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= 031410
(160 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 = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 40/84 (47%), Gaps = 13/84 (15%)
Query: 27 VTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSH------------RVGRLGPGDIVFV 74
+ +++ P + SM+PTL L GD IL E ++ G GDIV
Sbjct: 2 IVRSFIYEPFQIPSGSMMPTL-LIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVF 60
Query: 75 RSPVDPNKIVTKRIVGVEGDRVTY 98
+ P DP KR VG+ GD+VTY
Sbjct: 61 KYPEDPKLDYIKRAVGLPGDKVTY 84
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 84 VTKRI--VGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLI 141
VT RI V + D+V + + G T +VP G ++ GDN S DSR +G VP +
Sbjct: 160 VTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANL 219
Query: 142 EGKA 145
G+A
Sbjct: 220 VGRA 223
>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 = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 39/80 (48%), Gaps = 13/80 (16%)
Query: 31 YLWSPTLVFGPSMLPTLNLTGDVILAEYVSH------------RVGRLGPGDIVFVRSPV 78
+++ P + SM+PTL L GD IL E ++ G GDIV + P
Sbjct: 4 FIYEPFQIPSGSMMPTL-LIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPE 62
Query: 79 DPNKIVTKRIVGVEGDRVTY 98
DP KR VG+ GD+VTY
Sbjct: 63 DPKLDYIKRAVGLPGDKVTY 82
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 84 VTKRI--VGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLI 141
VT RI V + D+V + + G T +VP G ++ GDN S DSR +G VP +
Sbjct: 158 VTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANL 217
Query: 142 EGKA 145
G+A
Sbjct: 218 VGRA 221
>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 = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 39/80 (48%), Gaps = 13/80 (16%)
Query: 31 YLWSPTLVFGPSMLPTLNLTGDVILAEYVSH------------RVGRLGPGDIVFVRSPV 78
+++ P + SM+PTL L GD IL E ++ G GDIV + P
Sbjct: 5 FIYEPFQIPSGSMMPTL-LIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPE 63
Query: 79 DPNKIVTKRIVGVEGDRVTY 98
DP KR VG+ GD+VTY
Sbjct: 64 DPKLDYIKRAVGLPGDKVTY 83
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 84 VTKRI--VGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLI 141
VT RI V + D+V + + G T +VP G ++ GDN S DSR +G VP +
Sbjct: 159 VTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANL 218
Query: 142 EGKA 145
G+A
Sbjct: 219 VGRA 222
>pdb|2HMJ|A Chain A, Crystal Structure Of The Naphthalene 1,2-Dioxygenase
Phe-352-Val Mutant.
pdb|2HML|A Chain A, Crystal Structure Of The Naphthalene 1,2-Dioxygenase F352v
Mutant Bound To Phenanthrene.
pdb|2HMN|A Chain A, Crystal Structure Of The Naphthalene 1,2-Dioxygenase F352v
Mutant Bound To Anthracene
Length = 449
Score = 28.5 bits (62), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 47/126 (37%), Gaps = 12/126 (9%)
Query: 37 LVFGPSMLPTLNLT-GDVILAEYVSHRVGRLGPGDIVF-------VRSPVDPNKIVTKRI 88
+ FG + LN GDV Y SH + P + + V +P+D N
Sbjct: 270 MAFGGAKQERLNKEIGDVRARIYRSHLNCTVFPNNSMLTCSGVFKVWNPIDANTTEVWTY 329
Query: 89 VGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDN---LYASRDSRQFGPVPYGLIEGKA 145
VE D K R DS V P G W DN AS++ +++ L+
Sbjct: 330 AIVEKDMPEDLKRRLADSVQRTVGPAG-FWESDDNDNMETASQNGKKYQSRDSDLLSNLG 388
Query: 146 FFRQVW 151
F V+
Sbjct: 389 FGEDVY 394
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
0.325 0.143 0.468
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,419,737
Number of Sequences: 62578
Number of extensions: 228474
Number of successful extensions: 451
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 445
Number of HSP's gapped (non-prelim): 7
length of query: 160
length of database: 14,973,337
effective HSP length: 91
effective length of query: 69
effective length of database: 9,278,739
effective search space: 640232991
effective search space used: 640232991
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 47 (22.7 bits)