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= 004471
(751 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1NQE|A Chain A, Outer Membrane Cobalamin Transporter (btub) From E. Coli
pdb|1NQG|A Chain A, Outer Membrane Cobalamin Transporter (Btub) From E. Coli,
With Bound Calcium
pdb|1NQH|A Chain A, Outer Membrane Cobalamin Transporter (Btub) From E. Coli,
With Bound Calcium And Cyanocobalamin (Vitamin B12)
Substrate
pdb|1UJW|A Chain A, Structure Of The Complex Between Btub And Colicin E3
Receptor Binding Domain
pdb|2GUF|A Chain A, In Meso Crystal Structure Of The Cobalamin Transporter,
Btub
pdb|2YSU|A Chain A, Structure Of The Complex Between Btub And Colicin E2
Receptor Binding Domain
Length = 594
Score = 34.3 bits (77), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 28/74 (37%), Gaps = 9/74 (12%)
Query: 316 FEEGYRLLPQYCEQVKRTNPGSIASVYGNPA---------DNCFQRLFISFQASIYGFLN 366
F EGYR + Y K N G + YGNP + F+ L I G+ N
Sbjct: 379 FIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRN 438
Query: 367 ACRPLLGLDRTFLK 380
L+ D LK
Sbjct: 439 DVSDLIDYDDHTLK 452
>pdb|3RGM|A Chain A, Crystal Structure Of Spin-Labeled Btub T156r1
Length = 594
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 28/74 (37%), Gaps = 9/74 (12%)
Query: 316 FEEGYRLLPQYCEQVKRTNPGSIASVYGNPA---------DNCFQRLFISFQASIYGFLN 366
F EGYR + Y K N G + YGNP + F+ L I G+ N
Sbjct: 379 FIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRN 438
Query: 367 ACRPLLGLDRTFLK 380
L+ D LK
Sbjct: 439 DVSDLIDYDDHTLK 452
>pdb|3M8B|A Chain A, Crystal Structure Of Spin-Labeled Btub V10r1 In The Apo
State
pdb|3M8D|A Chain A, Crystal Structure Of Spin-Labeled Btub V10r1 With Bound
Calcium And Cyanocobalamin
Length = 594
Score = 34.3 bits (77), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 28/74 (37%), Gaps = 9/74 (12%)
Query: 316 FEEGYRLLPQYCEQVKRTNPGSIASVYGNPA---------DNCFQRLFISFQASIYGFLN 366
F EGYR + Y K N G + YGNP + F+ L I G+ N
Sbjct: 379 FIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRN 438
Query: 367 ACRPLLGLDRTFLK 380
L+ D LK
Sbjct: 439 DVSDLIDYDDHTLK 452
>pdb|2GSK|A Chain A, Structure Of The Btub:tonb Complex
Length = 590
Score = 34.3 bits (77), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 28/74 (37%), Gaps = 9/74 (12%)
Query: 316 FEEGYRLLPQYCEQVKRTNPGSIASVYGNPA---------DNCFQRLFISFQASIYGFLN 366
F EGYR + Y K N G + YGNP + F+ L I G+ N
Sbjct: 375 FIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRN 434
Query: 367 ACRPLLGLDRTFLK 380
L+ D LK
Sbjct: 435 DVSDLIDYDDHTLK 448
>pdb|1NQF|A Chain A, Outer Membrane Cobalamin Transporter (Btub) From E. Coli,
Methionine Substiution Construct For Se-Met Sad Phasing
Length = 594
Score = 34.3 bits (77), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 28/74 (37%), Gaps = 9/74 (12%)
Query: 316 FEEGYRLLPQYCEQVKRTNPGSIASVYGNPA---------DNCFQRLFISFQASIYGFLN 366
F EGYR + Y K N G + YGNP + F+ L I G+ N
Sbjct: 379 FIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRN 438
Query: 367 ACRPLLGLDRTFLK 380
L+ D LK
Sbjct: 439 DVSDLIDYDDHTLK 452
>pdb|3RGN|A Chain A, Crystal Structure Of Spin-Labeled Btub W371r1
Length = 594
Score = 34.3 bits (77), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 28/74 (37%), Gaps = 9/74 (12%)
Query: 316 FEEGYRLLPQYCEQVKRTNPGSIASVYGNPA---------DNCFQRLFISFQASIYGFLN 366
F EGYR + Y K N G + YGNP + F+ L I G+ N
Sbjct: 379 FIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRN 438
Query: 367 ACRPLLGLDRTFLK 380
L+ D LK
Sbjct: 439 DVSDLIDYDDHTLK 452
>pdb|1YYF|D Chain D, Correction Of X-Ray Intensities From An Hslv-Hslu Co-
Crystal Containing Lattice Translocation Defects
pdb|1YYF|C Chain C, Correction Of X-Ray Intensities From An Hslv-Hslu Co-
Crystal Containing Lattice Translocation Defects
Length = 181
Score = 30.8 bits (68), Expect = 2.7, Method: Composition-based stats.
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 463 MRHLSESFRKEFNNTILVNLLWEAAHALTVIE-FEAKILE 501
M+H + RK FN +L A A T+ E FEAK+ E
Sbjct: 34 MKHTARKVRKLFNGKVLAGFAGSVADAFTLFEKFEAKLEE 73
>pdb|2Z3A|A Chain A, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3A|B Chain B, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3A|C Chain C, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3A|D Chain D, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3A|E Chain E, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3A|F Chain F, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3A|G Chain G, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3A|H Chain H, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3A|I Chain I, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3A|J Chain J, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3A|K Chain K, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3A|L Chain L, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3B|A Chain A, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3B|B Chain B, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3B|C Chain C, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3B|D Chain D, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3B|E Chain E, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3B|F Chain F, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3B|G Chain G, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3B|H Chain H, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3B|I Chain I, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3B|J Chain J, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3B|K Chain K, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
pdb|2Z3B|L Chain L, Crystal Structure Of Bacillus Subtilis Codw, A Non-
Canonical Hslv-Like Peptidase With An Impaired Catalytic
Apparatus
Length = 180
Score = 30.8 bits (68), Expect = 2.7, Method: Composition-based stats.
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 463 MRHLSESFRKEFNNTILVNLLWEAAHALTVIE-FEAKILE 501
M+H + RK FN +L A A T+ E FEAK+ E
Sbjct: 33 MKHTARKVRKLFNGKVLAGFAGSVADAFTLFEKFEAKLEE 72
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 0.135 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,830,255
Number of Sequences: 62578
Number of extensions: 947870
Number of successful extensions: 2010
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 1986
Number of HSP's gapped (non-prelim): 28
length of query: 751
length of database: 14,973,337
effective HSP length: 106
effective length of query: 645
effective length of database: 8,340,069
effective search space: 5379344505
effective search space used: 5379344505
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: 55 (25.8 bits)