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= psy4862
(81 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease
Length = 977
Score = 85.1 bits (209), Expect = 9e-18, Method: Composition-based stats.
Identities = 38/52 (73%), Positives = 44/52 (84%)
Query: 30 EVGVHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
EVGVHIADV+HF+KPGT LD E A R T+VYLVDKRIDM+P LL +LCSL+
Sbjct: 541 EVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLK 592
>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 1003
Score = 85.1 bits (209), Expect = 1e-17, Method: Composition-based stats.
Identities = 38/52 (73%), Positives = 44/52 (84%)
Query: 30 EVGVHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
EVGVHIADV+HF+KPGT LD E A R T+VYLVDKRIDM+P LL +LCSL+
Sbjct: 567 EVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLK 618
>pdb|2VNU|D Chain D, Crystal Structure Of Sc Rrp44
Length = 760
Score = 83.2 bits (204), Expect = 3e-17, Method: Composition-based stats.
Identities = 37/52 (71%), Positives = 43/52 (82%)
Query: 30 EVGVHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
EVGVHIADV+HF+KPGT LD E A R T+VYLVDKRID +P LL +LCSL+
Sbjct: 324 EVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDXLPXLLGTDLCSLK 375
>pdb|2IX1|A Chain A, Rnase Ii D209n Mutant
Length = 664
Score = 43.1 bits (100), Expect = 4e-05, Method: Composition-based stats.
Identities = 24/49 (48%), Positives = 31/49 (63%)
Query: 33 VHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
V IAD + +I G+ LD+ A +RA T YL I M+P LS +LCSLR
Sbjct: 246 VAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLR 294
>pdb|2IX0|A Chain A, Rnase Ii
Length = 663
Score = 42.7 bits (99), Expect = 4e-05, Method: Composition-based stats.
Identities = 24/49 (48%), Positives = 31/49 (63%)
Query: 33 VHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
V IAD + +I G+ LD+ A +RA T YL I M+P LS +LCSLR
Sbjct: 245 VAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLR 293
>pdb|2R7D|A Chain A, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7D|B Chain B, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7D|C Chain C, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7F|A Chain A, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Hexagonal Crystal Form.
Northeast Structural Genomics Target Drr63
Length = 469
Score = 41.2 bits (95), Expect = 1e-04, Method: Composition-based stats.
Identities = 18/38 (47%), Positives = 25/38 (65%)
Query: 33 VHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVP 70
VH+ADV+ + P +PLD EA R T+YL D+ I +P
Sbjct: 118 VHVADVAALVAPDSPLDLEARARGATLYLPDRTIGXLP 155
>pdb|2ID0|A Chain A, Escherichia Coli Rnase Ii
pdb|2ID0|B Chain B, Escherichia Coli Rnase Ii
pdb|2ID0|C Chain C, Escherichia Coli Rnase Ii
pdb|2ID0|D Chain D, Escherichia Coli Rnase Ii
Length = 644
Score = 40.8 bits (94), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/49 (46%), Positives = 30/49 (61%)
Query: 33 VHIADVSHFIKPGTPLDEEAALRATTVYLVDKRIDMVPGLLSGNLCSLR 81
V IAD + +I G+ LD+ A +RA T YL I +P LS +LCSLR
Sbjct: 226 VAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPXLPRELSDDLCSLR 274
>pdb|1HBM|C Chain C, Methyl-Coenzyme M Reductase Enzyme Product Complex
pdb|1HBM|F Chain F, Methyl-Coenzyme M Reductase Enzyme Product Complex
pdb|1HBN|C Chain C, Methyl-Coenzyme M Reductase
pdb|1HBN|F Chain F, Methyl-Coenzyme M Reductase
pdb|1HBO|C Chain C, Methyl-Coenzyme M Reductase Mcr-Red1-Silent
pdb|1HBO|F Chain F, Methyl-Coenzyme M Reductase Mcr-Red1-Silent
pdb|1HBU|C Chain C, Methyl-Coenzyme M Reductase In The Mcr-Red1-Silent State
In Complex With Coenzyme M
pdb|1HBU|F Chain F, Methyl-Coenzyme M Reductase In The Mcr-Red1-Silent State
In Complex With Coenzyme M
pdb|3M1V|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M1V|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2R|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2R|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2U|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2U|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2V|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2V|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M30|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M30|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M32|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M32|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
Length = 248
Score = 28.1 bits (61), Expect = 1.4, Method: Composition-based stats.
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 45 GTPLDEEAALRATTVYLVD 63
G PLDEE + TT+Y VD
Sbjct: 201 GEPLDEETLMEKTTIYRVD 219
>pdb|1MRO|C Chain C, Methyl-Coenzyme M Reductase
pdb|1MRO|F Chain F, Methyl-Coenzyme M Reductase
Length = 247
Score = 27.7 bits (60), Expect = 1.5, Method: Composition-based stats.
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 45 GTPLDEEAALRATTVYLVD 63
G PLDEE + TT+Y VD
Sbjct: 201 GEPLDEETLMEKTTIYRVD 219
>pdb|3POT|C Chain C, Structural Analysis Of A Ni(Iii)-Methyl Species In
Methyl-Coenzyme M Reductase From Methanothermobacter
Marburgensis
pdb|3POT|F Chain F, Structural Analysis Of A Ni(Iii)-Methyl Species In
Methyl-Coenzyme M Reductase From Methanothermobacter
Marburgensis
Length = 249
Score = 27.7 bits (60), Expect = 1.5, Method: Composition-based stats.
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 45 GTPLDEEAALRATTVYLVD 63
G PLDEE + TT+Y VD
Sbjct: 202 GEPLDEETLMEKTTIYRVD 220
>pdb|4DD5|A Chain A, Biosynthetic Thiolase (Thla1) From Clostridium Difficile
Length = 396
Score = 25.4 bits (54), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 29 GEVGVHIADVSHFIKPGTPLDEEAALR 55
G G + D +IKPGT +++ A LR
Sbjct: 211 GRKGDTVVDKDEYIKPGTTMEKLAKLR 237
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
0.321 0.139 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,583,248
Number of Sequences: 62578
Number of extensions: 42981
Number of successful extensions: 76
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 64
Number of HSP's gapped (non-prelim): 12
length of query: 81
length of database: 14,973,337
effective HSP length: 50
effective length of query: 31
effective length of database: 11,844,437
effective search space: 367177547
effective search space used: 367177547
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: 45 (21.9 bits)