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= 012077
(471 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3CMU|A Chain A, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
Length = 2050
Score = 33.9 bits (76), Expect = 0.19, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVTGSSPKACENPVGDHYLLKSIKNKI 181
+G KI A WL +NP+ A I KK R LL+ S+P + G S + I
Sbjct: 967 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLL--SNPNSTTGSTGSMASTGSTGSAI 1024
Query: 182 D 182
D
Sbjct: 1025 D 1025
Score = 32.7 bits (73), Expect = 0.40, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVTGSSPKACENPVG 169
+G KI A WL +NP+ A I KK R LL+ S+P + G
Sbjct: 618 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLL--SNPNSTTGSTG 663
Score = 32.7 bits (73), Expect = 0.40, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVTGSSPKACENPVG 169
+G KI A WL +NP+ A I KK R LL+ S+P + G
Sbjct: 1316 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLL--SNPNSTTGATG 1361
Score = 32.0 bits (71), Expect = 0.74, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVT 157
+G KI A WL +NP+ A I KK R LL++
Sbjct: 269 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLS 304
Score = 32.0 bits (71), Expect = 0.74, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVT 157
+G KI A WL +NP+ A I KK R LL++
Sbjct: 1662 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLS 1697
Score = 32.0 bits (71), Expect = 0.74, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVT 157
+G KI A WL +NP+ A I KK R LL++
Sbjct: 2010 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLS 2045
>pdb|3CMV|A Chain A, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMV|B Chain B, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMV|C Chain C, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMV|D Chain D, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMV|E Chain E, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMV|F Chain F, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMV|G Chain G, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMV|H Chain H, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
Length = 1357
Score = 33.1 bits (74), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVTGSSPKACENPVG 169
+G KI A WL +NP+ A I KK R LL+ S+P + G
Sbjct: 618 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLL--SNPNSTTGSTG 663
Score = 32.3 bits (72), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVT 157
+G KI A WL +NP+ A I KK R LL++
Sbjct: 269 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLS 304
Score = 32.3 bits (72), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVT 157
+G KI A WL +NP+ A I KK R LL++
Sbjct: 967 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLS 1002
Score = 32.3 bits (72), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVT 157
+G KI A WL +NP+ A I KK R LL++
Sbjct: 1317 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLS 1352
>pdb|3CMT|A Chain A, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMT|D Chain D, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMW|A Chain A, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMW|C Chain C, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMX|A Chain A, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMX|D Chain D, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
Length = 1706
Score = 32.7 bits (73), Expect = 0.40, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVTGSSPKACENPVG 169
+G KI A WL +NP+ A I KK R LL+ S+P + G
Sbjct: 618 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLL--SNPNSTTGSTG 663
Score = 32.7 bits (73), Expect = 0.40, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVTGSSPKACENPVG 169
+G KI A WL +NP+ A I KK R LL+ S+P + G
Sbjct: 1317 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLL--SNPNSTTGSTG 1362
Score = 32.0 bits (71), Expect = 0.74, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVT 157
+G KI A WL +NP+ A I KK R LL++
Sbjct: 269 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLS 304
Score = 32.0 bits (71), Expect = 0.74, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVT 157
+G KI A WL +NP+ A I KK R LL++
Sbjct: 967 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLS 1002
Score = 32.0 bits (71), Expect = 0.74, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVT 157
+G KI A WL +NP+ A I KK R LL++
Sbjct: 1666 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLS 1701
>pdb|1U94|A Chain A, Crystal Structure Of E. Coli Reca In A Compressed Helical
Filament Form 2
pdb|1U98|A Chain A, "crystal Structure Of E. Coli Reca In A Compressed Helical
Filament Form3"
pdb|1U99|A Chain A, "crystal Structures Of E. Coli Reca In A Compressed
Helical Filament Form 4"
pdb|1XMS|A Chain A, "e. Coli Reca In Complex With Mnamp-Pnp"
pdb|1XMV|A Chain A, "e. Coli Reca In Complex With Mgadp"
Length = 356
Score = 32.3 bits (72), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVT 157
+G KI A WL +NP+ A I KK R LL++
Sbjct: 298 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLS 333
>pdb|2REC|A Chain A, Reca Hexamer Model, Electron Microscopy
pdb|2REC|B Chain B, Reca Hexamer Model, Electron Microscopy
pdb|2REC|C Chain C, Reca Hexamer Model, Electron Microscopy
pdb|2REC|D Chain D, Reca Hexamer Model, Electron Microscopy
pdb|2REC|E Chain E, Reca Hexamer Model, Electron Microscopy
pdb|2REC|F Chain F, Reca Hexamer Model, Electron Microscopy
Length = 353
Score = 32.3 bits (72), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVT 157
+G KI A WL +NP+ A I KK R LL++
Sbjct: 295 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLS 330
>pdb|1N03|A Chain A, Model For Active Reca Filament
pdb|1N03|B Chain B, Model For Active Reca Filament
pdb|1N03|C Chain C, Model For Active Reca Filament
pdb|1N03|D Chain D, Model For Active Reca Filament
pdb|1N03|E Chain E, Model For Active Reca Filament
pdb|1N03|F Chain F, Model For Active Reca Filament
pdb|1N03|G Chain G, Model For Active Reca Filament
pdb|1REA|A Chain A, Structure Of The Reca Protein-Adp Complex
pdb|2REB|A Chain A, The Structure Of The E. Coli Reca Protein Monomer And
Polymer
Length = 352
Score = 32.0 bits (71), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVT 157
+G KI A WL +NP+ A I KK R LL++
Sbjct: 294 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLS 329
>pdb|1AA3|A Chain A, C-Terminal Domain Of The E. Coli Reca, Nmr, Minimized
Average Structure
Length = 63
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 122 RGPKISNWDAQRAQWLNENPDFANFINKKPRVLLVT 157
+G KI A WL +NP+ A I KK R LL++
Sbjct: 27 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLS 62
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
0.320 0.137 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,357,544
Number of Sequences: 62578
Number of extensions: 690520
Number of successful extensions: 1326
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1305
Number of HSP's gapped (non-prelim): 24
length of query: 471
length of database: 14,973,337
effective HSP length: 102
effective length of query: 369
effective length of database: 8,590,381
effective search space: 3169850589
effective search space used: 3169850589
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: 53 (25.0 bits)