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= 008209
(574 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 = 727 bits (1877), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 357/550 (64%), Positives = 437/550 (79%), Gaps = 19/550 (3%)
Query: 12 RYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSA 71
+Y+TDGMLLREAM D L RY I+LDEAHERTLATD+L GLLK+V+K RPDLK+++MSA
Sbjct: 189 KYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSA 248
Query: 72 TLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILV 131
TL+AEKFQ YF APL+ VPGR +PVE++YT E +RDYL++AIRTV+QIH E +GDIL+
Sbjct: 249 TLDAEKFQRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILL 308
Query: 132 FLTGEEEIEDACRKITKEITNMGDQV------GPVKVVPLYSTLPPAMQQKIFEXXXXXX 185
FLTGE+EIEDA RKI+ E GDQ+ GP+ V PLY +LPP QQ+IFE
Sbjct: 309 FLTGEDEIEDAVRKISLE----GDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESH 364
Query: 186 XXXXXXXRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKASAH 245
RK+V+STNIAETSLTIDGIVYV+DPGF+KQKVYNPR+RVESLLVSPISKASA
Sbjct: 365 NGRPG--RKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQ 422
Query: 246 QRSGRAGRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDF 305
QR+GRAGRT+PGKCFRLYTE++F +L Q+YPEILRSNL++TVL LKKLGIDDLVHFDF
Sbjct: 423 QRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKLGIDDLVHFDF 482
Query: 306 MDPPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEI 365
MDPPAPET+MRALE LNYL LDD+GNLT +G S+FPLDP ++ ML+ S ++ CS EI
Sbjct: 483 MDPPAPETMMRALEELNYLACLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQEI 542
Query: 366 LSISAMLSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDP----SW 421
L+I AMLSVPN F+RP + +K AD+AK F H DGDH+TLLNVYHA+K + W
Sbjct: 543 LTIVAMLSVPNVFIRPTKDKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIHKW 602
Query: 422 CYDNFVNHRALKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAH 481
C D+++N+R+L +ADN+R QL R+M R+NL+L + D+ S Y+ NIRKA+ +G+FMQVA
Sbjct: 603 CRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDYESPKYFDNIRKALASGFFMQVAK 662
Query: 482 LERTGQ--YLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDI 539
+R+G Y+TVKDNQ V +HPS L H EWVIYNE+VLTS+N+IRTVT VR EWLI+I
Sbjct: 663 -KRSGAKGYITVKDNQDVLIHPSTVLGHDAEWVIYNEFVLTSKNYIRTVTSVRPEWLIEI 721
Query: 540 APHYYDLSNF 549
AP YYDLSNF
Sbjct: 722 APAYYDLSNF 731
>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 = 727 bits (1877), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 357/550 (64%), Positives = 437/550 (79%), Gaps = 19/550 (3%)
Query: 12 RYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSA 71
+Y+TDGMLLREAM D L RY I+LDEAHERTLATD+L GLLK+V+K RPDLK+++MSA
Sbjct: 189 KYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSA 248
Query: 72 TLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILV 131
TL+AEKFQ YF APL+ VPGR +PVE++YT E +RDYL++AIRTV+QIH E +GDIL+
Sbjct: 249 TLDAEKFQRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILL 308
Query: 132 FLTGEEEIEDACRKITKEITNMGDQV------GPVKVVPLYSTLPPAMQQKIFEXXXXXX 185
FLTGE+EIEDA RKI+ E GDQ+ GP+ V PLY +LPP QQ+IFE
Sbjct: 309 FLTGEDEIEDAVRKISLE----GDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESH 364
Query: 186 XXXXXXXRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKASAH 245
RK+V+STNIAETSLTIDGIVYV+DPGF+KQKVYNPR+RVESLLVSPISKASA
Sbjct: 365 NGRPG--RKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQ 422
Query: 246 QRSGRAGRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDF 305
QR+GRAGRT+PGKCFRLYTE++F +L Q+YPEILRSNL++TVL LKKLGIDDLVHFDF
Sbjct: 423 QRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKLGIDDLVHFDF 482
Query: 306 MDPPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEI 365
MDPPAPET+MRALE LNYL LDD+GNLT +G S+FPLDP ++ ML+ S ++ CS EI
Sbjct: 483 MDPPAPETMMRALEELNYLACLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQEI 542
Query: 366 LSISAMLSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDP----SW 421
L+I AMLSVPN F+RP + +K AD+AK F H DGDH+TLLNVYHA+K + W
Sbjct: 543 LTIVAMLSVPNVFIRPTKDKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIHKW 602
Query: 422 CYDNFVNHRALKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAH 481
C D+++N+R+L +ADN+R QL R+M R+NL+L + D+ S Y+ NIRKA+ +G+FMQVA
Sbjct: 603 CRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDYESPKYFDNIRKALASGFFMQVAK 662
Query: 482 LERTGQ--YLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDI 539
+R+G Y+TVKDNQ V +HPS L H EWVIYNE+VLTS+N+IRTVT VR EWLI+I
Sbjct: 663 -KRSGAKGYITVKDNQDVLIHPSTVLGHDAEWVIYNEFVLTSKNYIRTVTSVRPEWLIEI 721
Query: 540 APHYYDLSNF 549
AP YYDLSNF
Sbjct: 722 APAYYDLSNF 731
>pdb|3I4U|A Chain A, Crystal Structure Analysis Of A Helicase Associated Domain
Length = 270
Score = 217 bits (552), Expect = 2e-56, Method: Compositional matrix adjust.
Identities = 103/236 (43%), Positives = 159/236 (67%), Gaps = 5/236 (2%)
Query: 312 ETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILSISAM 371
ETL+ A+E L LGALDD+G LT +G +M+EFPL+P + KML+ S CS E+L+I +M
Sbjct: 18 ETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSM 77
Query: 372 LSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDPSWCYDNFVNHRA 431
LSV N F RP++ Q AD+ KA+F +GDHLTLL VY+++K N WCY+NF+ R+
Sbjct: 78 LSVQNVFYRPKDKQALADQKKAKFHQTEGDHLTLLAVYNSWKNNKFSNPWCYENFIQARS 137
Query: 432 LKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAHLERTGQYLTV 491
L+ A ++R+Q++ IM R L + S ++ V ++KA+ +G+F A + Y T+
Sbjct: 138 LRRAQDIRKQMLGIMDRHKLDVVSCGKST----VRVQKAICSGFFRNAAKKDPQEGYRTL 193
Query: 492 KDNQVVHLHPSNCL-DHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDIAPHYYDL 546
D QVV++HPS+ L + +PEWV+Y+E VLT++ ++R VT + WL++ AP ++ +
Sbjct: 194 IDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAPAFFKV 249
>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 = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 49/78 (62%), Gaps = 2/78 (2%)
Query: 13 YLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSAT 72
+ T G+LLR+ + +++DE HER + TD L +L++V++ P++++V+ SAT
Sbjct: 160 FCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLXSAT 217
Query: 73 LEAEKFQGYFYGAPLMKV 90
++ F YF+ P+++V
Sbjct: 218 IDTSXFCEYFFNCPIIEV 235
>pdb|3FY3|A Chain A, Crystal Structure Of Truncated Hemolysin A From P.
Mirabilis
Length = 236
Score = 33.1 bits (74), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 43/99 (43%), Gaps = 7/99 (7%)
Query: 434 SADNVRQQLVRIMARFNLKLCSN---DFNSRDYYVNIRKAMLAGYFMQVAHLERT----G 486
SA N Q++ I+ N + N DFN A+ AG HL G
Sbjct: 15 SAVNGGTQVINIVTPNNEGISHNQYQDFNVGKPGAVFNNALEAGQSQLAGHLNANSNLNG 74
Query: 487 QYLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFI 525
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 = 0.81, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 57 VLKNRPDLKLVVMSATLE---AEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYL 110
+ KNRPDLK+ ++ +++ G + A +M+ P L E+ E E DY+
Sbjct: 84 IAKNRPDLKVCIIESSVAPGGGSWLGGQLFSAMVMRKPAHLFLQELEIPYEDEGDYV 140
>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 = 7.3, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 308 PPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILS 367
P P+ + L+V+N ++D + + EK+S P+ L S ++ CS E+ +
Sbjct: 15 PRLPKAIAELLDVVN-----NEDSTVKAVSEKLSHDPVLSARVLRLANSARFGCSREVGT 69
Query: 368 I 368
I
Sbjct: 70 I 70
>pdb|3FEW|X Chain X, Structure And Function Of Colicin S4, A Colicin With A
Duplicated Receptor Binding Domain
Length = 505
Score = 28.9 bits (63), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 46/105 (43%), Gaps = 9/105 (8%)
Query: 319 EVLNYLGALDDDGNLTEMGEKMSEFPLD---PQMSKMLVESPKYNCSNEILSISAMLSVP 375
E+ LG D+ E ++ +E D P + K V+ +++ + +LSV
Sbjct: 179 EIYEALGFNKDESQRQEKAKQQAEDAWDRLPPNVRKFDVDVEQFHYLVVLDDYGNVLSVT 238
Query: 376 NCFVRPREAQKAADEAKARFGHIDG-DHLTLLNVYHAYKQNNEDP 419
VRP + KA+ G +D DH T +Y A NNE+P
Sbjct: 239 RTGVRPYVGSE-----KAKAGIMDKVDHKTPEEIYEALGFNNEEP 278
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 0.137 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,064,498
Number of Sequences: 62578
Number of extensions: 638849
Number of successful extensions: 1495
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1480
Number of HSP's gapped (non-prelim): 9
length of query: 574
length of database: 14,973,337
effective HSP length: 104
effective length of query: 470
effective length of database: 8,465,225
effective search space: 3978655750
effective search space used: 3978655750
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)