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= psy7201
(65 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DUO|A Chain A, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN, CA2+-
Bound Form
pdb|2DUO|B Chain B, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN, CA2+-
Bound Form
pdb|2DUP|A Chain A, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
METAL-Free Form
pdb|2DUP|B Chain B, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
METAL-Free Form
pdb|2DUQ|A Chain A, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
Ca2+MAN-Bound Form
pdb|2DUQ|B Chain B, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
Ca2+MAN-Bound Form
pdb|2DUR|A Chain A, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
CA2+MAN2-Bound Form
pdb|2DUR|B Chain B, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
CA2+MAN2-Bound Form
pdb|2E6V|A Chain A, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
Ca2+MAN3GLCNAC-Bound Form
pdb|2E6V|B Chain B, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
Ca2+MAN3GLCNAC-Bound Form
pdb|2E6V|C Chain C, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
Ca2+MAN3GLCNAC-Bound Form
pdb|2E6V|D Chain D, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
Ca2+MAN3GLCNAC-Bound Form
pdb|2E6V|E Chain E, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
Ca2+MAN3GLCNAC-Bound Form
Length = 253
Score = 74.3 bits (181), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 29/49 (59%), Positives = 39/49 (79%)
Query: 2 TDFENKAAWKECFKVSGVKLPTGYYFGVSAATGDLSDNHDVLGIRTYEL 50
TD E+K WK C ++GV+LPTGYYFG SA TGDLSDNHD++ ++ ++L
Sbjct: 180 TDLEDKNEWKNCIDITGVRLPTGYYFGASAGTGDLSDNHDIISMKLFQL 228
>pdb|1R1Z|A Chain A, The Crystal Structure Of The Carbohydrate Recognition
Domain Of The Glycoprotein Sorting Receptor P58ERGIC-53
Reveals A Novel Metal Binding Site And Conformational
Changes Associated With Calcium Ion Binding
pdb|1R1Z|B Chain B, The Crystal Structure Of The Carbohydrate Recognition
Domain Of The Glycoprotein Sorting Receptor P58ERGIC-53
Reveals A Novel Metal Binding Site And Conformational
Changes Associated With Calcium Ion Binding
pdb|1R1Z|C Chain C, The Crystal Structure Of The Carbohydrate Recognition
Domain Of The Glycoprotein Sorting Receptor P58ERGIC-53
Reveals A Novel Metal Binding Site And Conformational
Changes Associated With Calcium Ion Binding
pdb|1R1Z|D Chain D, The Crystal Structure Of The Carbohydrate Recognition
Domain Of The Glycoprotein Sorting Receptor P58ERGIC-53
Reveals A Novel Metal Binding Site And Conformational
Changes Associated With Calcium Ion Binding
Length = 263
Score = 50.1 bits (118), Expect = 3e-07, Method: Composition-based stats.
Identities = 23/51 (45%), Positives = 36/51 (70%)
Query: 6 NKAAWKECFKVSGVKLPTGYYFGVSAATGDLSDNHDVLGIRTYELEFPGEK 56
+K ++ C KV + +PT +FG+SAATG L+D+HDVL T++L PG++
Sbjct: 210 DKNDYEFCAKVENMVIPTQGHFGISAATGGLADDHDVLSFLTFQLTEPGKE 260
>pdb|1GV9|A Chain A, P58ERGIC-53
Length = 260
Score = 50.1 bits (118), Expect = 3e-07, Method: Composition-based stats.
Identities = 23/51 (45%), Positives = 36/51 (70%)
Query: 6 NKAAWKECFKVSGVKLPTGYYFGVSAATGDLSDNHDVLGIRTYELEFPGEK 56
+K ++ C KV + +PT +FG+SAATG L+D+HDVL T++L PG++
Sbjct: 207 DKNDYEFCAKVENMVIPTQGHFGISAATGGLADDHDVLSFLTFQLTEPGKE 257
>pdb|3A4U|A Chain A, Crystal Structure Of Mcfd2 In Complex With Carbohydrate
Recognition Domain Of Ergic-53
Length = 255
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 35/51 (68%)
Query: 6 NKAAWKECFKVSGVKLPTGYYFGVSAATGDLSDNHDVLGIRTYELEFPGEK 56
+K ++ C KV + +P +FG+SAATG L+D+HDVL T++L PG++
Sbjct: 193 DKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQLTEPGKE 243
>pdb|3LCP|A Chain A, Crystal Structure Of The Carbohydrate Recognition Domain
Of Complex With Mcfd2
pdb|3LCP|B Chain B, Crystal Structure Of The Carbohydrate Recognition Domain
Of Complex With Mcfd2
Length = 247
Score = 48.1 bits (113), Expect = 1e-06, Method: Composition-based stats.
Identities = 22/51 (43%), Positives = 35/51 (68%)
Query: 6 NKAAWKECFKVSGVKLPTGYYFGVSAATGDLSDNHDVLGIRTYELEFPGEK 56
+K ++ C KV + +P +FG+SAATG L+D+HDVL T++L PG++
Sbjct: 193 DKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQLTEPGKE 243
>pdb|2A6Y|A Chain A, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Tetragonal Crystal Form
Length = 256
Score = 27.7 bits (60), Expect = 1.8, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 3/43 (6%)
Query: 11 KECFKVSGVKLPTGYY-FGVSAATGDLSDNHDVLGIRTYELEF 52
K CF+ V+ P+G Y GV+A G +++N + I ++++F
Sbjct: 185 KVCFQTRKVRFPSGSYRIGVTAQNGAVNNNAESFEI--FKMQF 225
>pdb|2A6Z|A Chain A, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Monoclinic Crystal Form 1
pdb|2A70|A Chain A, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Monoclinic Crystal Form 2
pdb|2A70|B Chain B, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Monoclinic Crystal Form 2
pdb|2A71|A Chain A, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Orthorhombic Crystal Form
pdb|2A71|B Chain B, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Orthorhombic Crystal Form
pdb|2A71|C Chain C, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Orthorhombic Crystal Form
pdb|2A71|D Chain D, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Orthorhombic Crystal Form
Length = 222
Score = 27.3 bits (59), Expect = 2.1, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 3/43 (6%)
Query: 11 KECFKVSGVKLPTG-YYFGVSAATGDLSDNHDVLGIRTYELEF 52
K CF+ V+ P+G Y GV+A G +++N + I ++++F
Sbjct: 178 KVCFQTRKVRFPSGSYRIGVTAQNGAVNNNAESFEI--FKMQF 218
>pdb|3IT9|A Chain A, Crystal Structure Of Penicillin-Binding Protein 6 (Pbp6)
From E. Coli In Apo State
pdb|3IT9|B Chain B, Crystal Structure Of Penicillin-Binding Protein 6 (Pbp6)
From E. Coli In Apo State
pdb|3IT9|C Chain C, Crystal Structure Of Penicillin-Binding Protein 6 (Pbp6)
From E. Coli In Apo State
pdb|3IT9|D Chain D, Crystal Structure Of Penicillin-Binding Protein 6 (Pbp6)
From E. Coli In Apo State
pdb|3ITA|A Chain A, Crystal Structure Of Penicillin-Binding Protein 6 (Pbp6)
From E. Coli In Acyl-Enzyme Complex With Ampicillin
pdb|3ITA|B Chain B, Crystal Structure Of Penicillin-Binding Protein 6 (Pbp6)
From E. Coli In Acyl-Enzyme Complex With Ampicillin
pdb|3ITA|C Chain C, Crystal Structure Of Penicillin-Binding Protein 6 (Pbp6)
From E. Coli In Acyl-Enzyme Complex With Ampicillin
pdb|3ITA|D Chain D, Crystal Structure Of Penicillin-Binding Protein 6 (Pbp6)
From E. Coli In Acyl-Enzyme Complex With Ampicillin
pdb|3ITB|A Chain A, Crystal Structure Of Penicillin-Binding Protein 6 (Pbp6)
From E. Coli In Complex With A Substrate Fragment
pdb|3ITB|B Chain B, Crystal Structure Of Penicillin-Binding Protein 6 (Pbp6)
From E. Coli In Complex With A Substrate Fragment
pdb|3ITB|C Chain C, Crystal Structure Of Penicillin-Binding Protein 6 (Pbp6)
From E. Coli In Complex With A Substrate Fragment
pdb|3ITB|D Chain D, Crystal Structure Of Penicillin-Binding Protein 6 (Pbp6)
From E. Coli In Complex With A Substrate Fragment
Length = 352
Score = 26.6 bits (57), Expect = 4.2, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 6 NKAAWKECFKVSGVKLPT----GYYFGVSAATGDLSDNHDVLGIRTYELEF-PGEKL 57
N+ W V G+K T GY SA GD+ VLG +T + F EKL
Sbjct: 195 NRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKL 251
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
0.316 0.137 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,299,022
Number of Sequences: 62578
Number of extensions: 76741
Number of successful extensions: 141
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 135
Number of HSP's gapped (non-prelim): 9
length of query: 65
length of database: 14,973,337
effective HSP length: 36
effective length of query: 29
effective length of database: 12,720,529
effective search space: 368895341
effective search space used: 368895341
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 45 (21.9 bits)