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= 007386
(605 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2A1R|A Chain A, Crystal Structure Of Parn Nuclease Domain
pdb|2A1R|B Chain B, Crystal Structure Of Parn Nuclease Domain
pdb|2A1S|A Chain A, Crystal Structure Of Native Parn Nuclease Domain
pdb|2A1S|B Chain B, Crystal Structure Of Native Parn Nuclease Domain
pdb|2A1S|C Chain C, Crystal Structure Of Native Parn Nuclease Domain
pdb|2A1S|D Chain D, Crystal Structure Of Native Parn Nuclease Domain
Length = 430
Score = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 86/359 (23%), Positives = 156/359 (43%), Gaps = 54/359 (15%)
Query: 8 NFFIFQRQELPLDGAA--YEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKALKH 65
NF++F + P + ++ +F+CQ++S+DFLA FDFN G+ YL++E+E + +
Sbjct: 89 NFYVFPK---PFNRSSPDVKFVCQSSSIDFLASQGFDFNKVFRNGIPYLNQEEERQLREQ 145
Query: 66 VNSTYEDESLDSWHSLKEIRDTHLFNIPDILFAERMK--DRLSEWLGGLLRNRDEGSEVQ 123
+ E S + + P + ++ K D++ E + LL++ + +
Sbjct: 146 YD---EKRSQANGAGALSYVSPNTSKCPVTIPEDQKKFIDQVVEKIEDLLQSEENKN--- 199
Query: 124 PSFNDSKQQFETIFFKMRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNV 183
+ P GF + L+ Q + K+ K + + E V
Sbjct: 200 --------------LDLEPC---TGF--QRKLIYQTLSWKYPKGIHVETLETEKKERYIV 240
Query: 184 IVYIESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAH 243
I ++ E K+ ++ EQ+ + ++GF VI +++ KL++GHN LD+ H
Sbjct: 241 ISKVDEEERKRREQQKHAKEQE-----ELNDAVGFSRVIHAIANSGKLVIGHNMLLDVMH 295
Query: 244 IYSKFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCP 303
+F+ PLP EF FP ++DTK++ + ++ F +
Sbjct: 296 TVHQFYCPLPADLSEFKEMTTCVFPRLLDTKLMAS----------------TQPFKDIIN 339
Query: 304 QIALGSKSTHLALQPSVKVEVE-VDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 361
+L L P +VE + S + S HEAGYDA++TG F ++LG
Sbjct: 340 NTSLAELEKRLKETPFNPPKVESAEGFPSYDTASEQLHEAGYDAYITGLCFISMANYLG 398
>pdb|3D45|A Chain A, Crystal Structure Of Mouse Parn In Complex With M7gpppg
pdb|3D45|B Chain B, Crystal Structure Of Mouse Parn In Complex With M7gpppg
Length = 507
Score = 90.5 bits (223), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 108/469 (23%), Positives = 196/469 (41%), Gaps = 75/469 (15%)
Query: 8 NFFIFQRQELPLDGAAYEFLCQTTSMDFLAKYQFDFNACIHEGVSYLSREQEDKALKHVN 67
NF++F + +F+CQ++S+DFLA FDFN G+ YL++E+E + +
Sbjct: 91 NFYVFPK-PFSRSSPDVKFVCQSSSIDFLASQGFDFNKVFCSGIPYLNQEEERQLREQF- 148
Query: 68 STYEDESLDSWHSLKEIRDTHLFNIPDILFAERMKDRLSEWLGGLLRNRDEGS-EVQPSF 126
DE + + + IP+ ++ D++ E + L++ ++ S E+ P
Sbjct: 149 ----DEKRSQANGAGALAKCPV-TIPED--QKKFIDQVIEKIEDFLQSEEKRSLELDPC- 200
Query: 127 NDSKQQFETIFFKMRPAISLNGFTSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVY 186
GF + L+ Q + K+ K + + + VI
Sbjct: 201 --------------------TGF--QRKLIYQTLSWKYPKGIHVETLETDKKERHIVISK 238
Query: 187 IESESDKKMLMKEVKDEQKIDAEMSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYS 246
++ E K+ ++ EQ+ + ++GF VI +++ KL+VGHN LD+ H
Sbjct: 239 VDEEERKRREQEKYTKEQE-----ELNDAVGFSRVIHAIANSGKLVVGHNMLLDVMHTIH 293
Query: 247 KFFGPLPLTAEEFISSVNKYFPHIIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIA 306
+F+ PLP EF FP ++DTK++ + ++ F + +
Sbjct: 294 QFYCPLPADLNEFKEMAICVFPRLLDTKLMAS----------------TQPFKDIINNTS 337
Query: 307 LGSKSTHLALQPSVKVEVE-VDDIRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLGIDFK 365
L L P +VE + S + S HEAGYDA++TG F ++LG
Sbjct: 338 LAELEKRLKETPFDPPKVESAEGFPSYDTASEQLHEAGYDAYITGLCFISMANYLGSLLS 397
Query: 366 QQSSSENLAHNEKLREHVNLLYLSWTNGEIINLSTGNRTSESLASNKRKNHYPKILFECI 425
+ A ++ + N L+L ++++ N L +++H
Sbjct: 398 PPKMCVS-ARSKLIEPFFNKLFLM----RVMDIPYLNLEGPDL--QPKRDH--------- 441
Query: 426 VIVWGFPSHLKAWDIRECISKVYGPTSVISVYHVDETAVFVQFSRAEMV 474
V+ FP K D+ + S +G I + +D+T+ FV S+ E V
Sbjct: 442 VLHVTFPKEWKTSDLYQLFS-AFG---NIQISWIDDTSAFVSLSQPEQV 486
>pdb|4ECN|A Chain A, Crystal Structure Of A Leucine-Rich Repeat Protein
(Bt_0210) From Bacteroides Thetaiotaomicron Vpi-5482 At
2.80 A Resolution
Length = 876
Score = 28.9 bits (63), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 70 YEDESLDSWHSLKEIRDTHLFNIPD 94
YE+E L SW +LK++ D L+N P+
Sbjct: 480 YENEEL-SWSNLKDLTDVELYNCPN 503
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 0.133 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,973,877
Number of Sequences: 62578
Number of extensions: 682622
Number of successful extensions: 1470
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1464
Number of HSP's gapped (non-prelim): 8
length of query: 605
length of database: 14,973,337
effective HSP length: 104
effective length of query: 501
effective length of database: 8,465,225
effective search space: 4241077725
effective search space used: 4241077725
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)