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= 021124
(317 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1I36|A Chain A, Structure Of Conserved Protein Mth1747 Of Unknown Function
Reveals Structural Similarity With 3-Hydroxyacid
Dehydrogenases
pdb|1I36|B Chain B, Structure Of Conserved Protein Mth1747 Of Unknown Function
Reveals Structural Similarity With 3-Hydroxyacid
Dehydrogenases
Length = 264
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 27/150 (18%), Positives = 68/150 (45%), Gaps = 18/150 (12%)
Query: 45 LNYQTLSPK--DLAKAVLTQGGWADLLCSGRQSPQSVDVALVFVGRELQ----------S 92
++ +SP+ +A +++ +GG+ D G + D+ ++ GR+ + +
Sbjct: 85 VDINNISPETVRMASSLIEKGGFVDAAIMGSVRRKGADIRIIASGRDAEEFMKLNRYGLN 144
Query: 93 SHISGNKHADLALVDTLKVSFTKSNFSMAFPYIVSAGEETMESSLFS--EFTEACVDDFK 150
+ G + D + + L+ S+TK ++ + + +A +E + E+TE +DF+
Sbjct: 145 IEVRGREPGDASAIKMLRSSYTKGVSALLWETLTAAHRLGLEEDVLEMLEYTEG--NDFR 202
Query: 151 VANVAFSESCTVEGENFLKLADLHSVHDHL 180
+ ++ +S + + ++ V D L
Sbjct: 203 ESAISRLKSSCIHARR--RYEEMKEVQDML 230
>pdb|2AYI|A Chain A, Wild-Type Ampt From Thermus Thermophilus
pdb|2AYI|B Chain B, Wild-Type Ampt From Thermus Thermophilus
pdb|2AYI|C Chain C, Wild-Type Ampt From Thermus Thermophilus
pdb|2AYI|D Chain D, Wild-Type Ampt From Thermus Thermophilus
pdb|2AYI|E Chain E, Wild-Type Ampt From Thermus Thermophilus
Length = 408
Score = 31.2 bits (69), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 45/98 (45%), Gaps = 8/98 (8%)
Query: 150 KVANVAFSESCTVE-GENFLKLADLHSVHDHLRLRAEKSLKGQADLIVVCYGDTQSMKQP 208
K+A +A +E G+ + A + +V D +RL AEK+ + A L V YGD + ++
Sbjct: 10 KLAELAIRVGLNLEKGQEVIATAPIEAV-DFVRLLAEKAYREGASLFTVIYGDQELARKR 68
Query: 209 KQPRPESEV------ISELIDSVEKSGAKYTVLYVSDP 240
PE + + E + + GA + SDP
Sbjct: 69 LALAPEEGLDKAPAWLYEGMARAFREGAARLAVSGSDP 106
>pdb|3NQ8|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution R4 85A
Length = 269
Score = 30.8 bits (68), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 44/166 (26%), Positives = 73/166 (43%), Gaps = 32/166 (19%)
Query: 97 GNKHADLALVDT-LKVSFTKSNFSMAFPY-IVSAGEETMESSLFSEFTEACVDDFKVANV 154
GN D+AL +T +++ ++ FPY + AG E + L EAC ANV
Sbjct: 81 GNDDIDIALAETRAAIAYGADGVAVVFPYRALMAGNEQVGFDLVKACKEAC----AAANV 136
Query: 155 AFS---ESCTVEGENFLKLADLHSVHDHLRLRAEKSLKGQADLIVVCYGDTQSMKQPKQP 211
S E+ ++ E ++ A +E S+K AD IV G P+
Sbjct: 137 LLSVIIETGELKDEALIRKA------------SEISIKAGADYIVTSTGKVAVGATPESA 184
Query: 212 RPESEVISELIDSVEKSGAKYTVLYVSDPVRSVQYPSHQELERFLA 257
R EVI ++ G + TV ++ PV V+ + ++ +++LA
Sbjct: 185 RIMMEVIRDM-------GVENTVGFI--PVGGVR--TAEDAQKYLA 219
>pdb|3NQ2|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution R2 35G
pdb|3NQ2|B Chain B, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution R2 35G
Length = 264
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 44/166 (26%), Positives = 73/166 (43%), Gaps = 32/166 (19%)
Query: 97 GNKHADLALVDT-LKVSFTKSNFSMAFPY-IVSAGEETMESSLFSEFTEACVDDFKVANV 154
GN D+AL +T +++ ++ FPY + AG E + L EAC ANV
Sbjct: 80 GNDDIDIALAETRAAIAYGADGVAVVFPYRALMAGNEQVGFDLVKACKEAC----AAANV 135
Query: 155 AFS---ESCTVEGENFLKLADLHSVHDHLRLRAEKSLKGQADLIVVCYGDTQSMKQPKQP 211
S E+ ++ E ++ A +E S+K AD IV G P+
Sbjct: 136 LLSVIIETGELKDEALIRKA------------SEISIKAGADHIVTSTGKVAEGATPESA 183
Query: 212 RPESEVISELIDSVEKSGAKYTVLYVSDPVRSVQYPSHQELERFLA 257
R EVI ++ G + TV ++ PV V+ + ++ +++LA
Sbjct: 184 RIMMEVIRDM-------GVEKTVGFI--PVGGVR--TAEDAQKYLA 218
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 223 DSVEKSGAKYTVLYVSDPVRS-VQYPSHQELERFLAESVAGNKSANNTGC 271
D ++ K V V DPV S V P +E +FL + V G + N+ GC
Sbjct: 33 DLIKADKEKLPVHVVVDPVLSKVLRPHQREGVKFLWDCVTGRRIENSYGC 82
>pdb|3NPW|A Chain A, In Silico Designed Of An Improved Kemp Eliminase Ke70
Mutant By Computational Design And Directed Evolution
pdb|3NPW|B Chain B, In Silico Designed Of An Improved Kemp Eliminase Ke70
Mutant By Computational Design And Directed Evolution
Length = 264
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 44/166 (26%), Positives = 72/166 (43%), Gaps = 32/166 (19%)
Query: 97 GNKHADLALVDT-LKVSFTKSNFSMAFPY-IVSAGEETMESSLFSEFTEACVDDFKVANV 154
GN D+AL +T +++ ++ FPY + AG E + L EAC ANV
Sbjct: 80 GNDDIDIALAETRAAIAYGADGVAVVFPYRALMAGNEQVGFDLVKACKEAC----AAANV 135
Query: 155 AFS---ESCTVEGENFLKLADLHSVHDHLRLRAEKSLKGQADLIVVCYGDTQSMKQPKQP 211
S E+ ++ E ++ A +E S+K AD IV G P+
Sbjct: 136 LLSVIIETGELKDEALIRKA------------SEISIKAGADHIVTSTGKVAVGATPESA 183
Query: 212 RPESEVISELIDSVEKSGAKYTVLYVSDPVRSVQYPSHQELERFLA 257
R EVI ++ G + TV ++ P V+ + +E +++LA
Sbjct: 184 RIMMEVIRDM-------GVEKTVGFI--PAGGVR--TAEEAQKYLA 218
>pdb|3NPX|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
pdb|3NPX|B Chain B, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
Length = 264
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 44/166 (26%), Positives = 72/166 (43%), Gaps = 32/166 (19%)
Query: 97 GNKHADLALVDT-LKVSFTKSNFSMAFPY-IVSAGEETMESSLFSEFTEACVDDFKVANV 154
GN D+AL +T +++ ++ FPY + AG E + L EAC ANV
Sbjct: 80 GNDDIDIALAETRAAIAYGADGVAVVFPYRALMAGNEQVGFDLVKACKEAC----AAANV 135
Query: 155 AFS---ESCTVEGENFLKLADLHSVHDHLRLRAEKSLKGQADLIVVCYGDTQSMKQPKQP 211
S E+ ++ E ++ A +E S+K AD IV G P+
Sbjct: 136 LLSVIIETGELKDEALIRKA------------SEISIKAGADHIVTSTGKVAVGATPESA 183
Query: 212 RPESEVISELIDSVEKSGAKYTVLYVSDPVRSVQYPSHQELERFLA 257
R EVI ++ G + TV ++ P V+ + +E +++LA
Sbjct: 184 RIMMEVIRDM-------GVEKTVGFI--PAGGVR--TAEEAQKYLA 218
>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED
Pnpase
Length = 559
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 122 FPYIVSAGEETMESSLFSEFTEAC------VD---DFKVANVAFSESCTVEGENFLKLAD 172
FPY V E ES+ S C +D K A + EG+N++ L+D
Sbjct: 427 FPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSD 486
Query: 173 LHSVHDHL 180
+ DHL
Sbjct: 487 ILGDEDHL 494
>pdb|3H1C|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|B Chain B, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|C Chain C, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|G Chain G, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|I Chain I, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|K Chain K, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|M Chain M, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|O Chain O, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|R Chain R, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|T Chain T, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|V Chain V, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|X Chain X, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
Length = 549
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 122 FPYIVSAGEETMESSLFSEFTEAC------VD---DFKVANVAFSESCTVEGENFLKLAD 172
FPY V E ES+ S C +D K A + EG+N++ L+D
Sbjct: 421 FPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSD 480
Query: 173 LHSVHDHL 180
+ DHL
Sbjct: 481 ILGDEDHL 488
>pdb|3GCM|A Chain A, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|B Chain B, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|C Chain C, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GLL|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core
pdb|3GME|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase In
Complex With Rnase E And Manganese
Length = 549
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 122 FPYIVSAGEETMESSLFSEFTEAC------VD---DFKVANVAFSESCTVEGENFLKLAD 172
FPY V E ES+ S C +D K A + EG+N++ L+D
Sbjct: 421 FPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSD 480
Query: 173 LHSVHDHL 180
+ DHL
Sbjct: 481 ILGDEDHL 488
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 122 FPYIVSAGEETMESSLFSEFTEAC------VD---DFKVANVAFSESCTVEGENFLKLAD 172
FPY V E ES+ S C +D K A + EG+N++ L+D
Sbjct: 427 FPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSD 486
Query: 173 LHSVHDHL 180
+ DHL
Sbjct: 487 ILGDEDHL 494
>pdb|3Q2D|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
pdb|3Q2D|B Chain B, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
Length = 272
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 41/163 (25%), Positives = 71/163 (43%), Gaps = 26/163 (15%)
Query: 97 GNKHADLALVDT-LKVSFTKSNFSMAFPY-IVSAGEETMESSLFSEFTEACVDDFKVANV 154
GN D+AL +T +++ + ++ FPY + AG E + L EAC V
Sbjct: 81 GNDDIDIALAETRAAIAYGADSVAVVFPYRALMAGNEQVGFDLVKACKEACAA-ANVLLA 139
Query: 155 AFSESCTVEGENFLKLADLHSVHDHLRLRAEKSLKGQADLIVVCYGDTQSMKQPKQPRPE 214
E+ ++ E ++ A +E S+K AD IV G P+ R
Sbjct: 140 VIIETGELKDEALIRKA------------SEISIKAGADNIVTSTGKVAVGATPESARIM 187
Query: 215 SEVISELIDSVEKSGAKYTVLYVSDPVRSVQYPSHQELERFLA 257
EVI ++ G + TV ++ PV V+ + ++ +++LA
Sbjct: 188 MEVIRDM-------GVEKTVGFI--PVGGVR--TAEDAQKYLA 219
>pdb|3NR0|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution R6 610A
pdb|3NR0|B Chain B, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution R6 610A
Length = 271
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 41/163 (25%), Positives = 71/163 (43%), Gaps = 26/163 (15%)
Query: 97 GNKHADLALVDT-LKVSFTKSNFSMAFPY-IVSAGEETMESSLFSEFTEACVDDFKVANV 154
GN D+AL +T +++ + ++ FPY + AG E + L EAC V
Sbjct: 80 GNDDIDIALAETRAAIAYGADSVAVVFPYRALMAGNEQVGFDLVKACKEACAA-ANVLLA 138
Query: 155 AFSESCTVEGENFLKLADLHSVHDHLRLRAEKSLKGQADLIVVCYGDTQSMKQPKQPRPE 214
E+ ++ E ++ A +E S+K AD IV G P+ R
Sbjct: 139 VIIETGELKDEALIRKA------------SEISIKAGADNIVTSTGKVAVGATPESARIM 186
Query: 215 SEVISELIDSVEKSGAKYTVLYVSDPVRSVQYPSHQELERFLA 257
EVI ++ G + TV ++ PV V+ + ++ +++LA
Sbjct: 187 MEVIRDM-------GVEKTVGFI--PVGGVR--TAEDAQKYLA 218
>pdb|3NPU|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
pdb|3NPU|B Chain B, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
pdb|3NPV|B Chain B, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
pdb|3NPV|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
Length = 263
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 39/137 (28%), Positives = 59/137 (43%), Gaps = 23/137 (16%)
Query: 97 GNKHADLALVDT-LKVSFTKSNFSMAFPY-IVSAGEETMESSLFSEFTEACVDDFKVANV 154
GN D+AL +T +++ ++ FPY + AG E + L EAC ANV
Sbjct: 79 GNDDIDIALAETRAAIAYGADGVAVVFPYRALMAGNEQVGFDLVKACKEAC----AAANV 134
Query: 155 AFS---ESCTVEGENFLKLADLHSVHDHLRLRAEKSLKGQADLIVVCYGDTQSMKQPKQP 211
S E+ ++ E ++ A +E S+K AD IV G P+
Sbjct: 135 LLSVIIETGELKDEALIRKA------------SEISIKAGADHIVTSTGKVAVGATPESA 182
Query: 212 RPESEVISELIDSVEKS 228
R EVI ++ VEK+
Sbjct: 183 RIMMEVIRDM--GVEKT 197
>pdb|2P0Y|A Chain A, Crystal Structure Of Q88yi3_lacpl From Lactobacillus
Plantarum. Northeast Structural Genomics Consortium
Target Lpr6
Length = 341
Score = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 130 EETMESSLFSEFTEACVDDFKVANVAFSESCTVEGENFLKLADLHSVHDHLRLRAE-KSL 188
E+ + F+E ++ DF+ ++C V NFLKL D + HD ++ AE +L
Sbjct: 269 EDYXDFHKFNEVSKQVSHDFRGLR---EQNCRVISSNFLKLRDNGAFHDGDQVVAELXNL 325
Query: 189 KGQADL 194
G +D+
Sbjct: 326 VGHSDV 331
>pdb|2XE4|A Chain A, Structure Of Oligopeptidase B From Leishmania Major
Length = 751
Score = 27.7 bits (60), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 10/76 (13%)
Query: 31 LWSTHHQKISSNNALNYQTLSPKDLAKAVLTQGGWADLLCSGRQSPQSVDVALVFVGREL 90
+W K+ S + Y+ +P L A + + + LC G QSP++ +V L+ + +
Sbjct: 249 VWRHVMGKLQSEDVCLYEEHNP--LFSAFMYKAADTNTLCIGSQSPETAEVHLLDLRK-- 304
Query: 91 QSSHISGNKHADLALV 106
GN H L +V
Sbjct: 305 ------GNAHNTLEIV 314
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 0.129 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,245,118
Number of Sequences: 62578
Number of extensions: 296929
Number of successful extensions: 691
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 688
Number of HSP's gapped (non-prelim): 23
length of query: 317
length of database: 14,973,337
effective HSP length: 99
effective length of query: 218
effective length of database: 8,778,115
effective search space: 1913629070
effective search space used: 1913629070
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)