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= 021373
(313 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1T7D|A Chain A, Crystal Structure Of Escherichia Coli Type I Signal
Peptidase In Complex With A Lipopeptide Inhibitor
pdb|1T7D|B Chain B, Crystal Structure Of Escherichia Coli Type I Signal
Peptidase In Complex With A Lipopeptide Inhibitor
pdb|3S04|A Chain A, Crystal Structure Of Escherichia Coli Type I Signal
Peptidase In Complex With An Arylomycin Lipoglycopeptide
Antibiotic
pdb|3S04|B Chain B, Crystal Structure Of Escherichia Coli Type I Signal
Peptidase In Complex With An Arylomycin Lipoglycopeptide
Antibiotic
Length = 250
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 34/91 (37%), Positives = 41/91 (45%), Gaps = 23/91 (25%)
Query: 163 LAFRSFVAEPRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPC------------SNDIVIF 210
+ RSF+ EP IPS SM PT +GD I+ EK Y + P DIV+F
Sbjct: 1 MIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVF 60
Query: 211 KSP--PVLQEVGYTDDDVFIKRVVAKEGDVV 239
K P P L +IKR V GD V
Sbjct: 61 KYPEDPKLD---------YIKRAVGLPGDKV 82
Score = 31.2 bits (69), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 260 EAPSYNMTPITVPENSVFVMGDNRNNSYDSH 290
+ P + VP F+MGDNR+NS DS
Sbjct: 179 QQPGQQLATWIVPPGQYFMMGDNRDNSADSR 209
>pdb|1KN9|A Chain A, Crystal Structure Of A Bacterial Signal Peptidase Apo-
Enzyme, Implications For Signal Peptide Binding And The
Ser-Lys Dyad Mechanism.
pdb|1KN9|B Chain B, Crystal Structure Of A Bacterial Signal Peptidase Apo-
Enzyme, Implications For Signal Peptide Binding And The
Ser-Lys Dyad Mechanism.
pdb|1KN9|C Chain C, Crystal Structure Of A Bacterial Signal Peptidase Apo-
Enzyme, Implications For Signal Peptide Binding And The
Ser-Lys Dyad Mechanism.
pdb|1KN9|D Chain D, Crystal Structure Of A Bacterial Signal Peptidase Apo-
Enzyme, Implications For Signal Peptide Binding And The
Ser-Lys Dyad Mechanism.
pdb|3IIQ|A Chain A, Crystallographic Analysis Of Bacterial Signal Peptidase In
Ternary Complex With Arylomycin A2 And A Beta-Sultam
Inhibitor
pdb|3IIQ|B Chain B, Crystallographic Analysis Of Bacterial Signal Peptidase In
Ternary Complex With Arylomycin A2 And A Beta-Sultam
Inhibitor
Length = 249
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 34/88 (38%), Positives = 40/88 (45%), Gaps = 23/88 (26%)
Query: 166 RSFVAEPRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPC------------SNDIVIFKSP 213
RSF+ EP IPS SM PT +GD I+ EK Y + P DIV+FK P
Sbjct: 3 RSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYP 62
Query: 214 --PVLQEVGYTDDDVFIKRVVAKEGDVV 239
P L +IKR V GD V
Sbjct: 63 EDPKLD---------YIKRAVGLPGDKV 81
Score = 31.2 bits (69), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 260 EAPSYNMTPITVPENSVFVMGDNRNNSYDSH 290
+ P + VP F+MGDNR+NS DS
Sbjct: 178 QQPGQQLATWIVPPGQYFMMGDNRDNSADSR 208
>pdb|1B12|A Chain A, Crystal Structure Of Type 1 Signal Peptidase From
Escherichia Coli In Complex With A Beta-Lactam Inhibitor
pdb|1B12|B Chain B, Crystal Structure Of Type 1 Signal Peptidase From
Escherichia Coli In Complex With A Beta-Lactam Inhibitor
pdb|1B12|C Chain C, Crystal Structure Of Type 1 Signal Peptidase From
Escherichia Coli In Complex With A Beta-Lactam Inhibitor
pdb|1B12|D Chain D, Crystal Structure Of Type 1 Signal Peptidase From
Escherichia Coli In Complex With A Beta-Lactam Inhibitor
Length = 248
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 34/88 (38%), Positives = 40/88 (45%), Gaps = 23/88 (26%)
Query: 166 RSFVAEPRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPC------------SNDIVIFKSP 213
RSF+ EP IPS SM PT +GD I+ EK Y + P DIV+FK P
Sbjct: 2 RSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYP 61
Query: 214 --PVLQEVGYTDDDVFIKRVVAKEGDVV 239
P L +IKR V GD V
Sbjct: 62 EDPKLD---------YIKRAVGLPGDKV 80
Score = 31.2 bits (69), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 260 EAPSYNMTPITVPENSVFVMGDNRNNSYDSH 290
+ P + VP F+MGDNR+NS DS
Sbjct: 177 QQPGQQLATWIVPPGQYFMMGDNRDNSADSR 207
>pdb|2X34|A Chain A, Structure Of A Polyisoprenoid Binding Domain From
Saccharophagus Degradans Implicated In Plant Cell Wall
Breakdown
pdb|2X34|B Chain B, Structure Of A Polyisoprenoid Binding Domain From
Saccharophagus Degradans Implicated In Plant Cell Wall
Breakdown
Length = 181
Score = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 10/67 (14%)
Query: 237 DVVEVREGKLIVNGVVRNEDYILEAPSYNMTPITVPENSVFVMG--------DNRNNSYD 288
D+ V G + NG R DY+ E +Y++ +TVP + V G + + + D
Sbjct: 48 DLNSVNTGIDVRNG--RXRDYLFETATYSVATVTVPVDLAAVAGLAVGEDXLVDVSATLD 105
Query: 289 SHGAPPC 295
HG P
Sbjct: 106 LHGVPGV 112
>pdb|3U5Z|G Chain G, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|H Chain H, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|F Chain F, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|Q Chain Q, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|R Chain R, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|P Chain P, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U60|G Chain G, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U60|H Chain H, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U60|F Chain F, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U61|G Chain G, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
pdb|3U61|H Chain H, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
pdb|3U61|F Chain F, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
Length = 228
Score = 28.1 bits (61), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 239 VEVREGKLIVNGVVRNEDYILEAPSYNMT 267
+ V+EGK+++NG + ED L Y++T
Sbjct: 140 ITVKEGKIVINGFNKVEDSALTRVKYSLT 168
>pdb|1CZD|A Chain A, Crystal Structure Of The Processivity Clamp Gp45 From
Bacteriophage T4
pdb|1CZD|B Chain B, Crystal Structure Of The Processivity Clamp Gp45 From
Bacteriophage T4
pdb|1CZD|C Chain C, Crystal Structure Of The Processivity Clamp Gp45 From
Bacteriophage T4
Length = 228
Score = 28.1 bits (61), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 239 VEVREGKLIVNGVVRNEDYILEAPSYNMT 267
+ V+EGK+++NG + ED L Y++T
Sbjct: 140 ITVKEGKIVINGFNKVEDSALTRVKYSLT 168
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
0.317 0.134 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,593,647
Number of Sequences: 62578
Number of extensions: 333613
Number of successful extensions: 860
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 849
Number of HSP's gapped (non-prelim): 13
length of query: 313
length of database: 14,973,337
effective HSP length: 99
effective length of query: 214
effective length of database: 8,778,115
effective search space: 1878516610
effective search space used: 1878516610
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)