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= 019676
(337 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 27/46 (58%)
Query: 260 EAPSYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSV 305
+ P + VP F+MGDNR+NS DS WG +P N++GR+
Sbjct: 177 QQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRAT 222
Score = 46.2 bits (108), Expect = 3e-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
>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 = 2e-05, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 27/45 (60%)
Query: 260 EAPSYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRS 304
+ P + VP F+MGDNR+NS DS WG +P N++GR+
Sbjct: 179 QQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRA 223
Score = 46.2 bits (108), Expect = 2e-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
>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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 27/45 (60%)
Query: 260 EAPSYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRS 304
+ P + VP F+MGDNR+NS DS WG +P N++GR+
Sbjct: 178 QQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRA 222
Score = 46.2 bits (108), Expect = 3e-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
>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 = 6.9, 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 = 7.5, 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 0.135 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,589,570
Number of Sequences: 62578
Number of extensions: 381308
Number of successful extensions: 1029
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: 1018
Number of HSP's gapped (non-prelim): 13
length of query: 337
length of database: 14,973,337
effective HSP length: 99
effective length of query: 238
effective length of database: 8,778,115
effective search space: 2089191370
effective search space used: 2089191370
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)