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= psy12225
(396 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3TCF|A Chain A, Crystal Structure Of E. Coli Oppa Complexed With
Endogenous Ligands
pdb|3TCF|B Chain B, Crystal Structure Of E. Coli Oppa Complexed With
Endogenous Ligands
pdb|3TCF|C Chain C, Crystal Structure Of E. Coli Oppa Complexed With
Endogenous Ligands
pdb|3TCF|D Chain D, Crystal Structure Of E. Coli Oppa Complexed With
Endogenous Ligands
pdb|3TCF|E Chain E, Crystal Structure Of E. Coli Oppa Complexed With
Endogenous Ligands
pdb|3TCF|F Chain F, Crystal Structure Of E. Coli Oppa Complexed With
Endogenous Ligands
pdb|3TCF|G Chain G, Crystal Structure Of E. Coli Oppa Complexed With
Endogenous Ligands
pdb|3TCF|H Chain H, Crystal Structure Of E. Coli Oppa Complexed With
Endogenous Ligands
pdb|3TCG|A Chain A, Crystal Structure Of E. Coli Oppa Complexed With The
Tripeptide Kge
pdb|3TCG|B Chain B, Crystal Structure Of E. Coli Oppa Complexed With The
Tripeptide Kge
pdb|3TCG|C Chain C, Crystal Structure Of E. Coli Oppa Complexed With The
Tripeptide Kge
pdb|3TCG|D Chain D, Crystal Structure Of E. Coli Oppa Complexed With The
Tripeptide Kge
pdb|3TCG|E Chain E, Crystal Structure Of E. Coli Oppa Complexed With The
Tripeptide Kge
pdb|3TCG|F Chain F, Crystal Structure Of E. Coli Oppa Complexed With The
Tripeptide Kge
pdb|3TCG|G Chain G, Crystal Structure Of E. Coli Oppa Complexed With The
Tripeptide Kge
pdb|3TCG|H Chain H, Crystal Structure Of E. Coli Oppa Complexed With The
Tripeptide Kge
pdb|3TCH|A Chain A, Crystal Structure Of E. Coli Oppa In An Open Conformation
Length = 524
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 247 ITSVPAGLETPDSIELRKKKIESDMETNEAP-QLFQVLTEKRPDKLGPGMMASTHMYEV 304
+T +P E D R +I DM N P +LFQ L ++ PD++ T+ YE+
Sbjct: 222 VTYLPIASEVTDVNRYRSGEI--DMTNNSMPIELFQKLKKEIPDEVHVDPYLCTYYYEI 278
>pdb|2Z23|A Chain A, Crystal Structure Of Y.Pestis Oligo Peptide Binding
Protein Oppa With Tri-Lysine Ligand
Length = 517
Score = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 247 ITSVPAGLETPDSIELRKKKIESDMETNEAP-QLFQVLTEKRPDKLGPGMMASTHMYEV 304
+T +P E D R +I DM N P +LFQ L ++ PD++ T+ YE+
Sbjct: 221 VTYLPISSEVTDVNRYRSGEI--DMTYNNMPIELFQKLKKEIPDQVHVDPYLCTYYYEI 277
>pdb|1GXU|A Chain A, Hydrogenase Maturation Protein Hypf
"acylphosphatase-Like" N-Terminal Domain (Hypf-Acp) In
Complex With A Substrate. Crystal Grown In The Presence
Of Carbamoylphosphate
Length = 91
Score = 28.9 bits (63), Expect = 4.7, Method: Composition-based stats.
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 43 FKWQTKPRLSIHGDLYYEGKEFETKLKE 70
F WQ +L++HGD+ +G E +L+E
Sbjct: 25 FVWQLAQQLNLHGDVCNDGDGVEVRLRE 52
>pdb|1GXT|A Chain A, Hydrogenase Maturation Protein Hypf
"acylphosphatase-Like" N-Terminal Domain (Hypf-Acp) In
Complex With Sulfate
Length = 91
Score = 28.9 bits (63), Expect = 5.0, Method: Composition-based stats.
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 43 FKWQTKPRLSIHGDLYYEGKEFETKLKE 70
F WQ +L++HGD+ +G E +L+E
Sbjct: 25 FVWQLAQQLNLHGDVCNDGDGVEVRLRE 52
>pdb|2Z8D|A Chain A, The Galacto-N-Biose-LACTO-N-Biose I-Binding Protein
(Gl-Bp) Of The Abc Transporter From Bifidobacterium
Longum In Complex With Lacto-N- Biose
pdb|2Z8D|B Chain B, The Galacto-N-Biose-LACTO-N-Biose I-Binding Protein
(Gl-Bp) Of The Abc Transporter From Bifidobacterium
Longum In Complex With Lacto-N- Biose
pdb|2Z8E|A Chain A, The Galacto-n-biose-/lacto-n-biose I-binding Protein
(gl-bp) Of The Abc Transporter From Bifidobacterium
Longum In Complex With Galacto- N-biose
pdb|2Z8E|B Chain B, The Galacto-n-biose-/lacto-n-biose I-binding Protein
(gl-bp) Of The Abc Transporter From Bifidobacterium
Longum In Complex With Galacto- N-biose
pdb|2Z8F|A Chain A, The Galacto-N-Biose-LACTO-N-Biose I-Binding Protein
(Gl-Bp) Of The Abc Transporter From Bifidobacterium
Longum In Complex With Lacto-N- Tetraose
pdb|2Z8F|B Chain B, The Galacto-N-Biose-LACTO-N-Biose I-Binding Protein
(Gl-Bp) Of The Abc Transporter From Bifidobacterium
Longum In Complex With Lacto-N- Tetraose
Length = 412
Score = 28.5 bits (62), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 265 KKIESDMETNEAPQLFQVLTEKRPDKLGPGMMASTHMY 302
KK+E+D+++ EAP L QV + P+ G++ Y
Sbjct: 63 KKLETDVKSGEAPDLAQVGYAELPEVFTKGLLQDVTQY 100
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
0.312 0.132 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,082,776
Number of Sequences: 62578
Number of extensions: 472511
Number of successful extensions: 742
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 727
Number of HSP's gapped (non-prelim): 12
length of query: 396
length of database: 14,973,337
effective HSP length: 101
effective length of query: 295
effective length of database: 8,652,959
effective search space: 2552622905
effective search space used: 2552622905
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)