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= 023805
(277 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 51/173 (29%), Positives = 79/173 (45%), Gaps = 17/173 (9%)
Query: 11 GTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSS 70
G A V D ETT Q ++E GA+ + ++V+ + TLIKP ++ KSS
Sbjct: 10 GDATFVVLDFETT--GLDPQVDEIIEIGAVKIQGGQIVD--EYHTLIKPS--REISRKSS 63
Query: 71 RCDGITREAVESAPEFEEVADKIFSILNGRVWAGHNIR---RFDCARIKEAFAEIGKPAP 127
GIT+E +E+ EEV + L + HN RF IK+ +G
Sbjct: 64 EITGITQEMLENKRSIEEVLPEFLGFLEDSIIVAHNANFDYRFLRLWIKKV---MGLDWE 120
Query: 128 VPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLGQ-QKHRSLDDVRMNLEVL 179
P ID+L + R+ ++ ++ GLG + HR+LDD R+ +V
Sbjct: 121 RP--YIDTLALAKSLLKLRSYSLD--SVVEKLGLGPFRHHRALDDARVTAQVF 169
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 39/138 (28%), Positives = 60/138 (43%), Gaps = 11/138 (7%)
Query: 16 VFFDLETTVPRRAGQRFW---VLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRC 72
+ D ETT + G + ++E GA+ V R+L +F +KP L V ++
Sbjct: 9 IVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTG-NNFHVYLKPDRL--VDPEAFGV 65
Query: 73 DGITREAVESAPEFEEVADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAP---VP 129
GI E + P F EVAD+ + G HN FD + F+ + + P
Sbjct: 66 HGIADEFLLDKPTFAEVADEFMDYIRGAELVIHN-AAFDIGFMDYEFSLLKRDIPKTNTF 124
Query: 130 VGMIDSLGVLTEKF-GRR 146
+ DSL V + F G+R
Sbjct: 125 CKVTDSLAVARKMFPGKR 142
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 44/149 (29%), Positives = 65/149 (43%), Gaps = 12/149 (8%)
Query: 5 IPSQAAGTAEIVFFDLETTVPRRAGQRFW---VLEFGAIIVCPRKLVELESFSTLIKPKD 61
I A T +IV D ETT + G + ++E GA+ V R+L +F +KP
Sbjct: 2 IEFSTAITRQIVL-DTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTG-NNFHVYLKPDR 59
Query: 62 LSAVALKSSRCDGITREAVESAPEFEEVADKIFSILNGRVWAGHNIRRFDCARIKEAFAE 121
L V ++ GI E + P F EVAD+ + G HN FD + F+
Sbjct: 60 L--VDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHN-AAFDIGFMDYEFSL 116
Query: 122 IGKPAP---VPVGMIDSLGVLTEKF-GRR 146
+ + P + DSL V + F G+R
Sbjct: 117 LKRDIPKTNTFCKVTDSLAVARKMFPGKR 145
>pdb|2B5E|A Chain A, Crystal Structure Of Yeast Protein Disulfide Isomerase
pdb|3BOA|A Chain A, Crystal Structure Of Yeast Protein Disulfide Isomerase
Length = 504
Score = 27.7 bits (60), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 131 GMIDSLGVLTEKFGRRAGNMKMATLASYFGLGQQKHRSLDDVRMNL 176
G+++ + + KFGR AGN+ M F + H +D++ L
Sbjct: 268 GLMNFVSIDARKFGRHAGNLNMKEQFPLFAI----HDMTEDLKYGL 309
>pdb|3B9W|A Chain A, The 1.3 A Resolution Structure Of Nitrosomonas Europaea
Rh50 And Mechanistic Implications For Nh3 Transport By
Rhesus Family Proteins
Length = 407
Score = 27.7 bits (60), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 132 MIDSLGVLTEKFGRRAGNMKMATLASYFGLG 162
++D+ LTE F AG++ + +YFGLG
Sbjct: 125 VLDNASGLTEGFQDSAGSIAIHAFGAYFGLG 155
>pdb|1ST6|A Chain A, Crystal Structure Of A Cytoskeletal Protein
Length = 1069
Score = 27.7 bits (60), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 24/41 (58%)
Query: 225 KSPPISLGYQRSAVPYTRTSLGKMTESVKNLLCKSQGSQPL 265
K+ + G +R + T +LG+MT+ + +L + QG+ P+
Sbjct: 311 KAGELCAGKERREILGTCKTLGQMTDQLADLRARGQGATPM 351
>pdb|3BHS|A Chain A, Nitrosomonas Europaea Rh50 And Mechanism Of Conduction By
Rhesus Protein Family Of Channels
Length = 406
Score = 27.7 bits (60), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 132 MIDSLGVLTEKFGRRAGNMKMATLASYFGLG 162
++D+ LTE F AG++ + +YFGLG
Sbjct: 124 VLDNASGLTEGFQDSAGSIAIHAFGAYFGLG 154
>pdb|3B9Y|A Chain A, Crystal Structure Of The Nitrosomonas Europaea Rh Protein
pdb|3B9Z|A Chain A, Crystal Structure Of The Nitrosomonas Europaea Rh Protein
Complexed With Carbon Dioxide
Length = 388
Score = 27.7 bits (60), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 132 MIDSLGVLTEKFGRRAGNMKMATLASYFGLG 162
++D+ LTE F AG++ + +YFGLG
Sbjct: 119 VLDNASGLTEGFQDSAGSIAIHAFGAYFGLG 149
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
0.319 0.133 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,281,716
Number of Sequences: 62578
Number of extensions: 266089
Number of successful extensions: 599
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 593
Number of HSP's gapped (non-prelim): 10
length of query: 277
length of database: 14,973,337
effective HSP length: 98
effective length of query: 179
effective length of database: 8,840,693
effective search space: 1582484047
effective search space used: 1582484047
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: 51 (24.3 bits)