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= 030940
(169 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XFG|A Chain A, Reassembly And Co-Crystallization Of A Family 9
Processive Endoglucanase From Separately Expressed Gh9
And Cbm3c Modules
Length = 466
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 60 GEEPPESLFMKELKRRGMTPTSLLEDSSRTDSGLDD 95
GE +++F E +R G +S L + R DSGLDD
Sbjct: 27 GEALQKAIFFYECQRSGKLDSSTLRLNWRGDSGLDD 62
>pdb|3SE8|L Chain L, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc03 In Complex With Hiv-1 Gp120
Length = 209
Score = 27.3 bits (59), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 73 KRRGMTPTSLLEDSSRTDSGLDDK 96
KRRG P L+ D+SR SG+ D+
Sbjct: 37 KRRGQVPRLLIYDTSRRASGVPDR 60
>pdb|3POT|B Chain B, Structural Analysis Of A Ni(Iii)-Methyl Species In
Methyl-Coenzyme M Reductase From Methanothermobacter
Marburgensis
pdb|3POT|E Chain E, Structural Analysis Of A Ni(Iii)-Methyl Species In
Methyl-Coenzyme M Reductase From Methanothermobacter
Marburgensis
Length = 443
Score = 26.2 bits (56), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 94 DDKTKLKEEDIGFSRRNTVSTEIDKSLADQRERSMALNSEGLEGRLTI-----PLIKKHS 148
DD+ L EE + + + KS+ +R++A+N EG+E L P K
Sbjct: 12 DDRGNLVEEQVPLEALSPLRNPAIKSIVQGIKRTVAVNLEGIENALKTAKVGGPACKIMG 71
Query: 149 RELIL 153
REL L
Sbjct: 72 RELDL 76
>pdb|1MRO|B Chain B, Methyl-Coenzyme M Reductase
pdb|1MRO|E Chain E, Methyl-Coenzyme M Reductase
pdb|1HBM|B Chain B, Methyl-Coenzyme M Reductase Enzyme Product Complex
pdb|1HBM|E Chain E, Methyl-Coenzyme M Reductase Enzyme Product Complex
pdb|1HBN|B Chain B, Methyl-Coenzyme M Reductase
pdb|1HBN|E Chain E, Methyl-Coenzyme M Reductase
pdb|1HBO|B Chain B, Methyl-Coenzyme M Reductase Mcr-Red1-Silent
pdb|1HBO|E Chain E, Methyl-Coenzyme M Reductase Mcr-Red1-Silent
pdb|1HBU|B Chain B, Methyl-Coenzyme M Reductase In The Mcr-Red1-Silent State
In Complex With Coenzyme M
pdb|1HBU|E Chain E, Methyl-Coenzyme M Reductase In The Mcr-Red1-Silent State
In Complex With Coenzyme M
pdb|3M1V|B Chain B, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M1V|E Chain E, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2R|B Chain B, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2R|E Chain E, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2U|B Chain B, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2U|E Chain E, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2V|B Chain B, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2V|E Chain E, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M30|B Chain B, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M30|E Chain E, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M32|B Chain B, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M32|E Chain E, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
Length = 442
Score = 26.2 bits (56), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 94 DDKTKLKEEDIGFSRRNTVSTEIDKSLADQRERSMALNSEGLEGRLTI-----PLIKKHS 148
DD+ L EE + + + KS+ +R++A+N EG+E L P K
Sbjct: 11 DDRGNLVEEQVPLEALSPLRNPAIKSIVQGIKRTVAVNLEGIENALKTAKVGGPACKIMG 70
Query: 149 RELIL 153
REL L
Sbjct: 71 RELDL 75
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
0.317 0.134 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,345,063
Number of Sequences: 62578
Number of extensions: 157988
Number of successful extensions: 365
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 361
Number of HSP's gapped (non-prelim): 10
length of query: 169
length of database: 14,973,337
effective HSP length: 92
effective length of query: 77
effective length of database: 9,216,161
effective search space: 709644397
effective search space used: 709644397
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)