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= 020531
(325 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 = 50.8 bits (120), 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
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 5/60 (8%)
Query: 267 TAGDCVEVHGGKLLVNGVAQDE-DFILEPLAYEMDPVVVPEGYVFVLGDNRNNSFDSHNW 325
T GD ++L +AQD+ + ++ +VP G F++GDNR+NS DS W
Sbjct: 155 TLGDVTH----RILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYW 210
>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 = 50.4 bits (119), 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
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 5/60 (8%)
Query: 267 TAGDCVEVHGGKLLVNGVAQDE-DFILEPLAYEMDPVVVPEGYVFVLGDNRNNSFDSHNW 325
T GD ++L +AQD+ + ++ +VP G F++GDNR+NS DS W
Sbjct: 156 TLGDVTH----RILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYW 211
>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 = 50.1 bits (118), 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
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 5/60 (8%)
Query: 267 TAGDCVEVHGGKLLVNGVAQDE-DFILEPLAYEMDPVVVPEGYVFVLGDNRNNSFDSHNW 325
T GD ++L +AQD+ + ++ +VP G F++GDNR+NS DS W
Sbjct: 154 TLGDVTH----RILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYW 209
>pdb|2AF5|A Chain A, 2.5a X-Ray Structure Of Engineered Ospa Protein
Length = 297
Score = 31.2 bits (69), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 48/177 (27%), Positives = 80/177 (45%), Gaps = 17/177 (9%)
Query: 148 TTDKIQFSGSENLNGVSLQLKTSGSWLSKLLNVCSDDAKAAFTALTV------SFLFKSF 201
T DK++ G+ + N S L+ + SK+ SDD T L V + + K
Sbjct: 35 TVDKLELKGTSDKNNGSGVLEGVKADKSKVKLTISDD--LGQTTLEVFKEDGKTLVSKKV 92
Query: 202 LAEPRSIPSASMNPTLDVGDRIL--AEKVS---YFFKRPEVSDIVIFRAPPILQEIGFSS 256
++ +S N ++ ++ + A+K S F ++ E+S+ I RA E F+
Sbjct: 93 TSKDKSSTEEKFNEKGELSEKKITRADKSSTEEKFNEKGELSEKKITRADKSSTEEKFNE 152
Query: 257 -GDVFIKRIVATAGDCVEVHGGKLLVNGVAQD--EDFILE-PLAYEMDPVVVPEGYV 309
G+V K I G +E G K +G A++ + ++LE L E +VV EG V
Sbjct: 153 KGEVSEKIITRADGTRLEYTGIKSDGSGKAKEVLKGYVLEGTLTAEKTTLVVKEGTV 209
>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 = 30.0 bits (66), Expect = 2.0, 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|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 = 4.8, 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
>pdb|2DYT|A Chain A, The Crystal Structure Of Saccharomyces Cerevisiae Atg3
Length = 312
Score = 28.1 bits (61), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 2/37 (5%)
Query: 268 AGDCVEVHGGKLLVNGVAQ--DEDFILEPLAYEMDPV 302
A CVEV G +++ G A+ DED +LE + E + V
Sbjct: 82 AEQCVEVEGPDVIMKGFAEDGDEDDVLEYIGSETEHV 118
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
0.320 0.136 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,912,689
Number of Sequences: 62578
Number of extensions: 405777
Number of successful extensions: 770
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 763
Number of HSP's gapped (non-prelim): 12
length of query: 325
length of database: 14,973,337
effective HSP length: 99
effective length of query: 226
effective length of database: 8,778,115
effective search space: 1983853990
effective search space used: 1983853990
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)