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= 029367
(194 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 = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 38/75 (50%), Gaps = 17/75 (22%)
Query: 57 IPSSSMYPTLRIGDRIIVEKASYYFRNPSIH------------DIVTFRAPFQYPGLGEE 104
IPS SM PTL IGD I+VEK +Y ++P DIV F+ P + P L
Sbjct: 12 IPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYP-EDPKLD-- 68
Query: 105 DVFIKRIVAKAGDLV 119
+IKR V GD V
Sbjct: 69 --YIKRAVGLPGDKV 81
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 23/33 (69%)
Query: 151 VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGR 183
VP G +++GDNR+NS DS WG +P N+ GR
Sbjct: 189 VPPGQYFMMGDNRDNSADSRYWGFVPEANLVGR 221
>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 = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 38/75 (50%), Gaps = 17/75 (22%)
Query: 57 IPSSSMYPTLRIGDRIIVEKASYYFRNPSIH------------DIVTFRAPFQYPGLGEE 104
IPS SM PTL IGD I+VEK +Y ++P DIV F+ P + P L
Sbjct: 11 IPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYP-EDPKLD-- 67
Query: 105 DVFIKRIVAKAGDLV 119
+IKR V GD V
Sbjct: 68 --YIKRAVGLPGDKV 80
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 23/33 (69%)
Query: 151 VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGR 183
VP G +++GDNR+NS DS WG +P N+ GR
Sbjct: 188 VPPGQYFMMGDNRDNSADSRYWGFVPEANLVGR 220
>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 = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 38/75 (50%), Gaps = 17/75 (22%)
Query: 57 IPSSSMYPTLRIGDRIIVEKASYYFRNPSIH------------DIVTFRAPFQYPGLGEE 104
IPS SM PTL IGD I+VEK +Y ++P DIV F+ P + P L
Sbjct: 13 IPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYP-EDPKLD-- 69
Query: 105 DVFIKRIVAKAGDLV 119
+IKR V GD V
Sbjct: 70 --YIKRAVGLPGDKV 82
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 23/33 (69%)
Query: 151 VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGR 183
VP G +++GDNR+NS DS WG +P N+ GR
Sbjct: 190 VPPGQYFMMGDNRDNSADSRYWGFVPEANLVGR 222
>pdb|3LUY|A Chain A, Putative Chorismate Mutase From Bifidobacterium
Adolescentis
Length = 329
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 112 VAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLT 149
VA+ D + R + + +G+AQ + FIAEH T T
Sbjct: 101 VAQGADPAEARIATAHPHGLAQCKRFIAEHRLSTQPAT 138
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 0.142 0.456
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,337,144
Number of Sequences: 62578
Number of extensions: 267244
Number of successful extensions: 743
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 736
Number of HSP's gapped (non-prelim): 7
length of query: 194
length of database: 14,973,337
effective HSP length: 94
effective length of query: 100
effective length of database: 9,091,005
effective search space: 909100500
effective search space used: 909100500
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: 49 (23.5 bits)