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= 025093
(258 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3JTF|A Chain A, The Cbs Domain Pair Structure Of A Magnesium And Cobalt
Efflux Protein From Bordetella Parapertussis In Complex
With Amp
pdb|3JTF|B Chain B, The Cbs Domain Pair Structure Of A Magnesium And Cobalt
Efflux Protein From Bordetella Parapertussis In Complex
With Amp
Length = 129
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 203 EKTASDAMTPIAETFAIDINAKLDKELMNLILEKGHSRVPVYYEEPTNIIGLIL 256
E+T +D P + +DI+ L +L+ I+E HSR PVY ++ NIIG++L
Sbjct: 4 ERTVADIXVPRSRXDLLDISQPL-PQLLATIIETAHSRFPVYEDDRDNIIGILL 56
>pdb|4HG0|A Chain A, Crystal Structure Of Magnesium And Cobalt Efflux Protein
Corc, Northeast Structural Genomics Consortium (nesg)
Target Er40
Length = 292
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 44/89 (49%), Gaps = 5/89 (5%)
Query: 167 RAELKTLVNLHGNEAGKGGELTHDETTIIAGALELTEKTASDAMTPIAETFAIDINAKLD 226
R EL L+ ++G+ + D + G ++ ++ D P ++ + N LD
Sbjct: 34 RDELLALIR----DSGQNDLIDEDTRDXLEGVXDIADQRVRDIXIPRSQXITLKRNQTLD 89
Query: 227 KELMNLILEKGHSRVPVYYEEPTNIIGLI 255
E +++I+E HSR PV E+ +I G++
Sbjct: 90 -ECLDVIIESAHSRFPVISEDKDHIEGIL 117
>pdb|3LHH|A Chain A, The Crystal Structure Of Cbs Domain Protein From
Shewanella Oneidensis Mr-1
Length = 172
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 1/76 (1%)
Query: 180 EAGKGGELTHDETTIIAGALELTEKTASDAMTPIAETFAIDINAKLDKELMNLILEKGHS 239
E G + H+E + L E+T S P ++ +D+N LD L + + HS
Sbjct: 18 EGSSAGVIEHNEHAXVKNVFRLDERTISSLXVPRSDIVFLDLNLPLDANLRT-VXQSPHS 76
Query: 240 RVPVYYEEPTNIIGLI 255
R PV + +G+I
Sbjct: 77 RFPVCRNNVDDXVGII 92
>pdb|3NQR|A Chain A, A Putative Cbs Domain-Containing Protein From Salmonella
Typhimurium Lt2
pdb|3NQR|B Chain B, A Putative Cbs Domain-Containing Protein From Salmonella
Typhimurium Lt2
pdb|3NQR|C Chain C, A Putative Cbs Domain-Containing Protein From Salmonella
Typhimurium Lt2
pdb|3NQR|D Chain D, A Putative Cbs Domain-Containing Protein From Salmonella
Typhimurium Lt2
Length = 127
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 203 EKTASDAMTPIAETFAIDINAKLDKELMNLILEKGHSRVPVYYEEPTNIIGLI 255
++ D P ++ + N LD E +++I+E HSR PV E+ +I G++
Sbjct: 2 DQRVRDIXIPRSQXITLKRNQTLD-ECLDVIIESAHSRFPVISEDKDHIEGIL 53
>pdb|1JRK|A Chain A, Crystal Structure Of A Nudix Protein From Pyrobaculum
Aerophilum Reveals A Dimer With Intertwined Beta Sheets
pdb|1JRK|B Chain B, Crystal Structure Of A Nudix Protein From Pyrobaculum
Aerophilum Reveals A Dimer With Intertwined Beta Sheets
pdb|1JRK|C Chain C, Crystal Structure Of A Nudix Protein From Pyrobaculum
Aerophilum Reveals A Dimer With Intertwined Beta Sheets
pdb|1JRK|D Chain D, Crystal Structure Of A Nudix Protein From Pyrobaculum
Aerophilum Reveals A Dimer With Intertwined Beta Sheets
pdb|1K26|A Chain A, Structure Of A Nudix Protein From Pyrobaculum Aerophilum
Solved By The Single Wavelength Anomolous Scattering
Method
pdb|1K26|B Chain B, Structure Of A Nudix Protein From Pyrobaculum Aerophilum
Solved By The Single Wavelength Anomolous Scattering
Method
pdb|1K2E|A Chain A, Crystal Structure Of A Nudix Protein From Pyrobaculum
Aerophilum
pdb|1K2E|B Chain B, Crystal Structure Of A Nudix Protein From Pyrobaculum
Aerophilum
Length = 156
Score = 27.3 bits (59), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 45/97 (46%), Gaps = 13/97 (13%)
Query: 155 VLLGHGRVALFRRAELKTLVNLHGNEAGKGGELTHDETTIIAGALELTEKTASDAMTPIA 214
VL+ +G+V L + L + GG + H+ET I A E E+T + PI
Sbjct: 7 VLVENGKVLLVKHKRLGVYIY-------PGGHVEHNETPIEAVKREFEEETGI-VVEPIG 58
Query: 215 ETFAIDINAKLDKELMNLILEKGHSRVPVYYEEPTNI 251
T+ I +++ + +ILE+ V Y E T+I
Sbjct: 59 FTYGIIDENAVERPMPLVILEE-----VVKYPEETHI 90
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
0.324 0.140 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,295,866
Number of Sequences: 62578
Number of extensions: 224012
Number of successful extensions: 453
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 449
Number of HSP's gapped (non-prelim): 12
length of query: 258
length of database: 14,973,337
effective HSP length: 97
effective length of query: 161
effective length of database: 8,903,271
effective search space: 1433426631
effective search space used: 1433426631
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)