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= psy8196
(230 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1J53|A Chain A, Structure Of The N-Terminal Exonuclease Domain Of The
Epsilon Subunit Of E.Coli Dna Polymerase Iii At Ph 8.5
pdb|1J54|A Chain A, Structure Of The N-Terminal Exonuclease Domain Of The
Epsilon Subunit Of E.Coli Dna Polymerase Iii At Ph 5.8
pdb|2IDO|A Chain A, Structure Of The E. Coli Pol Iii Epsilon-Hot Proofreading
Complex
pdb|2IDO|C Chain C, Structure Of The E. Coli Pol Iii Epsilon-Hot Proofreading
Complex
pdb|2XY8|A Chain A, Paramagnetic-Based Nmr Structure Of The Complex Between
The N-Terminal Epsilon Domain And The Theta Domain Of
The Dna Polymerase Iii
Length = 186
Score = 188 bits (478), Expect = 2e-48, Method: Compositional matrix adjust.
Identities = 92/179 (51%), Positives = 121/179 (67%), Gaps = 5/179 (2%)
Query: 3 RHIVLDIETTGLNII----DGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIH 58
R IVLD ETTG+N I +GH+IIEIG VE+ NR++TGNN H Y+ P R + A +H
Sbjct: 7 RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVH 66
Query: 59 GXXXXXXXXXXXXSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYS-NFTKYIYR 117
G +E+ D F++Y+ +E++IHNAAFD+GF+D E SLL T +
Sbjct: 67 GIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCK 126
Query: 118 ITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNL 176
+TD+L +ARK+ GKRNSLDALC RY I RTLHG LLDA++LAEVYLAMT GQ+++
Sbjct: 127 VTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTGGQTSM 185
>pdb|2GUI|A Chain A, Structure And Function Of Cyclized Versions Of The
Proofread Exonuclease Subunit Of E. Coli Dna Polymerase
Iii
Length = 194
Score = 188 bits (478), Expect = 2e-48, Method: Compositional matrix adjust.
Identities = 92/179 (51%), Positives = 121/179 (67%), Gaps = 5/179 (2%)
Query: 3 RHIVLDIETTGLNII----DGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIH 58
R IVLD ETTG+N I +GH+IIEIG VE+ NR++TGNN H Y+ P R + A +H
Sbjct: 10 RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVH 69
Query: 59 GXXXXXXXXXXXXSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYS-NFTKYIYR 117
G +E+ D F++Y+ +E++IHNAAFD+GF+D E SLL T +
Sbjct: 70 GIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCK 129
Query: 118 ITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNL 176
+TD+L +ARK+ GKRNSLDALC RY I RTLHG LLDA++LAEVYLAMT GQ+++
Sbjct: 130 VTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTGGQTSM 188
>pdb|2P1J|A Chain A, Crystal Structure Of A Polc-Type Dna Polymerase Iii
Exonuclease Domain From Thermotoga Maritima
pdb|2P1J|B Chain B, Crystal Structure Of A Polc-Type Dna Polymerase Iii
Exonuclease Domain From Thermotoga Maritima
Length = 186
Score = 67.0 bits (162), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 53/165 (32%), Positives = 84/165 (50%), Gaps = 11/165 (6%)
Query: 5 IVLDIETTGLNI-IDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGXXXX 63
+VLD ETTGL+ +D IIEIG V+I+ QI + H I P R+ + + I G
Sbjct: 15 VVLDFETTGLDPQVD--EIIEIGAVKIQGGQIV-DEYHTLIKPSREISRKSSEITGITQE 71
Query: 64 XXXXXXXXSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMEL-SLLGYSNFTKYIYRITDTL 122
E++ FL ++ +S I+ HNA FD FL + + ++G YI DTL
Sbjct: 72 MLENKRSIEEVLPEFLGFLEDSIIVAHNANFDYRFLRLWIKKVMGLDWERPYI----DTL 127
Query: 123 LMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYL 167
+A+ + + SLD++ ++ + H L DA + A+V+L
Sbjct: 128 ALAKSLLKLRSYSLDSVVEKLGLGPFRH--HRALDDARVTAQVFL 170
>pdb|2F96|A Chain A, 2.1 A Crystal Structure Of Pseudomonas Aeruginosa Rnase T
(Ribonuclease T)
pdb|2F96|B Chain B, 2.1 A Crystal Structure Of Pseudomonas Aeruginosa Rnase T
(Ribonuclease T)
Length = 224
Score = 30.4 bits (67), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 39/181 (21%), Positives = 69/181 (38%), Gaps = 19/181 (10%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEI----KNRQITGNNLHYYINP--GRDSEKSALAIH 58
+V+D+ET G N ++EI + K + + I P G + E +AL
Sbjct: 32 VVVDVETGGFNSAT-DALLEIAATTVGXDEKGFLFPEHTYFFRIEPFEGANIEPAALEFT 90
Query: 59 GXXXXXXXXXXXXSE--IVDNF--------LNYVSNSEIIIHNAAFDVGFLDMELSLLGY 108
G E + + F N + ++ HN++FD+GFL+ ++ G
Sbjct: 91 GIKLDHPLRXAVQEEAALTEIFRGIRKALKANGCKRAILVGHNSSFDLGFLNAAVARTGI 150
Query: 109 SNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLA 168
+ + DT +A + + L C +R H D E AE++
Sbjct: 151 KRNPFHPFSSFDTATLAGLAY--GQTVLAKACQAAGXEFDNREAHSARYDTEKTAELFCG 208
Query: 169 M 169
+
Sbjct: 209 I 209
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 0.138 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,772,455
Number of Sequences: 62578
Number of extensions: 190448
Number of successful extensions: 335
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 324
Number of HSP's gapped (non-prelim): 8
length of query: 230
length of database: 14,973,337
effective HSP length: 96
effective length of query: 134
effective length of database: 8,965,849
effective search space: 1201423766
effective search space used: 1201423766
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: 50 (23.9 bits)