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= 021403
(313 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 = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 35/90 (38%), Positives = 44/90 (48%), Gaps = 23/90 (25%)
Query: 197 LFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFK------------RPEVSDIVIFR 244
+ +SF+ EP IPS SM PTL +GD IL EK +Y K P+ DIV+F+
Sbjct: 1 MVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFK 60
Query: 245 AP--PILQEIGFSSGDVFIKRIVATAGDCV 272
P P L +IKR V GD V
Sbjct: 61 YPEDPKLD---------YIKRAVGLPGDKV 81
>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 = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 35/91 (38%), Positives = 44/91 (48%), Gaps = 23/91 (25%)
Query: 196 FLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFK------------RPEVSDIVIF 243
+ +SF+ EP IPS SM PTL +GD IL EK +Y K P+ DIV+F
Sbjct: 1 MIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVF 60
Query: 244 RAP--PILQEIGFSSGDVFIKRIVATAGDCV 272
+ P P L +IKR V GD V
Sbjct: 61 KYPEDPKLD---------YIKRAVGLPGDKV 82
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 35/88 (39%), Positives = 43/88 (48%), Gaps = 23/88 (26%)
Query: 199 KSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFK------------RPEVSDIVIFRAP 246
+SF+ EP IPS SM PTL +GD IL EK +Y K P+ DIV+F+ P
Sbjct: 2 RSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYP 61
Query: 247 --PILQEIGFSSGDVFIKRIVATAGDCV 272
P L +IKR V GD V
Sbjct: 62 EDPKLD---------YIKRAVGLPGDKV 80
>pdb|3OWT|A Chain A, Crystal Structure Of S. Cerevisiae Rap1-Sir3 Complex
pdb|3OWT|B Chain B, Crystal Structure Of S. Cerevisiae Rap1-Sir3 Complex
Length = 157
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 13 VAQNLAHSAGIRFGFSTTSTRSFH-ECLFRPRVFCHSKKTDLDPPPN 58
+ Q+L GIR FST+ + + PR F + K +++PPPN
Sbjct: 66 LVQDLCDETGIRKNFSTSILTCLSGDLMVFPRYFLNMFKDNVNPPPN 112
>pdb|2DYT|A Chain A, The Crystal Structure Of Saccharomyces Cerevisiae Atg3
Length = 312
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 268 AGDCVEVHGGKLLVNGVAQ--DEDFILEPLAYEMDPVVMFP 306
A CVEV G +++ G A+ DED +LE + E + V P
Sbjct: 82 AEQCVEVEGPDVIMKGFAEDGDEDDVLEYIGSETEHVQSTP 122
>pdb|3CZ6|A Chain A, Crystal Structure Of The Rap1 C-Terminus
pdb|3CZ6|B Chain B, Crystal Structure Of The Rap1 C-Terminus
Length = 168
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 25/51 (49%), Gaps = 9/51 (17%)
Query: 13 VAQNLAHSAGIRFGFSTTSTRSFHECL-----FRPRVFCHSKKTDLDPPPN 58
+ Q+L GIR FST S CL PR F + K +++PPPN
Sbjct: 66 LVQDLCDETGIRKNFST----SILTCLSGDLXVFPRYFLNXFKDNVNPPPN 112
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 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,265,006
Number of Sequences: 62578
Number of extensions: 372186
Number of successful extensions: 674
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 671
Number of HSP's gapped (non-prelim): 7
length of query: 313
length of database: 14,973,337
effective HSP length: 99
effective length of query: 214
effective length of database: 8,778,115
effective search space: 1878516610
effective search space used: 1878516610
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: 51 (24.3 bits)