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= 011120
(493 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SIL|A Chain A, Sialidase From Salmonella Typhimurium
Length = 379
Score = 32.3 bits (72), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 61/145 (42%), Gaps = 19/145 (13%)
Query: 228 KSSIYEVNGEPITKHKGSLVFLFKDYNCTVEYYRSPFLVVQSRPPAKAPKEVRLTLKVDQ 287
KS +++ GE T KG+ + + T +Y+R P + S+ + R DQ
Sbjct: 2 KSVVFKAEGEHFTDQKGNTI-VGSGSGGTTKYFRIPAMCTTSKGTIVVFADARHNTASDQ 60
Query: 288 --LDWSSRKWRDADVLIFNTGHWWNFEKTIREGCYFEER--GELKKKM--SVETAFEKAI 341
+D ++ + D G WN + I + +R +L + M + A +
Sbjct: 61 SFIDTAAARSTDG-------GKTWNKKIAI-----YNDRVNSKLSRVMDPTCIVANIQGR 108
Query: 342 ETLIHWIGSQVNMDKTQVLFRTYAP 366
ET++ +G N DKT +R AP
Sbjct: 109 ETILVMVGKWNNNDKTWGAYRDKAP 133
>pdb|1DIL|A Chain A, Sialidase From Salmonella Typhimurium Complexed With Apana
And Epana Inhibitors
pdb|1DIM|A Chain A, Sialidase From Salmonella Typhimurium Complexed With Epana
Inhibitor
pdb|2SIL|A Chain A, The Structures Of Salmonella Typhimurium Lt2 Neuraminidase
And Its Complex With A Transition State Analogue At 1.6
Angstroms Resolution
pdb|2SIM|A Chain A, The Structures Of Salmonella Typhimurium Lt2 Neuraminidase
And Its Complex With A Transition State Analogue At 1.6
Angstroms Resolution
Length = 381
Score = 32.3 bits (72), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 61/145 (42%), Gaps = 19/145 (13%)
Query: 228 KSSIYEVNGEPITKHKGSLVFLFKDYNCTVEYYRSPFLVVQSRPPAKAPKEVRLTLKVDQ 287
KS +++ GE T KG+ + + T +Y+R P + S+ + R DQ
Sbjct: 4 KSVVFKAEGEHFTDQKGNTI-VGSGSGGTTKYFRIPAMCTTSKGTIVVFADARHNTASDQ 62
Query: 288 --LDWSSRKWRDADVLIFNTGHWWNFEKTIREGCYFEER--GELKKKM--SVETAFEKAI 341
+D ++ + D G WN + I + +R +L + M + A +
Sbjct: 63 SFIDTAAARSTDG-------GKTWNKKIAI-----YNDRVNSKLSRVMDPTCIVANIQGR 110
Query: 342 ETLIHWIGSQVNMDKTQVLFRTYAP 366
ET++ +G N DKT +R AP
Sbjct: 111 ETILVMVGKWNNNDKTWGAYRDKAP 135
>pdb|1XHX|A Chain A, Phi29 Dna Polymerase, Orthorhombic Crystal Form
pdb|1XHX|B Chain B, Phi29 Dna Polymerase, Orthorhombic Crystal Form
pdb|1XHX|C Chain C, Phi29 Dna Polymerase, Orthorhombic Crystal Form
pdb|1XHX|D Chain D, Phi29 Dna Polymerase, Orthorhombic Crystal Form
pdb|1XHZ|A Chain A, Phi29 Dna Polymerase, Orthorhombic Crystal Form, Ssdna
Complex
pdb|1XHZ|B Chain B, Phi29 Dna Polymerase, Orthorhombic Crystal Form, Ssdna
Complex
pdb|1XHZ|C Chain C, Phi29 Dna Polymerase, Orthorhombic Crystal Form, Ssdna
Complex
pdb|1XHZ|D Chain D, Phi29 Dna Polymerase, Orthorhombic Crystal Form, Ssdna
Complex
pdb|1XI1|A Chain A, Phi29 Dna Polymerase Ssdna Complex, Monoclinic Crystal
Form
pdb|1XI1|B Chain B, Phi29 Dna Polymerase Ssdna Complex, Monoclinic Crystal
Form
pdb|2EX3|A Chain A, Bacteriophage Phi29 Dna Polymerase Bound To Terminal
Protein
pdb|2EX3|C Chain C, Bacteriophage Phi29 Dna Polymerase Bound To Terminal
Protein
pdb|2EX3|E Chain E, Bacteriophage Phi29 Dna Polymerase Bound To Terminal
Protein
pdb|2EX3|G Chain G, Bacteriophage Phi29 Dna Polymerase Bound To Terminal
Protein
pdb|2EX3|I Chain I, Bacteriophage Phi29 Dna Polymerase Bound To Terminal
Protein
pdb|2EX3|K Chain K, Bacteriophage Phi29 Dna Polymerase Bound To Terminal
Protein
pdb|2PY5|A Chain A, Phi29 Dna Polymerase Complexed With Single-stranded Dna
pdb|2PY5|B Chain B, Phi29 Dna Polymerase Complexed With Single-stranded Dna
pdb|2PYJ|A Chain A, Phi29 Dna Polymerase Complexed With Primer-Template Dna
And Incoming Nucleotide Substrates (Ternary Complex)
pdb|2PYJ|B Chain B, Phi29 Dna Polymerase Complexed With Primer-Template Dna
And Incoming Nucleotide Substrates (Ternary Complex)
pdb|2PYL|A Chain A, Phi29 Dna Polymerase Complexed With Primer-Template Dna
And Incoming Nucleotide Substrates (Ternary Complex)
pdb|2PZS|A Chain A, Phi29 Dna Polymerase Complexed With Primer-Template Dna
(Post-Translocation Binary Complex)
pdb|2PZS|B Chain B, Phi29 Dna Polymerase Complexed With Primer-Template Dna
(Post-Translocation Binary Complex)
pdb|2PZS|C Chain C, Phi29 Dna Polymerase Complexed With Primer-Template Dna
(Post-Translocation Binary Complex)
pdb|2PZS|D Chain D, Phi29 Dna Polymerase Complexed With Primer-Template Dna
(Post-Translocation Binary Complex)
Length = 575
Score = 29.3 bits (64), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 21/29 (72%), Gaps = 2/29 (6%)
Query: 135 VFDGNWVWDDNYPLY-RSSDCLF-LDEGF 161
VF+G +VWD++YPL+ + C F L EG+
Sbjct: 270 VFEGKYVWDEDYPLHIQHIRCEFELKEGY 298
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
0.323 0.139 0.456
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,231,856
Number of Sequences: 62578
Number of extensions: 627298
Number of successful extensions: 989
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 986
Number of HSP's gapped (non-prelim): 3
length of query: 493
length of database: 14,973,337
effective HSP length: 103
effective length of query: 390
effective length of database: 8,527,803
effective search space: 3325843170
effective search space used: 3325843170
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)