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= 043662
(330 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1DJ0|A Chain A, The Crystal Structure Of E. Coli Pseudouridine Synthase I
At 1.5 Angstrom Resolution
pdb|1DJ0|B Chain B, The Crystal Structure Of E. Coli Pseudouridine Synthase I
At 1.5 Angstrom Resolution
Length = 264
Score = 138 bits (348), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 93/269 (34%), Positives = 142/269 (52%), Gaps = 12/269 (4%)
Query: 47 PGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVH 106
P +K L I YDG++Y GWQ Q ++Q +EKAL +++ E + + A RTD GVH
Sbjct: 2 PVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKAL---SQVANEPITVFCAGRTDAGVH 58
Query: 107 AWGQVAHF-ITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKI 165
GQV HF T D ++ +N LP DI VR + +FHARFSA ++ Y Y I
Sbjct: 59 GTGQVVHFETTALRKDAAWTL--GVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYII 116
Query: 166 YNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFR 225
YN + H L+ M +AA+ +G++DF++F VQ R P ++V
Sbjct: 117 YNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSR--TPWRNVMH 174
Query: 226 FDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYA 285
+V G + ++++ + F++ VRN+V L+++G P + ++LA +DR LA A
Sbjct: 175 INVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRT-LA--A 231
Query: 286 LSAPPHGLCLVEVKYNEEH-LRLPAACPL 313
+A GL LV V Y + + L P PL
Sbjct: 232 ATAKAEGLYLVAVDYPDRYDLPKPPMGPL 260
>pdb|2NQP|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|B Chain B, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|C Chain C, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|D Chain D, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|B Chain B, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|C Chain C, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|D Chain D, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NRE|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
Length = 270
Score = 138 bits (348), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 94/269 (34%), Positives = 141/269 (52%), Gaps = 12/269 (4%)
Query: 47 PGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVH 106
P +K L I YDG++Y GWQ Q ++Q +EKAL +V E + + A RTD GVH
Sbjct: 8 PVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVAN---EPITVFCAGRTDAGVH 64
Query: 107 AWGQVAHF-ITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKI 165
GQV HF T D ++ +N LP DI VR + +FHARFSA ++ Y Y I
Sbjct: 65 GTGQVVHFETTALRKDAAWTL--GVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYII 122
Query: 166 YNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFR 225
YN + H L+ M +AA+ +G++DF++F VQ R P ++V
Sbjct: 123 YNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSR--TPWRNVMH 180
Query: 226 FDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYA 285
+V G + ++++ + F++ VRN+V L+++G P + ++LA +DR LA A
Sbjct: 181 INVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRT-LA--A 237
Query: 286 LSAPPHGLCLVEVKYNEEH-LRLPAACPL 313
+A GL LV V Y + + L P PL
Sbjct: 238 ATAKAEGLYLVAVDYPDRYDLPKPPMGPL 266
>pdb|1VS3|A Chain A, Crystal Structure Of The Trna Pseudouridine Synthase Trua
From Thermus Thermophilus Hb8
pdb|1VS3|B Chain B, Crystal Structure Of The Trna Pseudouridine Synthase Trua
From Thermus Thermophilus Hb8
Length = 249
Score = 117 bits (293), Expect = 8e-27, Method: Compositional matrix adjust.
Identities = 86/252 (34%), Positives = 119/252 (47%), Gaps = 9/252 (3%)
Query: 53 LVIAYDGTRYAGWQFQTSP-PTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQV 111
L+ YDGT +AG Q Q T+Q +E+AL + L + V A RTD GVHA
Sbjct: 6 LLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIGALPKA----VAAGRTDAGVHALAMP 61
Query: 112 AHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVM 171
H + S +E + ALN LLP D++V P+FHAR A + Y Y+I
Sbjct: 62 FH-VDVESAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRPHP 120
Query: 172 DPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEM 231
P RH A L+ M +A +G+H+F F + +++ + E
Sbjct: 121 SPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRPGERELLEARLQVAEGEA 180
Query: 232 GALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPH 291
G ++L G FL QVR MV LL++G PP+ + IL T DR+ +AP H
Sbjct: 181 GLEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGP---TAPAH 237
Query: 292 GLCLVEVKYNEE 303
GL VE Y EE
Sbjct: 238 GLYFVEAAYPEE 249
>pdb|3ETC|A Chain A, 2.1 A Structure Of Acyl-Adenylate Synthetase From
Methanosarcina Acetivorans Containing A Link Between
Lys256 And Cys298
pdb|3ETC|B Chain B, 2.1 A Structure Of Acyl-Adenylate Synthetase From
Methanosarcina Acetivorans Containing A Link Between
Lys256 And Cys298
Length = 580
Score = 31.2 bits (69), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 188 TTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGA 233
T+L+ Q FV K DF ++ + Q N ++L P F +DV+++ A
Sbjct: 25 TSLLSQ----FVSKTDFESYEDFQENFKILVPENFNFAYDVVDVYA 66
>pdb|1P91|A Chain A, Crystal Structure Of Rlma(I) Enzyme: 23s Rrna N1-G745
Methyltransferase (Northeast Structural Genomics
Consortium Target Er19)
pdb|1P91|B Chain B, Crystal Structure Of Rlma(I) Enzyme: 23s Rrna N1-G745
Methyltransferase (Northeast Structural Genomics
Consortium Target Er19)
Length = 269
Score = 28.1 bits (61), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 31/116 (26%), Positives = 47/116 (40%), Gaps = 15/116 (12%)
Query: 219 PVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDR 278
P + F DV ++ ++ + Y QV VA ++ D + +I A
Sbjct: 108 PEITTFGLDVSKVA------IKAAAKRYPQVTFCVASSHRLPFSDTSXDAIIRIYAPCKA 161
Query: 279 KELAK------YALSAPPHGLCLVEVK---YNEEHLRLPAACPLSSFGRHHSVRKC 325
+ELA+ + ++A P L E+K YNE HL P A L F S C
Sbjct: 162 EELARVVKPGGWVITATPGPRHLXELKGLIYNEVHLHAPHAEQLEGFTLQQSAELC 217
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
0.322 0.138 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,338,468
Number of Sequences: 62578
Number of extensions: 432287
Number of successful extensions: 809
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 794
Number of HSP's gapped (non-prelim): 6
length of query: 330
length of database: 14,973,337
effective HSP length: 99
effective length of query: 231
effective length of database: 8,778,115
effective search space: 2027744565
effective search space used: 2027744565
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)