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= psy15891
(899 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IKM|A Chain A, Crystal Structure Of Human Mitochondrial Dna Polymerase
Holoenzyme
pdb|3IKM|D Chain D, Crystal Structure Of Human Mitochondrial Dna Polymerase
Holoenzyme
Length = 1172
Score = 701 bits (1810), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 402/955 (42%), Positives = 537/955 (56%), Gaps = 134/955 (14%)
Query: 6 WTNVSSLNS--LSEVYKLYCEGKVLDKTDRNIFVEGSLEDIENNWHNLMTYCAKDTLATF 63
W ++SS+NS L+EV++LY G L+K R +FV+G+++DI N+ +LM YCA+D AT
Sbjct: 278 WLDISSVNSNSLAEVHRLYVGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVWATH 337
Query: 64 EVIQALFPLFLERFPHPVTLAGMLELSTAYLPDTLATFEVIQALFPLFLERFPHPVTLAG 123
EV Q PLFLER PHPVTLAG
Sbjct: 338 --------------------------------------EVFQQQLPLFLERCPHPVTLAG 359
Query: 124 MLELSTAYLPVNNNWVKYFNESCQTFNDLNVEMKSLLMDKCDQACSLLHDDKYKDSLWLW 183
MLE+ +YLPVN NW +Y E+ T+ +L EMK LMD + AC LL ++YK+ WLW
Sbjct: 360 MLEMGVSYLPVNQNWERYLAEAQGTYEELQREMKKSLMDLANDACQLLSGERYKEDPWLW 419
Query: 184 DQDWSVXXXXXXXXXXXXXSVDQETEEPEEFYEINKNGEDQT-------EDEFVK--RRR 234
D +W + ++ P E + DQ E+EF + R
Sbjct: 420 DLEWDLQEFKQKKAKKVKKEPATASKLPIEGAGAPGDPMDQEDLGPCSEEEEFQQDVMAR 479
Query: 235 ELVEKFKPLMQTKDRLPVNSSYLIGYPEWYRKLCVKPHSADKDAVSKQELIHDGISDTSE 294
++K K T + LP +L G+P WYRKLC + + D
Sbjct: 480 ACLQKLK---GTTELLPKRPQHLPGHPGWYRKLCPR------------------LDDP-- 516
Query: 295 AWIPGPSLISTSMQITPKLLSLTWKSMPLHFIRGHGWGYLVPYSTD--IKVPDAENI--- 349
AW PGPSL+S M++TPKL++LTW PLH+ HGWGYLVP D K+P +
Sbjct: 517 AWTPGPSLLSLQMRVTPKLMALTWDGFPLHYSERHGWGYLVPGRRDNLAKLPTGTTLESA 576
Query: 350 ----PLEQLKQLY---------NNITKQDNCEAN----VDNAQNSLRDSVETNISFIDCS 392
P ++ LY + Q+ A DN +++ +VE + +++
Sbjct: 577 GVVCPYRAIESLYRKHCLEQGKQQLMPQEAGLAEEFLLTDN--SAIWQTVE-ELDYLEVE 633
Query: 393 KSAKRLEVIANVLDKKKLAEXXXXXXXXXXXXXPREIG-----------FIKLPHKDGEH 441
AK +E + + + LA G F KLPHKDG
Sbjct: 634 AEAK-MENLRAAVPGQPLALTARGGPKDTQPSYHHGNGPYNDVDIPGCWFFKLPHKDGNS 692
Query: 442 LNVGNPLSRDFINKFSDNSLAGVDIGAK--RIIEISRMLSYWRNNHERVKKQFVVWLNKK 499
NVG+P ++DF+ K D +L GA R +EI++M+S+WRN H+R+ Q VVWL +
Sbjct: 693 CNVGSPFAKDFLPKMEDGTLQAGPGGASGPRALEINKMISFWRNAHKRISSQMVVWLPRS 752
Query: 500 DLPRRLVE--NIESEGRDYGVILPQLIVSGTLTRRAVEATWMTASNAVGERVGSELRAMI 557
LPR ++ + + EG YG ILPQ++ +GT+TRRAVE TW+TASNA +RVGSEL+AM+
Sbjct: 753 ALPRAVIRHPDYDEEGL-YGAILPQVVTAGTITRRAVEPTWLTASNARPDRVGSELKAMV 811
Query: 558 QAPDGYSIIGADVDSQELWIASVIGDSYCAKEHGATPLGWMTLSGQKSNATDMHSITAKA 617
QAP GY+++GADVDSQELWIA+V+GD++ A HG T GWMTL G+KS TD+HS TA
Sbjct: 812 QAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTATT 871
Query: 618 VGISREHAKIINYARIYGAGERFAERLLKQFNPEMSKSDAKSKARKMYTLTKGKKLYRLK 677
VGISREHAKI NY RIYGAG+ FAERLL QFN +++ +A KA++MY TKG + YRL
Sbjct: 872 VGISREHAKIFNYGRIYGAGQPFAERLLMQFNHRLTQQEAAEKAQQMYAATKGLRWYRLS 931
Query: 678 DGHLEELIKRVYSKYE---------------AREVCSAYNTSVDKIFDKPQWYGGTESAM 722
D E L++ + + RE ++ + W GGTES M
Sbjct: 932 D-EGEWLVRELNLPVDRTEGGWISLQDLRKVQRETARKSQWKKWEVVAERAWKGGTESEM 990
Query: 723 FNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCM 782
FN+LE IATS P TP L C +SRALEP S +F+ +R+NWVVQS AVD+LHLMLV M
Sbjct: 991 FNKLESIATSDIPRTPVLGCCISRALEP-SAVQEEFMTSRVNWVVQSSAVDYLHLMLVAM 1049
Query: 783 RWLVSR---DTRFVISIHDEIRYLVPDEEKYETALALHVTNLLTRAFCIKKLDMTDIPLS 839
+WL D RF ISIHDE+RYLV +E++Y ALAL +TNLLTR KL + D+P S
Sbjct: 1050 KWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQS 1109
Query: 840 ISFFSGVEIDKVLRKESDNDCKTPSNPYGLCKGYGIPLGEILDIYQTIDKANGVI 894
++FFS V+ID+ LRKE DCKTPSNP G+ + YGIP GE LDIYQ I+ G +
Sbjct: 1110 VAFFSAVDIDRCLRKEVTMDCKTPSNPTGMERRYGIPQGEALDIYQIIELTKGSL 1164
>pdb|3C4R|A Chain A, Crystal Structure Of An Uncharacterized Protein Encoded By
Cryptic Prophage
pdb|3C4R|B Chain B, Crystal Structure Of An Uncharacterized Protein Encoded By
Cryptic Prophage
pdb|3C4R|C Chain C, Crystal Structure Of An Uncharacterized Protein Encoded By
Cryptic Prophage
pdb|3C4R|D Chain D, Crystal Structure Of An Uncharacterized Protein Encoded By
Cryptic Prophage
Length = 151
Score = 30.0 bits (66), Expect = 6.1, Method: Composition-based stats.
Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 4/87 (4%)
Query: 16 SEVYKLYCEGKVLDKTDRNIFVEGSLEDIENNWHNLMTYCAKDTLATFEVIQALFPLFLE 75
+E+ + Y E L T ++ + E + N + + KDT E IQAL P +E
Sbjct: 28 AEITRAYFE---LGXTFPELYDDSHPEALARNTQKIFRWVEKDTPDAVEKIQALLPA-IE 83
Query: 76 RFPHPVTLAGMLELSTAYLPDTLATFE 102
+ P+ +A S+AY + + T E
Sbjct: 84 KSXPPLLVARXRSHSSAYFRELVETRE 110
>pdb|2ZT9|C Chain C, Crystal Structure Of The Cytochrome B6f Complex From
Nostoc Sp. Pcc 7120
pdb|4H44|C Chain C, 2.70 A Cytochrome B6f Complex Structure From Nostoc Pcc
7120
Length = 289
Score = 30.0 bits (66), Expect = 6.7, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 518 VILPQLIVSGTLTRRAVEATWMTASNAVG---ERVGSELRAMIQAPDGYSIIGADVDSQE 574
V +PQ ++ T+ + V+ + T+ VG +VG + A++ P+G+ I D +E
Sbjct: 34 VEVPQSVLPDTVFKAVVKIPYDTSVQQVGADGSKVGLNVGAVLMLPEGFKIAPEDRIPEE 93
Query: 575 LWIASVIGDSY 585
L IGD Y
Sbjct: 94 L--KEEIGDVY 102
>pdb|1Q8I|A Chain A, Crystal Structure Of Escherichia Coli Dna Polymerase Ii
Length = 783
Score = 30.0 bits (66), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 525 VSGTLTRRAVEATWMTASNAVGERVGSELRAMIQAPDGYSIIGADVDSQELWIASVIGDS 584
V GT R + ++ G ++ + +A+I+A GY +I D DS +W+ +
Sbjct: 502 VLGTTACRFFDPRLASSITMRGHQIMRQTKALIEA-QGYDVIYGDTDSTFVWLKGAHSEE 560
Query: 585 YCAK 588
AK
Sbjct: 561 EAAK 564
>pdb|3K5L|A Chain A, Crystal Structure Of E.Coli Pol Ii-Abasic Dna-Datp Lt(0,
3) Ternary Complex
pdb|3K5M|A Chain A, Crystal Structure Of E.Coli Pol Ii-Abasic Dna-Ddgtp Lt(-2,
2) Ternary Complex
pdb|3K5N|A Chain A, Crystal Structure Of E.Coli Pol Ii-Abasic Dna Binary
Complex
pdb|3K5N|B Chain B, Crystal Structure Of E.Coli Pol Ii-Abasic Dna Binary
Complex
pdb|3K5O|A Chain A, Crystal Structure Of E.Coli Pol Ii
pdb|3K5O|B Chain B, Crystal Structure Of E.Coli Pol Ii
pdb|3K57|A Chain A, Crystal Structure Of E.Coli Pol Ii-Normal Dna-Datp Ternary
Complex
pdb|3K58|A Chain A, Crystal Structure Of E.Coli Pol Ii-Normal Dna-Dttp Ternary
Complex
pdb|3K59|A Chain A, Crystal Structure Of E.Coli Pol Ii-Normal Dna-Dctp Ternary
Complex
pdb|3MAQ|A Chain A, Crystal Structure Of E.coli Pol Ii-normal Dna-dgtp Ternary
Complex
Length = 786
Score = 29.6 bits (65), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 525 VSGTLTRRAVEATWMTASNAVGERVGSELRAMIQAPDGYSIIGADVDSQELWIASVIGDS 584
V GT R + ++ G ++ + +A+I+A GY +I D DS +W+ +
Sbjct: 505 VLGTTACRFFDPRLASSITMRGHQIMRQTKALIEA-QGYDVIYGDTDSTFVWLKGAHSEE 563
Query: 585 YCAK 588
AK
Sbjct: 564 EAAK 567
>pdb|1TU2|B Chain B, The Complex Of Nostoc Cytochrome F And Plastocyanin
Determin With Paramagnetic Nmr. Based On The Structures
Of Cytochrome F And Plastocyanin, 10 Structures
Length = 254
Score = 29.6 bits (65), Expect = 6.9, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 518 VILPQLIVSGTLTRRAVEATWMTASNAVG---ERVGSELRAMIQAPDGYSIIGADVDSQE 574
V +PQ ++ T+ + V+ + T+ VG +VG + A++ P+G+ I D +E
Sbjct: 34 VEVPQSVLPDTVFKAVVKIPYDTSVQQVGADGSKVGLNVGAVLMLPEGFKIAPEDRIPEE 93
Query: 575 LWIASVIGDSY 585
L IGD Y
Sbjct: 94 L--KEEIGDVY 102
>pdb|2YXD|A Chain A, Crystal Structure Of Cobalamin Biosynthesis Precorrin 8w
Decarboxylase (Cbit)
pdb|2YXD|B Chain B, Crystal Structure Of Cobalamin Biosynthesis Precorrin 8w
Decarboxylase (Cbit)
Length = 183
Score = 29.6 bits (65), Expect = 7.4, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 9/56 (16%)
Query: 361 ITKQDNCEANVDNAQ------NSLRDSVETNISFIDCSKSAKRLEVIANVLDKKKL 410
+TKQ+ + N+ N Q + D +E N +FI +K+ +E I +LDKKK+
Sbjct: 72 VTKQNLAKFNIKNCQIIKGRAEDVLDKLEFNKAFIGGTKN---IEKIIEILDKKKI 124
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
0.318 0.134 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,757,014
Number of Sequences: 62578
Number of extensions: 1110102
Number of successful extensions: 2792
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2780
Number of HSP's gapped (non-prelim): 11
length of query: 899
length of database: 14,973,337
effective HSP length: 108
effective length of query: 791
effective length of database: 8,214,913
effective search space: 6497996183
effective search space used: 6497996183
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)