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= 028706
(205 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 = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 12/58 (20%)
Query: 89 LSDDHVLMEKFCL-------QKYKFS-----HGDVIVFCSPSNHKEKHVKRIIGLPGD 134
L D +L+EKF QK GD++VF P + K ++KR +GLPGD
Sbjct: 23 LIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGD 80
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 22/37 (59%)
Query: 147 VPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHI 183
VP G ++ GDN +S DSR +G +P + GR T I
Sbjct: 190 VPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAI 226
>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 = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 12/58 (20%)
Query: 89 LSDDHVLMEKFCL-------QKYKFS-----HGDVIVFCSPSNHKEKHVKRIIGLPGD 134
L D +L+EKF QK GD++VF P + K ++KR +GLPGD
Sbjct: 22 LIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGD 79
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 22/37 (59%)
Query: 147 VPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHI 183
VP G ++ GDN +S DSR +G +P + GR T I
Sbjct: 189 VPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAI 225
>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 = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 12/58 (20%)
Query: 89 LSDDHVLMEKFCL-------QKYKFS-----HGDVIVFCSPSNHKEKHVKRIIGLPGD 134
L D +L+EKF QK GD++VF P + K ++KR +GLPGD
Sbjct: 21 LIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGD 78
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 22/37 (59%)
Query: 147 VPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHI 183
VP G ++ GDN +S DSR +G +P + GR T I
Sbjct: 188 VPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAI 224
>pdb|2C2A|A Chain A, Structure Of The Entire Cytoplasmic Portion Of A Sensor
Histidine Kinase Protein
Length = 258
Score = 27.3 bits (59), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 131 LPGDWIGTPMTNDVVKVPNGHCWVEGD 157
+PG +G +T ++V++ G WVE +
Sbjct: 208 VPGTGLGLAITKEIVELHGGRIWVESE 234
>pdb|3DGE|A Chain A, Structure Of A Histidine Kinase-response Regulator Complex
Reveals Insights Into Two-component Signaling And A
Novel Cis- Autophosphorylation Mechanism
pdb|3DGE|B Chain B, Structure Of A Histidine Kinase-response Regulator Complex
Reveals Insights Into Two-component Signaling And A
Novel Cis- Autophosphorylation Mechanism
Length = 258
Score = 27.3 bits (59), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 131 LPGDWIGTPMTNDVVKVPNGHCWVEGD 157
+PG +G +T ++V++ G WVE +
Sbjct: 208 VPGTGLGLAITKEIVELHGGRIWVESE 234
>pdb|4IWH|A Chain A, Crystal Structure Of A 3-isopropylmalate Dehydrogenase
From Burkholderia Pseudomallei
pdb|4IWH|B Chain B, Crystal Structure Of A 3-isopropylmalate Dehydrogenase
From Burkholderia Pseudomallei
Length = 363
Score = 26.9 bits (58), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 127 RIIGLPGDWIGTPMTNDVVKVPNG 150
+I LPGD IG + N+ VKV N
Sbjct: 10 KIAVLPGDGIGPEIVNEAVKVLNA 33
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
0.321 0.137 0.446
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,764,027
Number of Sequences: 62578
Number of extensions: 290126
Number of successful extensions: 521
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 512
Number of HSP's gapped (non-prelim): 9
length of query: 205
length of database: 14,973,337
effective HSP length: 94
effective length of query: 111
effective length of database: 9,091,005
effective search space: 1009101555
effective search space used: 1009101555
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)