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= 021285
(314 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 1e-05, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 27/45 (60%)
Query: 237 EAPSYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRS 281
+ P + VP F+MGDNR+NS DS WG +P N++GR+
Sbjct: 178 QQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRA 222
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 166 RSFVAEPRYIPSLSMYPTFDVGDRIVAEKEVGYTDDDVFIKRVVA----KEGDVV 216
RSF+ EP IPS SM PT +GD I+ EK D ++ K ++ K GD+V
Sbjct: 3 RSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIV 57
>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 = 19/45 (42%), Positives = 27/45 (60%)
Query: 237 EAPSYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRS 281
+ P + VP F+MGDNR+NS DS WG +P N++GR+
Sbjct: 179 QQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRA 223
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 163 LAFRSFVAEPRYIPSLSMYPTFDVGDRIVAEKEVGYTDDDVFIKRVVA----KEGDVV 216
+ RSF+ EP IPS SM PT +GD I+ EK D ++ K ++ K GD+V
Sbjct: 1 MIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIV 58
>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 = 1e-05, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 27/45 (60%)
Query: 237 EAPSYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRS 281
+ P + VP F+MGDNR+NS DS WG +P N++GR+
Sbjct: 177 QQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRA 221
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 166 RSFVAEPRYIPSLSMYPTFDVGDRIVAEKEVGYTDDDVFIKRVVA----KEGDVV 216
RSF+ EP IPS SM PT +GD I+ EK D ++ K ++ K GD+V
Sbjct: 2 RSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIV 56
>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 = 6.1, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 216 VEVREGKLIVNGVVRNEDYILEAPSYNMT 244
+ 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 = 6.4, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 216 VEVREGKLIVNGVVRNEDYILEAPSYNMT 244
+ 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
0.316 0.134 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,923,986
Number of Sequences: 62578
Number of extensions: 354536
Number of successful extensions: 958
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 950
Number of HSP's gapped (non-prelim): 9
length of query: 314
length of database: 14,973,337
effective HSP length: 99
effective length of query: 215
effective length of database: 8,778,115
effective search space: 1887294725
effective search space used: 1887294725
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: 51 (24.3 bits)