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= 044601
(213 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
Length = 775
Score = 33.1 bits (74), Expect = 0.11, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 34/52 (65%), Gaps = 5/52 (9%)
Query: 116 IQLNKELVKGFLRNAKLLLKEENGEIHVTHKEGDPYNKWELVKKAEKIGLTL 167
+ KE++K FLR +++E++ +I VT+ GD ++ L K+AEK+G+ L
Sbjct: 184 VSTEKEMIKRFLR----IIREKDPDIIVTYN-GDSFDFPYLAKRAEKLGIKL 230
>pdb|4AHC|A Chain A, Crystal Structure Of An Evolved Replicating Dna Polymerase
pdb|4AHC|B Chain B, Crystal Structure Of An Evolved Replicating Dna Polymerase
pdb|4AIL|C Chain C, Crystal Structure Of An Evolved Replicating Dna Polymerase
Length = 775
Score = 32.0 bits (71), Expect = 0.25, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 33/48 (68%), Gaps = 5/48 (10%)
Query: 120 KELVKGFLRNAKLLLKEENGEIHVTHKEGDPYNKWELVKKAEKIGLTL 167
+E++K FLR +++E++ +I VT+ GD ++ L K+AEK+G+ L
Sbjct: 188 REMIKRFLR----IIREKDPDIIVTYN-GDSFDFPYLAKRAEKLGIKL 230
>pdb|2UXY|A Chain A, Aliphatic Amidase
Length = 341
Score = 31.2 bits (69), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 138 NGEIHVTHKEGDPYNKWELVKKAEKIGLTLQEVVPFCKQD--YPGYDNKRAQGYLSDAP 194
GE H H PYN L+ +I ++++P+C + YPG Q Y+S+ P
Sbjct: 103 TGERHEEHPRKAPYNTLVLIDNNGEIVQKYRKIIPWCPIEGWYPG-----GQTYVSEGP 156
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna
PolymerasePCNA Monomer Mutant Complex
Length = 775
Score = 30.4 bits (67), Expect = 0.69, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 32/48 (66%), Gaps = 5/48 (10%)
Query: 120 KELVKGFLRNAKLLLKEENGEIHVTHKEGDPYNKWELVKKAEKIGLTL 167
+E +K FLR +++E++ +I VT+ GD ++ L K+AEK+G+ L
Sbjct: 188 REXIKRFLR----IIREKDPDIIVTYN-GDSFDFPYLAKRAEKLGIKL 230
>pdb|3S0Q|A Chain A, Peptidase Module Of The Peptidoglycan Hydrolase Ripa
(Rv1477) From Mycobacterium Tuberculosis, Catalytic Site
Mutant (Cys383ala) At 1.45 Resolution
Length = 215
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 3/57 (5%)
Query: 91 THKFDR---VIYNFPHVGFIFRENSYCQIQLNKELVKGFLRNAKLLLKEENGEIHVT 144
T FD V+Y+F VG S Q L +++ +R ++ NG HVT
Sbjct: 121 TVGFDASGLVLYSFAGVGIKLPHYSGSQYNLGRKIPSSQMRRGDVIFYGPNGSQHVT 177
>pdb|3PBC|A Chain A, Peptidase Module Of The Peptidoglycan Hydrolase Ripa
(Rv1477) From Mycobacterium Tuberculosis At 1.38
Resolution
Length = 214
Score = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 22/48 (45%)
Query: 97 VIYNFPHVGFIFRENSYCQIQLNKELVKGFLRNAKLLLKEENGEIHVT 144
V+Y+F VG S Q L +++ +R ++ NG HVT
Sbjct: 129 VLYSFAGVGIKLPHYSGSQYNLGRKIPSSQMRRGDVIFYGPNGSQHVT 176
>pdb|3NE0|A Chain A, Structure And Functional Regulation Of Ripa, A
Mycobacterial Enzyme Essential For Daughter Cell
Separation
Length = 214
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 22/48 (45%)
Query: 97 VIYNFPHVGFIFRENSYCQIQLNKELVKGFLRNAKLLLKEENGEIHVT 144
V+Y+F VG S Q L +++ +R ++ NG HVT
Sbjct: 129 VLYSFAGVGIKLPHYSGSQYNLGRKIPSSQMRRGDVIFYGPNGSQHVT 176
>pdb|2PLQ|A Chain A, Crystal Structure Of The Amidase From Geobacillus Pallidus
Rapc8
Length = 348
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 138 NGEIHVTHKEGDPYNKWELVKKAEKIGLTLQEVVPFCKQD--YPG 180
GE H H PYN L+ +I ++++P+C + YPG
Sbjct: 103 TGEKHEDHPNKAPYNTLVLINNKGEIVQKYRKIIPWCPIEGWYPG 147
>pdb|1W28|A Chain A, Conformational Flexibility Of The C-Terminus With
Implications For Substrate Binding And Catalysis In A
New Crystal Form Of Deacetoxycephalosporin C Synthase
pdb|1W2A|X Chain X, Deacetoxycephalosporin C Synthase (With His-Tag) Complexed
With Fe(Ii) And Ethylene Glycol
pdb|1W2N|A Chain A, Deacetoxycephalosporin C Synthase (With A N-Terminal His-
Tag) In Complex With Fe(Ii) And Ampicillin
pdb|1W2O|A Chain A, Deacetoxycephalosporin C Synthase (With A N-Terminal His-
Tag) In Complex With Fe(Ii) And Deacetoxycephalosporin C
Length = 331
Score = 27.3 bits (59), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 24 GDFSFSLCLAREFGFAHNMVATCLDTQETIANKYSN 59
DF+FS+ LARE GF ++ Q+ I Y N
Sbjct: 289 ADFTFSVPLARECGFDVSLDGETATFQDWIGGNYVN 324
>pdb|1HJF|A Chain A, Alteration Of The Co-Substrate Selectivity Of
Deacetoxycephalosporin C Synthase: The Role Of
Arginine-258
pdb|1HJG|A Chain A, Alteration Of The Co-Substrate Selectivity Of
Deacetoxycephalosporin C Synthase: The Role Of
Arginine-258
Length = 311
Score = 27.3 bits (59), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 24 GDFSFSLCLAREFGFAHNMVATCLDTQETIANKYSN 59
DF+FS+ LARE GF ++ Q+ I Y N
Sbjct: 269 ADFTFSVPLARECGFDVSLDGETATFQDWIGGNYVN 304
>pdb|1E5I|A Chain A, Delta-R306 Deacetoxycephalosporin C Synthase Complexed
With Iron And 2-Oxoglutarate
Length = 306
Score = 27.3 bits (59), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 24 GDFSFSLCLAREFGFAHNMVATCLDTQETIANKYSN 59
DF+FS+ LARE GF ++ Q+ I Y N
Sbjct: 269 ADFTFSVPLARECGFDVSLDGETATFQDWIGGNYVN 304
>pdb|1UNB|A Chain A, Deacetoxycephalosporin C Synthase Complexed With
2-Oxoglutarate And Ampicillin
pdb|1UO9|A Chain A, Deacetoxycephalosporin C Synthase Complexed With Succinate
pdb|1UOB|A Chain A, Deacetoxycephalosporin C Synthase Complexed With
2-Oxoglutarate And Penicillin G
pdb|1UOF|A Chain A, Deacetoxycephalosporin C Synthase Complexed With
Penicillin G
pdb|1UOG|A Chain A, Deacetoxycephalosporin C Synthase Complexed With
Deacetoxycephalosporin C
pdb|1DCS|A Chain A, Deacetoxycephalosporin C Synthase From S. Clavuligerus
pdb|1RXF|A Chain A, Deacetoxycephalosporin C Synthase Complexed With Fe(Ii)
pdb|1RXG|A Chain A, Deacetoxycephalosporin C Synthase Complexed With Fe(Ii)
And 2- Oxoglutarate
pdb|2JB8|A Chain A, Deacetoxycephalosporin C Synthase Complexed With
5-hydroxy- 4-keto Valeric Acid
Length = 311
Score = 27.3 bits (59), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 24 GDFSFSLCLAREFGFAHNMVATCLDTQETIANKYSN 59
DF+FS+ LARE GF ++ Q+ I Y N
Sbjct: 269 ADFTFSVPLARECGFDVSLDGETATFQDWIGGNYVN 304
>pdb|1E5H|A Chain A, Delta-R307a Deacetoxycephalosporin C Synthase Complexed
With Succinate And Carbon Dioxide
Length = 308
Score = 27.3 bits (59), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 24 GDFSFSLCLAREFGFAHNMVATCLDTQETIANKYSN 59
DF+FS+ LARE GF ++ Q+ I Y N
Sbjct: 269 ADFTFSVPLARECGFDVSLDGETATFQDWIGGNYVN 304
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 0.137 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,879,109
Number of Sequences: 62578
Number of extensions: 278890
Number of successful extensions: 698
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 689
Number of HSP's gapped (non-prelim): 18
length of query: 213
length of database: 14,973,337
effective HSP length: 95
effective length of query: 118
effective length of database: 9,028,427
effective search space: 1065354386
effective search space used: 1065354386
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)