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= 041464
(198 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1C3R|A Chain A, Crystal Structure Of An Hdac Homolog Complexed With
Trichostatin A
pdb|1C3R|B Chain B, Crystal Structure Of An Hdac Homolog Complexed With
Trichostatin A
pdb|1C3S|A Chain A, Crystal Structure Of An Hdac Homolog Complexed With Saha
Length = 375
Score = 30.8 bits (68), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 44/191 (23%), Positives = 75/191 (39%), Gaps = 37/191 (19%)
Query: 22 HAVDYT----VSNRAATTPGGMRFANEIGAEYTPNFIWRLFQQNTEADRKNIPQVDLFID 77
H DY + R+ + P G R IG P + +F ++ A + ++ F+
Sbjct: 61 HTEDYINTLMEAERSQSVPKGAREKYNIGGYENP-VSYAMFTGSSLATGSTVQAIEEFLK 119
Query: 78 DMKPGEIAFTSNNGIHY-------GDDFIQNIPVD---LIKQEFSGVMYHEMT--HANYV 125
G +AF G+H+ G +I N V L K+ F ++Y ++ H + V
Sbjct: 120 ----GNVAFNPAGGMHHAFKSRANGFCYINNPAVGIEYLRKKGFKRILYIDLDAHHCDGV 175
Query: 126 PEGWAKPGEGTMWNQGHSSVAARFLDYCNDLRNGFVAE----------LNKKMRDGYNDN 175
E + + + + S +Y GF+ E LN + G NDN
Sbjct: 176 QEAFYDTDQVFVLSLHQSP------EYAFPFEKGFLEEIGEGKGKGYNLNIPLPKGLNDN 229
Query: 176 FFMELLGKSID 186
F+ L KS++
Sbjct: 230 EFLFALEKSLE 240
>pdb|1C3P|A Chain A, Crystal Structure Of An Hdac Homolog From Aquifex Aeolicus
Length = 375
Score = 30.0 bits (66), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 44/191 (23%), Positives = 73/191 (38%), Gaps = 37/191 (19%)
Query: 22 HAVDYT----VSNRAATTPGGMRFANEIGAEYTPNFIWRLFQQNTEADRKNIPQVDLFID 77
H DY + R P G R IG P + +F ++ A + ++ F+
Sbjct: 61 HTEDYINTLMEAERCQCVPKGAREKYNIGGYENP-VSYAMFTGSSLATGSTVQAIEEFLK 119
Query: 78 DMKPGEIAFTSNNGIHY-------GDDFIQNIPVD---LIKQEFSGVMYHEMT--HANYV 125
G +AF G+H+ G +I N V L K+ F ++Y ++ H + V
Sbjct: 120 ----GNVAFNPAGGMHHAFKSRANGFCYINNPAVGIEYLRKKGFKRILYIDLDAHHCDGV 175
Query: 126 PEGWAKPGEGTMWNQGHSSVAARFLDYCNDLRNGFVAE----------LNKKMRDGYNDN 175
E + + + + S +Y GF+ E LN + G NDN
Sbjct: 176 QEAFYDTDQVFVLSLHQSP------EYAFPFEKGFLEEIGEGKGKGYNLNIPLPKGLNDN 229
Query: 176 FFMELLGKSID 186
F+ L KS++
Sbjct: 230 EFLFALEKSLE 240
>pdb|2X5D|A Chain A, Crystal Structure Of A Probable Aminotransferase From
Pseudomonas Aeruginosa
pdb|2X5D|B Chain B, Crystal Structure Of A Probable Aminotransferase From
Pseudomonas Aeruginosa
pdb|2X5D|C Chain C, Crystal Structure Of A Probable Aminotransferase From
Pseudomonas Aeruginosa
pdb|2X5D|D Chain D, Crystal Structure Of A Probable Aminotransferase From
Pseudomonas Aeruginosa
Length = 412
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 43/93 (46%), Gaps = 12/93 (12%)
Query: 58 FQQNTEADRKNIPQVDLFIDDMKPGEIAFTSNNGIHYGD-DFIQNIPVDLIKQEFSGVMY 116
F + A R++IP+ + I + F SN + DF + + V L KQ + ++
Sbjct: 159 FNELERAIRESIPKPRMMI-------LGFPSNPTAQCVELDFFERV-VALAKQ-YDVMVV 209
Query: 117 HEMTHANYVPEGWAKPGEGTMWNQGHSSVAARF 149
H++ +A+ V +GW P M G +A F
Sbjct: 210 HDLAYADIVYDGWKAP--SIMQVPGAKDIAVEF 240
>pdb|3ZS6|A Chain A, The Structural Characterization Of Burkholderia
Pseudomallei Oppa
Length = 506
Score = 28.1 bits (61), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 152 YCNDLRNGFVAELNKKMRDGYNDNFFMELLGKSIDQLWNDY 192
YCN + VAE N+K+ DG LL ++ D NDY
Sbjct: 431 YCNPKVDSLVAEANQKLDDGAR----AALLTQAHDLAMNDY 467
>pdb|3RFR|A Chain A, Crystal Structure Of Particulate Methane Monooxygenase
(Pmmo) From Methylocystis Sp. Strain M
pdb|3RFR|E Chain E, Crystal Structure Of Particulate Methane Monooxygenase
(Pmmo) From Methylocystis Sp. Strain M
pdb|3RFR|I Chain I, Crystal Structure Of Particulate Methane Monooxygenase
(Pmmo) From Methylocystis Sp. Strain M
Length = 419
Score = 27.7 bits (60), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 35 TPGGMRFANEIGAEYTPNFI 54
TP G RFA EIG P F+
Sbjct: 395 TPDGKRFAAEIGGPVIPKFV 414
>pdb|2X54|S Chain S, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 1 Of 2)
pdb|2X54|T Chain T, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 1 Of 2)
pdb|2X54|U Chain U, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 1 Of 2)
pdb|2X54|V Chain V, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 1 Of 2)
pdb|2X54|W Chain W, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 1 Of 2)
pdb|2X54|X Chain X, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 1 Of 2)
pdb|2X5A|S Chain S, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 2 Of 2)
pdb|2X5A|T Chain T, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 2 Of 2)
pdb|2X5A|U Chain U, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 2 Of 2)
pdb|2X5A|V Chain V, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 2 Of 2)
pdb|2X5A|W Chain W, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 2 Of 2)
pdb|2X5A|X Chain X, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 2 Of 2)
Length = 298
Score = 26.9 bits (58), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 31 RAATTPGGMRFANEIGAEYT 50
+ TP G+RF ++IG EYT
Sbjct: 206 KLPKTPAGVRFLDDIGNEYT 225
>pdb|2X53|S Chain S, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Sr
pdb|2X53|T Chain T, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Sr
pdb|2X53|U Chain U, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Sr
pdb|2X53|V Chain V, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Sr
pdb|2X53|W Chain W, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Sr
pdb|2X53|X Chain X, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Sr
Length = 298
Score = 26.9 bits (58), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 31 RAATTPGGMRFANEIGAEYT 50
+ TP G+RF ++IG EYT
Sbjct: 206 KLPKTPAGVRFLDDIGNEYT 225
>pdb|2WZP|P Chain P, Structures Of Lactococcal Phage P2 Baseplate Shed Light On
A Novel Mechanism Of Host Attachment And Activation In
Siphoviridae
pdb|2WZP|Q Chain Q, Structures Of Lactococcal Phage P2 Baseplate Shed Light On
A Novel Mechanism Of Host Attachment And Activation In
Siphoviridae
Length = 326
Score = 26.9 bits (58), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 31 RAATTPGGMRFANEIGAEYT 50
+ TP G+RF ++IG EYT
Sbjct: 234 KLPKTPAGVRFLDDIGNEYT 253
>pdb|3K3W|B Chain B, Thermostable Penicillin G Acylase From Alcaligenes
Faecalis In Orthorhombic Form
pdb|3ML0|B Chain B, Thermostable Penicillin G Acylase From Alcaligenes
Faecalis In Tetragonal Form
Length = 551
Score = 26.9 bits (58), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 75 FIDDMKPGEIAFTSNNGI---HYGDDF 98
F D M PG+ FT NG+ HY D
Sbjct: 491 FCDAMPPGQSGFTDRNGVRSPHYEDQL 517
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
0.320 0.137 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,580,313
Number of Sequences: 62578
Number of extensions: 281452
Number of successful extensions: 552
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 548
Number of HSP's gapped (non-prelim): 16
length of query: 198
length of database: 14,973,337
effective HSP length: 94
effective length of query: 104
effective length of database: 9,091,005
effective search space: 945464520
effective search space used: 945464520
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: 49 (23.5 bits)