKIRRELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFV 130
Query: 103 LEGVDIETPDRRRKMMIACTQPXXXXXXXXXXXXXEEMDVTIGEEVGYSIRFEDCSSART 162
L E P +ACTQP EEMDV +GEEVGYSIRFE+ +S +T
Sbjct: 131 LFD---EMP-HLENTQVACTQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKT 186
Query: 163 VLKYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVM 222
+LKY+TDGMLLREAM D L RY I+LDEAHERTLATD+L GLLK+V+K RPDLK+++M
Sbjct: 187 ILKYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIM 246
Query: 223 SATLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDI 282
SATL+AEKFQ YF APL+ VPGR +PVE++YT E +RDYL++AIRTV+QIH E +GDI
Sbjct: 247 SATLDAEKFQRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDI 306
Query: 283 LVFLTGEEEIEDACRKITKEITNMGDQV------GPVKVVPLYSTLPPAMQQKIFEXXXX 336
L+FLTGE+EIEDA RKI+ E GDQ+ GP+ V PLY +LPP QQ+IFE
Sbjct: 307 LLFLTGEDEIEDAVRKISLE----GDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPE 362
Query: 337 XXXXXXXXXRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKAS 396
RK+V+STNIAETSLTIDGIVYV+DPGF+KQKVYNPR+RVESLLVSPISKAS
Sbjct: 363 SHNGRPG--RKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKAS 420
Query: 397 AHQRSGRAGRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHF 456
A QR+GRAGRT+PGKCFRLYTE++F +L Q+YPEILRSNL++TVL LKKLGIDDLVHF
Sbjct: 421 AQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKLGIDDLVHF 480
Query: 457 DFMDPPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSN 516
DFMDPPAPET+MRALE LNYL LDD+GNLT +G S+FPLDP ++ ML+ S ++ CS
Sbjct: 481 DFMDPPAPETMMRALEELNYLACLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQ 540
Query: 517 EILSISAMLSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDP---- 572
EIL+I AMLSVPN F+RP + +K AD+AK F H DGDH+TLLNVYHA+K +
Sbjct: 541 EILTIVAMLSVPNVFIRPTKDKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIH 600
Query: 573 SWCYDNFVNHRALKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQV 632
WC D+++N+R+L +ADN+R QL R+M R+NL+L + D+ S Y+ NIRKA+ +G+FMQV
Sbjct: 601 KWCRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDYESPKYFDNIRKALASGFFMQV 660
Query: 633 AHLERTGQ--YLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEW 688
A +R+G Y+TVKDNQ V +HPS L H EWVIYNE+VLTS+N+IRTVT VR EW
Sbjct: 661 AK-KRSGAKGYITVKDNQDVLIHPSTVLGHDAEWVIYNEFVLTSKNYIRTVTSVRPEW 717
>pdb|3I4U|A Chain A, Crystal Structure Analysis Of A Helicase Associated Domain
Length = 270
Score = 207 bits (527), Expect = 2e-53, Method: Compositional matrix adjust.
Identities = 100/225 (44%), Positives = 151/225 (67%), Gaps = 5/225 (2%)
Query: 465 ETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILSISAM 524
ETL+ A+E L LGALDD+G LT +G +M+EFPL+P + KML+ S CS E+L+I +M
Sbjct: 18 ETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSM 77
Query: 525 LSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDPSWCYDNFVNHRA 584
LSV N F RP++ Q AD+ KA+F +GDHLTLL VY+++K N WCY+NF+ R+
Sbjct: 78 LSVQNVFYRPKDKQALADQKKAKFHQTEGDHLTLLAVYNSWKNNKFSNPWCYENFIQARS 137
Query: 585 LKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAHLERTGQYLTV 644
L+ A ++R+Q++ IM R L + S ++ V ++KA+ +G+F A + Y T+
Sbjct: 138 LRRAQDIRKQMLGIMDRHKLDVVSCGKST----VRVQKAICSGFFRNAAKKDPQEGYRTL 193
Query: 645 KDNQVVHLHPSNCL-DHKPEWVIYNEYVLTSRNFIRTVTDVRGEW 688
D QVV++HPS+ L + +PEWV+Y+E VLT++ ++R VT + W
Sbjct: 194 IDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRW 238
>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 = 110 bits (275), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 63/187 (33%), Positives = 103/187 (55%), Gaps = 5/187 (2%)
Query: 58 ILEKRKSLPVWQQKEEFLQVLKANQVIILVGETGSGKTTQIPQFVLEGVDIETPDRRRKM 117
IL++R+ LPV + + E L+ + N V+I+ G TG GKTTQ+PQF+L+ D DR +
Sbjct: 53 ILQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILD--DFIQNDRAAEC 110
Query: 118 MIACTQPXXXXXXXXXXXXXEEMDVTIGEEVGYSIRFEDC-SSARTVLKYLTDGMLLREA 176
I TQP E G+ GYS+RFE + + T G+LLR+
Sbjct: 111 NIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHASIXFCTVGVLLRKL 170
Query: 177 MTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSATLEAEKFQGYFY 236
+ +++DE HER + TD L +L++V++ P++++V+ SAT++ F YF+
Sbjct: 171 EAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLXSATIDTSXFCEYFF 228
Query: 237 GAPLMKV 243
P+++V
Sbjct: 229 NCPIIEV 235
>pdb|3FY3|A Chain A, Crystal Structure Of Truncated Hemolysin A From P.
Mirabilis
Length = 236
Score = 32.7 bits (73), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 43/99 (43%), Gaps = 7/99 (7%)
Query: 587 SADNVRQQLVRIMARFNLKLCSN---DFNSRDYYVNIRKAMLAGYFMQVAHLERT----G 639
SA N Q++ I+ N + N DFN A+ AG HL G
Sbjct: 15 SAVNGGTQVINIVTPNNEGISHNQYQDFNVGKPGAVFNNALEAGQSQLAGHLNANSNLNG 74
Query: 640 QYLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFI 678
Q ++ N+VV +PS L + + I EYVL++ N I
Sbjct: 75 QAASLILNEVVSRNPSFLLGQQEVFGIAAEYVLSNPNGI 113
>pdb|3FPZ|A Chain A, Saccharomyces Cerevisiae Thi4p Is A Suicide Thiamin
Thiazole Synthase
pdb|3FPZ|B Chain B, Saccharomyces Cerevisiae Thi4p Is A Suicide Thiamin
Thiazole Synthase
Length = 326
Score = 32.3 bits (72), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 210 VLKNRPDLKLVVMSATLE---AEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYL 263
+ KNRPDLK+ ++ +++ G + A +M+ P L E+ E E DY+
Sbjct: 84 IAKNRPDLKVCIIESSVAPGGGSWLGGQLFSAMVMRKPAHLFLQELEIPYEDEGDYV 140
>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 = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 7/55 (12%)
Query: 70 QKEEFLQVLKANQVIILVGETGSGKTTQIPQFVLEGVDIETPDRRRKMMIACTQP 124
QKE L L ++ I+ G G+GKTT + + +L+ V ++ + + C P
Sbjct: 194 QKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAV-------KQGLKVLCCAP 241
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 7/55 (12%)
Query: 70 QKEEFLQVLKANQVIILVGETGSGKTTQIPQFVLEGVDIETPDRRRKMMIACTQP 124
QKE L L ++ I+ G G+GKTT + + +L+ V ++ + + C P
Sbjct: 194 QKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAV-------KQGLKVLCCAP 241
>pdb|3FEW|X Chain X, Structure And Function Of Colicin S4, A Colicin With A
Duplicated Receptor Binding Domain
Length = 505
Score = 29.3 bits (64), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 46/105 (43%), Gaps = 9/105 (8%)
Query: 472 EVLNYLGALDDDGNLTEMGEKMSEFPLD---PQMSKMLVESPKYNCSNEILSISAMLSVP 528
E+ LG D+ E ++ +E D P + K V+ +++ + +LSV
Sbjct: 179 EIYEALGFNKDESQRQEKAKQQAEDAWDRLPPNVRKFDVDVEQFHYLVVLDDYGNVLSVT 238
Query: 529 NCFVRPREAQKAADEAKARFGHIDG-DHLTLLNVYHAYKQNNEDP 572
VRP + KA+ G +D DH T +Y A NNE+P
Sbjct: 239 RTGVRPYVGSE-----KAKAGIMDKVDHKTPEEIYEALGFNNEEP 278
>pdb|3M1T|A Chain A, Crystal Structure Of Putative Phosphohydrolase
(Yp_929327.1) From Shewanella Amazonensis Sb2b At 1.62 A
Resolution
Length = 275
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 461 PPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILS 520
P P+ + L+V+N ++D + + EK+S P+ L S ++ CS E+ +
Sbjct: 15 PRLPKAIAELLDVVN-----NEDSTVKAVSEKLSHDPVLSARVLRLANSARFGCSREVGT 69
Query: 521 I 521
I
Sbjct: 70 I 70
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 0.135 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,315,805
Number of Sequences: 62578
Number of extensions: 772800
Number of successful extensions: 2471
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 2441
Number of HSP's gapped (non-prelim): 23
length of query: 688
length of database: 14,973,337
effective HSP length: 105
effective length of query: 583
effective length of database: 8,402,647
effective search space: 4898743201
effective search space used: 4898743201
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)