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= 039213
(156 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3ZQ4|A Chain A, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
pdb|3ZQ4|C Chain C, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
pdb|3ZQ4|D Chain D, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
pdb|3ZQ4|E Chain E, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
Length = 555
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/29 (55%), Positives = 18/29 (62%)
Query: 43 VLPIGGLGEIGMNCMLVGNYDRYILIDAG 71
V +GGLGEIG N V D +LIDAG
Sbjct: 11 VFALGGLGEIGKNTYAVQFQDEIVLIDAG 39
>pdb|2XR1|A Chain A, Dimeric Archaeal Cleavage And Polyadenylation Specificity
Factor With N-Terminal Kh Domains (Kh-Cpsf) From
Methanosarcina Mazei
pdb|2XR1|B Chain B, Dimeric Archaeal Cleavage And Polyadenylation Specificity
Factor With N-Terminal Kh Domains (Kh-Cpsf) From
Methanosarcina Mazei
Length = 640
Score = 30.4 bits (67), Expect = 0.41, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 41 LRVLPIGGLGEIGMNCMLVGNYDRYILIDAG-DPGFGFQYTNICIFIYNGE-FNIQQIDE 98
+RV +GG E+G +C L+ + ILID G + G N+ ++Y E F + QID
Sbjct: 184 VRVTALGGCKEVGRSCFLLSTPESRILIDCGVNVG---SDENMTPYLYVPEVFPLNQIDA 240
Query: 99 SPLDGKVFDREALEEL 114
+ D + L L
Sbjct: 241 VIVTHAHLDHQGLVPL 256
>pdb|2ZAK|A Chain A, Orthorhombic Crystal Structure Of Precursor E. Coli
Isoaspartyl PeptidaseL-Asparaginase (Ecaiii) With
Active-Site T179a Mutation
pdb|2ZAK|B Chain B, Orthorhombic Crystal Structure Of Precursor E. Coli
Isoaspartyl PeptidaseL-Asparaginase (Ecaiii) With
Active-Site T179a Mutation
pdb|3C17|A Chain A, Hexagonal Crystal Structure Of Precursor E. Coli
Isoaspartyl Peptidase/l-asparaginase (ecaiii) With
Active-site T179a Mutation
pdb|3C17|B Chain B, Hexagonal Crystal Structure Of Precursor E. Coli
Isoaspartyl Peptidase/l-asparaginase (ecaiii) With
Active-site T179a Mutation
Length = 320
Score = 29.6 bits (65), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 9/51 (17%)
Query: 93 IQQIDESPL----DGKVFDREALEELSK---EGVTLVIKNGEMLGVSHLRN 136
++ ++E PL G VF R+ EL +G TL K G + GVSHLRN
Sbjct: 56 VRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTL--KAGAVAGVSHLRN 104
>pdb|3T3N|A Chain A, Molecular Basis For The Recognition And Cleavage Of Rna
(Uuccgu) By The Bifunctional 5'-3' ExoENDORIBONUCLEASE
RNASE J
pdb|3T3O|A Chain A, Molecular Basis For The Recognition And Cleavage Of Rna
(Cugg) By The Bifunctional 5'-3' ExoENDORIBONUCLEASE
RNASE J
Length = 562
Score = 29.3 bits (64), Expect = 0.98, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 41 LRVLPIGGLGEIGMNCMLVGNYDRYILIDAG 71
+ ++P+GG+GEIG N + D ++D G
Sbjct: 18 VEIIPLGGMGEIGKNITVFRFRDEIFVLDGG 48
Score = 28.9 bits (63), Expect = 1.3, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 3/47 (6%)
Query: 80 TNICIFIYNGEFNIQQIDESPLDGKVFDREALEELSKEGVTLVIKNG 126
T I ++ G+F ++D +P+DGKV + + EGV L+I +
Sbjct: 170 TPIGTIVHTGDF---KLDPTPIDGKVSHLAKVAQAGAEGVLLLIADA 213
>pdb|2ZAL|C Chain C, Crystal Structure Of E. Coli Isoaspartyl
AminopeptidaseL-Asparaginase In Complex With L-Aspartate
pdb|2ZAL|A Chain A, Crystal Structure Of E. Coli Isoaspartyl
AminopeptidaseL-Asparaginase In Complex With L-Aspartate
Length = 160
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 9/51 (17%)
Query: 93 IQQIDESPL----DGKVFDREALEELSK---EGVTLVIKNGEMLGVSHLRN 136
++ ++E PL G VF R+ EL +G TL K G + GVSHLRN
Sbjct: 56 VRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTL--KAGAVAGVSHLRN 104
>pdb|3BK1|A Chain A, Crystal Structure Analysis Of Rnase J
pdb|3BK2|A Chain A, Crystal Structure Analysis Of The Rnase JUMP COMPLEX
Length = 562
Score = 28.9 bits (63), Expect = 1.3, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 3/47 (6%)
Query: 80 TNICIFIYNGEFNIQQIDESPLDGKVFDREALEELSKEGVTLVIKNG 126
T I ++ G+F ++D +P+DGKV + + EGV L+I +
Sbjct: 169 TPIGTIVHTGDF---KLDPTPIDGKVSHLAKVAQAGAEGVLLLIADA 212
Score = 28.5 bits (62), Expect = 1.5, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 36 SNGPP---LRVLPIGGLGEIGMNCMLVGNYDRYILIDAG 71
S G P + ++P+GG GEIG N + D ++D G
Sbjct: 9 SQGGPQDHVEIIPLGGXGEIGKNITVFRFRDEIFVLDGG 47
>pdb|1JN9|A Chain A, Structure Of Putative Asparaginase Encoded By Escherichia
Coli Ybik Gene
pdb|1JN9|C Chain C, Structure Of Putative Asparaginase Encoded By Escherichia
Coli Ybik Gene
pdb|1K2X|A Chain A, Crystal Structure Of Putative Asparaginase Encoded By
Escherichia Coli Ybik Gene
pdb|1K2X|C Chain C, Crystal Structure Of Putative Asparaginase Encoded By
Escherichia Coli Ybik Gene
Length = 177
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 9/51 (17%)
Query: 93 IQQIDESPL----DGKVFDREALEELSK---EGVTLVIKNGEMLGVSHLRN 136
++ ++E PL G VF R+ EL +G TL K G + GVSHLRN
Sbjct: 56 VRLLEEXPLFNAGIGAVFTRDETHELDACVMDGNTL--KAGAVAGVSHLRN 104
>pdb|1T3M|A Chain A, Structure Of The Isoaspartyl Peptidase With L-Asparaginase
Activity From E. Coli
pdb|1T3M|C Chain C, Structure Of The Isoaspartyl Peptidase With L-Asparaginase
Activity From E. Coli
Length = 177
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 9/51 (17%)
Query: 93 IQQIDESPL----DGKVFDREALEELSK---EGVTLVIKNGEMLGVSHLRN 136
++ ++E PL G VF R+ EL +G TL K G + GVSHLRN
Sbjct: 56 VRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTL--KAGAVAGVSHLRN 104
>pdb|3AF5|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
From Pyrococcus Horikoshii
pdb|3AF6|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
From Pyrococcus Horikoshii Complexed With Rna-Analog
Length = 651
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 7/54 (12%)
Query: 41 LRVLPIGGLGEIGMNCMLVGNYDRYILIDAG-------DPGFGFQYTNICIFIY 87
+R+ +GG E+G + +LV + ++L+D G DP F + + F Y
Sbjct: 189 IRITGLGGFREVGRSALLVQTDESFVLVDFGVNVAMLNDPYKAFPHFDAPEFQY 242
>pdb|1HI9|A Chain A, Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis,
A Self-Compartmentalizing Protease.
pdb|1HI9|B Chain B, Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis,
A Self-Compartmentalizing Protease.
pdb|1HI9|C Chain C, Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis,
A Self-Compartmentalizing Protease.
pdb|1HI9|D Chain D, Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis,
A Self-Compartmentalizing Protease.
pdb|1HI9|E Chain E, Zn-Dependent D-Aminopeptidase Dppa From Bacillus Subtilis,
A Self-Compartmentalizing Protease
Length = 274
Score = 27.3 bits (59), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 49 LGEIGMNCMLVGNYDRYILIDAGD 72
+GE+G+N + G YD +L+ AGD
Sbjct: 131 VGELGLNAYVAGYYDVPVLMVAGD 154
>pdb|4HNL|A Chain A, Crystal Structure Of Enolase Egbg_01401 (Target
Efi-502226) From Enterococcus Gallinarum Eg2
Length = 421
Score = 26.9 bits (58), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 1/75 (1%)
Query: 76 GFQYTNICIFIYNGEFNIQQIDESPLDGKVFDR-EALEELSKEGVTLVIKNGEMLGVSHL 134
G++Y + Y G + Q E P+ G FD+ + +E K + K G + H
Sbjct: 168 GYRYIRCQLGFYGGNPSQLQTPEEPISGSYFDQTDYMETTLKMFAAIKEKYGNQFQMLHD 227
Query: 135 RNRRVLSNGFISLGK 149
+ R+ N I K
Sbjct: 228 VHERLHPNQAIQFAK 242
>pdb|2YCB|A Chain A, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
pdb|2YCB|B Chain B, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
Length = 636
Score = 26.2 bits (56), Expect = 7.2, Method: Composition-based stats.
Identities = 14/56 (25%), Positives = 27/56 (48%)
Query: 42 RVLPIGGLGEIGMNCMLVGNYDRYILIDAGDPGFGFQYTNICIFIYNGEFNIQQID 97
R+ +GG E+G +C+ + + +L+D G G N ++ EF + +D
Sbjct: 181 RLTAMGGFREVGRSCLYLQTPNSRVLLDCGVNVAGGDDKNSYPYLNVPEFTLDSLD 236
>pdb|3SKX|A Chain A, Crystal Structure Of The Atp Binding Domain Of
Archaeoglobus Fulgidus Copb
Length = 280
Score = 26.2 bits (56), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 23/31 (74%), Gaps = 2/31 (6%)
Query: 109 EALEELSKEGVTLV--IKNGEMLGVSHLRNR 137
E++E+L ++G T+V +KNGE+ GV L +R
Sbjct: 114 ESVEKLKQQGKTVVFILKNGEVSGVIALADR 144
>pdb|3SKY|A Chain A, 2.1a Crystal Structure Of The Phosphate Bound Atp Binding
Domain Of Archaeoglobus Fulgidus Copb
Length = 274
Score = 26.2 bits (56), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 23/31 (74%), Gaps = 2/31 (6%)
Query: 109 EALEELSKEGVTLV--IKNGEMLGVSHLRNR 137
E++E+L ++G T+V +KNGE+ GV L +R
Sbjct: 114 ESVEKLKQQGKTVVFILKNGEVSGVIALADR 144
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
0.319 0.142 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,478,505
Number of Sequences: 62578
Number of extensions: 199861
Number of successful extensions: 452
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 443
Number of HSP's gapped (non-prelim): 16
length of query: 156
length of database: 14,973,337
effective HSP length: 91
effective length of query: 65
effective length of database: 9,278,739
effective search space: 603118035
effective search space used: 603118035
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)