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= 047287
(210 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2VJX|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VJX|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VL4|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VL4|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VMF|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VMF|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VO5|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VO5|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VOT|A Chain A, Structural And Biochemical Evidence For A Boat-like
Transition State In Beta-mannosidases
pdb|2VOT|B Chain B, Structural And Biochemical Evidence For A Boat-like
Transition State In Beta-mannosidases
pdb|2VQT|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VQT|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VR4|A Chain A, Transition-state Mimicry In Mannoside Hydrolysis:
Characterisation Of Twenty Six Inhibitors And Insight
Into Binding From Linear Free Energy Relationships And
3-d Structure
pdb|2VR4|B Chain B, Transition-state Mimicry In Mannoside Hydrolysis:
Characterisation Of Twenty Six Inhibitors And Insight
Into Binding From Linear Free Energy Relationships And
3-d Structure
Length = 846
Score = 30.0 bits (66), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 28/49 (57%)
Query: 114 LLSEANKTLKQRTMTLRHADFAGLQLMEGYQVNTLQLNPSAEDCGYGLK 162
L+S+ T++Q T+ ++ DF G L + QV++L++ + C Y K
Sbjct: 669 LISDRLDTMEQMTLEMKVVDFDGKTLGKKIQVHSLEVPANTSKCVYRAK 717
>pdb|2WBK|A Chain A, Structure Of The Michaelis Complex Of Beta-Mannosidase,
Man2a, Provides Insight Into The Conformational
Itinerary Of Mannoside Hydrolysis
pdb|2WBK|B Chain B, Structure Of The Michaelis Complex Of Beta-Mannosidase,
Man2a, Provides Insight Into The Conformational
Itinerary Of Mannoside Hydrolysis
Length = 847
Score = 30.0 bits (66), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 28/49 (57%)
Query: 114 LLSEANKTLKQRTMTLRHADFAGLQLMEGYQVNTLQLNPSAEDCGYGLK 162
L+S+ T++Q T+ ++ DF G L + QV++L++ + C Y K
Sbjct: 669 LISDRLDTMEQMTLEMKVVDFDGKTLGKKIQVHSLEVPANTSKCVYRAK 717
>pdb|2JE8|A Chain A, Structure Of A Beta-Mannosidase From Bacteroides
Thetaiotaomicron
pdb|2JE8|B Chain B, Structure Of A Beta-Mannosidase From Bacteroides
Thetaiotaomicron
Length = 848
Score = 30.0 bits (66), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 28/49 (57%)
Query: 114 LLSEANKTLKQRTMTLRHADFAGLQLMEGYQVNTLQLNPSAEDCGYGLK 162
L+S+ T++Q T+ ++ DF G L + QV++L++ + C Y K
Sbjct: 671 LISDRLDTMEQMTLEMKVVDFDGKTLGKKIQVHSLEVPANTSKCVYRAK 719
>pdb|2VQU|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VQU|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
Length = 846
Score = 30.0 bits (66), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 28/49 (57%)
Query: 114 LLSEANKTLKQRTMTLRHADFAGLQLMEGYQVNTLQLNPSAEDCGYGLK 162
L+S+ T++Q T+ ++ DF G L + QV++L++ + C Y K
Sbjct: 669 LISDRLDTMEQMTLEMKVVDFDGKTLGKKIQVHSLEVPANTSKCVYRAK 717
>pdb|1D5A|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok. Deposition Of Second Native Structure At 2.4
Angstrom
Length = 733
Score = 30.0 bits (66), Expect = 0.97, Method: Composition-based stats.
Identities = 30/118 (25%), Positives = 49/118 (41%), Gaps = 5/118 (4%)
Query: 19 TLERYQKCNYGAPEPNVSAREALELSSQQEYLKLKARYEALQRSQRNLLGEELGPLNSKE 78
TLE + +G P V A E E + E L+ ARY LG+E P+ ++
Sbjct: 274 TLETVYEPVFGQPAEKVYAEEIAEAWASGEGLERVARYSMEDAKATYELGKEFFPMEAQ- 332
Query: 79 LESLERQLDMSLKQIRSTRTQYMLDTLTELQHKEQLLSEANKTLKQRTMTLRHADFAG 136
L R + SL + + T +++ + E+ NK +R + R +AG
Sbjct: 333 ---LSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNDVAPNKP-DERELARRTESYAG 386
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 29.6 bits (65), Expect = 1.4, Method: Composition-based stats.
Identities = 29/118 (24%), Positives = 49/118 (41%), Gaps = 5/118 (4%)
Query: 19 TLERYQKCNYGAPEPNVSAREALELSSQQEYLKLKARYEALQRSQRNLLGEELGPLNSKE 78
TLE + +G P+ V A E + E L+ ARY LG+E P+ ++
Sbjct: 274 TLEAVYEAIFGQPKEKVYAEEIAQAWETGEGLERVARYSMEDAKVTYELGKEFFPMEAQ- 332
Query: 79 LESLERQLDMSLKQIRSTRTQYMLDTLTELQHKEQLLSEANKTLKQRTMTLRHADFAG 136
L R + SL + + T +++ + E+ NK +R + R +AG
Sbjct: 333 ---LSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP-DERELARRRESYAG 386
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 29.3 bits (64), Expect = 1.4, Method: Composition-based stats.
Identities = 29/118 (24%), Positives = 49/118 (41%), Gaps = 5/118 (4%)
Query: 19 TLERYQKCNYGAPEPNVSAREALELSSQQEYLKLKARYEALQRSQRNLLGEELGPLNSKE 78
TLE + +G P+ V A E + E L+ ARY LG+E P+ ++
Sbjct: 274 TLEAVYEAIFGQPKEKVYAEEIAQAWETGEGLERVARYSMEDAKVTYELGKEFFPMEAQ- 332
Query: 79 LESLERQLDMSLKQIRSTRTQYMLDTLTELQHKEQLLSEANKTLKQRTMTLRHADFAG 136
L R + SL + + T +++ + E+ NK +R + R +AG
Sbjct: 333 ---LSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP-DERELARRRESYAG 386
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 29.3 bits (64), Expect = 1.4, Method: Composition-based stats.
Identities = 29/118 (24%), Positives = 49/118 (41%), Gaps = 5/118 (4%)
Query: 19 TLERYQKCNYGAPEPNVSAREALELSSQQEYLKLKARYEALQRSQRNLLGEELGPLNSKE 78
TLE + +G P+ V A E + E L+ ARY LG+E P+ ++
Sbjct: 274 TLEAVYEAIFGQPKEKVYAEEIAQAWETGEGLERVARYSMEDAKVTYELGKEFFPMEAQ- 332
Query: 79 LESLERQLDMSLKQIRSTRTQYMLDTLTELQHKEQLLSEANKTLKQRTMTLRHADFAG 136
L R + SL + + T +++ + E+ NK +R + R +AG
Sbjct: 333 ---LSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP-DERELARRRESYAG 386
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 29.3 bits (64), Expect = 1.5, Method: Composition-based stats.
Identities = 29/118 (24%), Positives = 49/118 (41%), Gaps = 5/118 (4%)
Query: 19 TLERYQKCNYGAPEPNVSAREALELSSQQEYLKLKARYEALQRSQRNLLGEELGPLNSKE 78
TLE + +G P+ V A E + E L+ ARY LG+E P+ ++
Sbjct: 274 TLEAVYEAIFGQPKEKVYAEEIAQAWETGEGLERVARYSMEDAKVTYELGKEFFPMEAQ- 332
Query: 79 LESLERQLDMSLKQIRSTRTQYMLDTLTELQHKEQLLSEANKTLKQRTMTLRHADFAG 136
L R + SL + + T +++ + E+ NK +R + R +AG
Sbjct: 333 ---LSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP-DERELARRRESYAG 386
>pdb|3STO|A Chain A, Serpin From The Trematode Schistosoma Haematobium
Length = 406
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 99 QYMLDTLTELQHKEQLLSEANKTLKQRTMTLRHADFAGLQLMEGYQVNTLQLNPSAEDCG 158
++ L+ TEL + ++LSE K LK+ T++LR F NTL L P+ + G
Sbjct: 263 KWSLNGATELLNGNKVLSEYVKNLKETTVSLRLPKFT--------LKNTLDLVPTLKSIG 314
>pdb|2OKT|A Chain A, Crystal Structure Of O-Succinylbenzoic Acid Synthetase
From Staphylococcus Aureus, Ligand-Free Form
pdb|2OLA|A Chain A, Crystal Structure Of O-Succinylbenzoic Acid Synthetase
From Staphylococcus Aureus, Cubic Crystal Form
Length = 342
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 7/78 (8%)
Query: 68 GEELGPLNSKELESLERQLDMSLKQIRSTRTQYMLDTLTELQHKEQLLSEANKTLKQRTM 127
G L++K+LESL+ +K + + + + L EL QL+ +AN++L ++
Sbjct: 123 GATASGLSNKQLESLKATKPTRIKLKWTPQIMHQIRVLRELDFHFQLVIDANESLDRQ-- 180
Query: 128 TLRHADFAGLQLMEGYQV 145
DF LQL+ QV
Sbjct: 181 -----DFTQLQLLAREQV 193
>pdb|3H70|A Chain A, Crystal Structure Of O-Succinylbenzoic Acid Synthetase
From Staphylococcus Aureus Complexed With Mg In The
Active Site
Length = 343
Score = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 7/78 (8%)
Query: 68 GEELGPLNSKELESLERQLDMSLKQIRSTRTQYMLDTLTELQHKEQLLSEANKTLKQRTM 127
G L++K+LESL+ +K + + + + L EL QL+ +AN++L ++
Sbjct: 124 GATASGLSNKQLESLKATKPTRIKLKWTPQIMHQIRVLRELDFHFQLVIDANESLDRQ-- 181
Query: 128 TLRHADFAGLQLMEGYQV 145
DF LQL+ QV
Sbjct: 182 -----DFTQLQLLAREQV 194
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 28.5 bits (62), Expect = 2.5, Method: Composition-based stats.
Identities = 31/119 (26%), Positives = 50/119 (42%), Gaps = 7/119 (5%)
Query: 19 TLERYQKCNYGAPEPNVSAREALELSSQQEYLKLKARYEALQRSQRNLLGEELGPLNSKE 78
TLE + +G P+ V A E + E L+ ARY LG E P+ ++
Sbjct: 274 TLEAVYEAVFGKPKEKVYAEEIAQAWESGEGLERVARYSMEDAKVTYELGREFFPMEAQ- 332
Query: 79 LESLERQLDMSLKQIRSTRTQYMLD-TLTELQHKEQLLSEANKTLKQRTMTLRHADFAG 136
L R + SL + + T +++ L +K L+ NK +R + R +AG
Sbjct: 333 ---LSRLIGQSLWDVSRSSTGNLVEWFLLRKAYKRNELA-PNKP-DERELARRRGGYAG 386
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 28.1 bits (61), Expect = 3.9, Method: Composition-based stats.
Identities = 29/118 (24%), Positives = 48/118 (40%), Gaps = 5/118 (4%)
Query: 19 TLERYQKCNYGAPEPNVSAREALELSSQQEYLKLKARYEALQRSQRNLLGEELGPLNSKE 78
TLE + +G P+ V A E E L+ ARY LG+E P+ ++
Sbjct: 274 TLETVYEPVFGQPKEKVYAEEIARAWESGEGLERVARYSMEDAKATYELGKEFFPMEAQ- 332
Query: 79 LESLERQLDMSLKQIRSTRTQYMLDTLTELQHKEQLLSEANKTLKQRTMTLRHADFAG 136
L R + SL + + T +++ + E+ NK +R + R +AG
Sbjct: 333 ---LSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNDVAPNKP-DERELARRTESYAG 386
>pdb|1F15|A Chain A, Cucumber Mosaic Virus (Strain Fny)
pdb|1F15|B Chain B, Cucumber Mosaic Virus (Strain Fny)
pdb|1F15|C Chain C, Cucumber Mosaic Virus (Strain Fny)
Length = 218
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 112 EQLLSEANKTLKQRTMTLRHADFAGLQLME-GYQVNTLQLNPSAEDCG--YG 160
Q LS NKTL T+ H F G + GY ++ L P D G YG
Sbjct: 36 SQQLSRLNKTLAAGRPTINHPTFVGSERCRPGYTFTSITLKPPKIDRGSYYG 87
>pdb|1QVR|A Chain A, Crystal Structure Analysis Of Clpb
pdb|1QVR|B Chain B, Crystal Structure Analysis Of Clpb
pdb|1QVR|C Chain C, Crystal Structure Analysis Of Clpb
Length = 854
Score = 27.3 bits (59), Expect = 5.9, Method: Composition-based stats.
Identities = 31/127 (24%), Positives = 59/127 (46%), Gaps = 17/127 (13%)
Query: 30 APEP-NVSAREALELSSQQEYLKLKARYEALQR-----SQRNLLGEELGPLNS------- 76
APE + R+ L+L ++E LK + ++ +R ++ L EE+ L +
Sbjct: 399 APEEIDALERKKLQLEIEREALKKEKDPDSQERLKAIEAEIAKLTEEIAKLRAEWERERE 458
Query: 77 --KELESLERQLDMSLKQIRSTRTQYMLDTLTELQHKEQLLSEANKTLKQRTMTLRHADF 134
++L + +LD ++I QY L+ EL++ E L + ++ + LR A F
Sbjct: 459 ILRKLREAQHRLDEVRREIELAERQYDLNRAAELRYGE--LPKLEAEVEALSEKLRGARF 516
Query: 135 AGLQLME 141
L++ E
Sbjct: 517 VRLEVTE 523
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 26.6 bits (57), Expect = 9.2, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 4/85 (4%)
Query: 19 TLERYQKCNYGAPEPNVSAREALELSSQQEYLKLKARYEALQRSQRNLLGEELGPLNSKE 78
TLE + +G P+ V A E E L+ ARY LG+E P+ ++
Sbjct: 274 TLEAVYEAVFGQPKEKVYAEEITTAWETGENLERVARYSMEDAKVTYELGKEFLPMEAQ- 332
Query: 79 LESLERQLDMSLKQIRSTRTQYMLD 103
L R + SL + + T +++
Sbjct: 333 ---LSRLIGQSLWDVSRSSTGNLVE 354
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 26.6 bits (57), Expect = 9.3, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 4/85 (4%)
Query: 19 TLERYQKCNYGAPEPNVSAREALELSSQQEYLKLKARYEALQRSQRNLLGEELGPLNSKE 78
TLE + +G P+ V A E E L+ ARY LG+E P+ ++
Sbjct: 274 TLEAVYEAVFGQPKEKVYAEEITTAWETGENLERVARYSMEDAKVTYELGKEFLPMEAQ- 332
Query: 79 LESLERQLDMSLKQIRSTRTQYMLD 103
L R + SL + + T +++
Sbjct: 333 ---LSRLIGQSLWDVSRSSTGNLVE 354
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
0.315 0.130 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,784,625
Number of Sequences: 62578
Number of extensions: 213465
Number of successful extensions: 569
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 554
Number of HSP's gapped (non-prelim): 29
length of query: 210
length of database: 14,973,337
effective HSP length: 95
effective length of query: 115
effective length of database: 9,028,427
effective search space: 1038269105
effective search space used: 1038269105
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: 49 (23.5 bits)