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= 005574
(690 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3BF0|A Chain A, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Native Crystals
pdb|3BF0|B Chain B, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Native Crystals
pdb|3BF0|C Chain C, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Native Crystals
pdb|3BF0|D Chain D, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Native Crystals
Length = 593
Score = 142 bits (358), Expect = 6e-34, Method: Compositional matrix adjust.
Identities = 128/483 (26%), Positives = 211/483 (43%), Gaps = 27/483 (5%)
Query: 140 SVLTMKLRGQIADQLKSRFSSGLSLPQICENFVKAAYDPRIVGIYLHIEPLSCG-WGKVE 198
S L+ +L G +D+L+ SL I +A D I GI + ++ + G ++
Sbjct: 53 SKLSRQLLGASSDRLQEN-----SLFDIVNTIRQAKDDRNITGIVMDLKNFAGGDQPSMQ 107
Query: 199 EIRRHVVDFKKSGKFIIGYVPVCGEKEYYLACACEELYAPPSAYFSLYGLTVQASFLGGV 258
I + + +F+ SGK + + +YYLA +++ P L+G + +
Sbjct: 108 YIGKALKEFRDSGKPVYAVGENYSQGQYYLASFANKIWLSPQGVVDLHGFATNGLYYKSL 167
Query: 259 LEKVGIEPQVQRIGKYKSAGDQLTRKTMSEENCEMLTALLDNIYGNWLDKVSSTKGKRKE 318
L+K+ + V R+G YKSA + R MS E + + ++ N+L+ V++ + E
Sbjct: 168 LDKLKVSTHVFRVGTYKSAVEPFIRDDMSPAAREADSRWIGELWQNYLNTVAANRQIPAE 227
Query: 319 DI--------ERFINDGVYKVERLKEEGFITNVLYDDEVISMLKERLGVQK-DKNLPMVD 369
+ E G + E + + E+ L + G K DKN +
Sbjct: 228 QVFPGAQGLLEGLTKTGGDTAKYALENKLVDALASSAEIEKALTKEFGWSKTDKNYRAIS 287
Query: 370 YRKYSGVRRWTLGLTGGGDQIAVIRASGXXXXXXXXXXXXXXXXXXEQLIEKIRKVRESK 429
Y Y+ T TG D I V+ A+G Q IR R
Sbjct: 288 YYDYA---LKTPADTG--DSIGVVFANGAIMDGEETQGNVGGDTTAAQ----IRDARLDP 338
Query: 430 RYKAAIIRIDSPGGDALASDLMWREIRLLSE-SKPVIASMSDVXXXXXXXXXXXXXTILA 488
+ KA ++R++SPGG AS+++ E+ KPV+ SM + I+A
Sbjct: 339 KVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVSMGGMAASGGYWISTPANYIVA 398
Query: 489 ENLTLTGSIGVVTGKFNLGKLYEKIGFNKEIISRGKYAEVLAAEQRPFRPDEAELFAKSA 548
TLTGSIG+ + + IG + + +S A+V + R P+ + S
Sbjct: 399 NPSTLTGSIGIFGVITTVENSLDSIGVHTDGVSTSPLADV--SITRALPPEAQLMMQLSI 456
Query: 549 QNAYKLFRDKAAFSRSMTVDKMEEYAQGRVWTGNDAASRGLVDALGGFSRAVAIAKQKAN 608
+N YK F A +R T +++++ AQG VWTG DA + GLVD+LG F AVA A + A
Sbjct: 457 ENGYKRFITLVADARHSTPEQIDKIAQGHVWTGQDAKANGLVDSLGDFDDAVAKAAELAK 516
Query: 609 IPE 611
+ +
Sbjct: 517 VKQ 519
>pdb|3BEZ|A Chain A, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Semet Crystals
pdb|3BEZ|B Chain B, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Semet Crystals
pdb|3BEZ|C Chain C, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Semet Crystals
pdb|3BEZ|D Chain D, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Semet Crystals
Length = 593
Score = 127 bits (319), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 127/482 (26%), Positives = 205/482 (42%), Gaps = 29/482 (6%)
Query: 140 SVLTMKLRGQIADQLKSRFSSGLSLPQICENFVKAAYDPRIVGIYLHIEPLSCG-WGKVE 198
S L+ +L G +D+L+ SL I +A D I GI ++ + G +
Sbjct: 53 SKLSRQLLGASSDRLQEN-----SLFDIVNTIRQAKDDRNITGIVXDLKNFAGGDQPSXQ 107
Query: 199 EIRRHVVDFKKSGKFIIGYVPVCGEKEYYLACACEELYAPPSAYFSLYGLTVQASFLGGV 258
I + + +F+ SGK + + +YYLA +++ P L+G + +
Sbjct: 108 YIGKALKEFRDSGKPVYAVGENYSQGQYYLASFANKIWLSPQGVVDLHGFATNGLYYKSL 167
Query: 259 LEKVGIEPQVQRIGKYKSAGDQLTRKTMSEENCEMLTALLDNIYGNWLDKVSSTKGKRKE 318
L+K+ + V R+G YKSA + R S E + + ++ N+L+ V++ + E
Sbjct: 168 LDKLKVSTHVFRVGTYKSAVEPFIRDDXSPAAREADSRWIGELWQNYLNTVAANRQIPAE 227
Query: 319 DI--------ERFINDGVYKVERLKEEGFITNVLYDDEVISMLKERLGVQK-DKNLPMVD 369
+ E G + E + + E+ L + G K DKN +
Sbjct: 228 QVFPGAQGLLEGLTKTGGDTAKYALENKLVDALASSAEIEKALTKEFGWSKTDKNYRAIS 287
Query: 370 YRKYSGVRRWTLGLTGGGDQIAVIRASGXXXXXXXXXXXXXXXXXXEQLIEKIRKVRESK 429
Y Y+ GD I V+ A+G Q IR R
Sbjct: 288 YYDYA-----LKTPADTGDSIGVVFANGAIXDGEETQGNVGGDTTAAQ----IRDARLDP 338
Query: 430 RYKAAIIRIDSPGGDALASDLMWREIRLLSE-SKPVIASMSDVXXXXXXXXXXXXXTILA 488
+ KA ++R++SPGG AS+++ E+ KPV+ S I+A
Sbjct: 339 KVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVSXGGXAASGGYWISTPANYIVA 398
Query: 489 ENLTLTGSIGVVTGKFNLGKLYEKIGFNKEIISRGKYAEVLAAEQRPFRPDEAELFAK-S 547
TLTGSIG+ + + IG + + +S A+V P EA+L + S
Sbjct: 399 NPSTLTGSIGIFGVITTVENSLDSIGVHTDGVSTSPLADVSITRALP---PEAQLXXQLS 455
Query: 548 AQNAYKLFRDKAAFSRSMTVDKMEEYAQGRVWTGNDAASRGLVDALGGFSRAVAIAKQKA 607
+N YK F A +R T +++++ AQG VWTG DA + GLVD+LG F AVA A + A
Sbjct: 456 IENGYKRFITLVADARHSTPEQIDKIAQGHVWTGQDAKANGLVDSLGDFDDAVAKAAELA 515
Query: 608 NI 609
+
Sbjct: 516 KV 517
>pdb|3RST|A Chain A, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
pdb|3RST|B Chain B, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
pdb|3RST|C Chain C, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
pdb|3RST|D Chain D, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
pdb|3RST|E Chain E, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
pdb|3RST|F Chain F, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
pdb|3RST|G Chain G, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
pdb|3RST|H Chain H, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
Length = 240
Score = 79.3 bits (194), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 49/190 (25%), Positives = 91/190 (47%), Gaps = 3/190 (1%)
Query: 418 LIEKIRKVRESKRYKAAIIRIDSPGGDALASDLMWREIRLLSES--KPVIASMSDVXXXX 475
++ + + ++ K K +++++SPGG S + +++ + + KP+ SM +
Sbjct: 34 FLKNLERAKDDKTVKGIVLKVNSPGGGVYESAEIHKKLEEIKKETKKPIYVSMGSMAASG 93
Query: 476 XXXXXXXXXTILAENLTLTGSIGVVTGKFNLGKLYEKIGFNKEIISRGKYAEVLAAEQRP 535
I A TLTGS+GV+ N KL +K+G + E I G +A++++ R
Sbjct: 94 GYYISTAADKIFATPETLTGSLGVIMESVNYSKLADKLGISFETIKSGAHADIMSP-SRE 152
Query: 536 FRPDEAELFAKSAQNAYKLFRDKAAFSRSMTVDKMEEYAQGRVWTGNDAASRGLVDALGG 595
+E + N+Y+ F D + R M ++++ A GRV+ G A LVD LG
Sbjct: 153 MTKEEKNIMQSMVDNSYEGFVDVISKGRGMPKAEVKKIADGRVYDGRQAKKLNLVDELGF 212
Query: 596 FSRAVAIAKQ 605
+ + K+
Sbjct: 213 YDDTITAMKK 222
Score = 59.3 bits (142), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 54/243 (22%), Positives = 112/243 (46%), Gaps = 15/243 (6%)
Query: 141 VLTMKLRGQIADQLKSRF---SSGLSLPQICENFVKAAYDPRIVGIYLHIEPLSCGWGKV 197
+ +++ G I D S + G + +N +A D + GI L + G +
Sbjct: 5 IAVLEVSGTIQDNGDSSSLLGADGYNHRTFLKNLERAKDDKTVKGIVLKVNSPGGGVYES 64
Query: 198 EEIRRHVVDFKKSGKFIIGYVPV---CGEKEYYLACACEELYAPPSAYFSLYGLTVQASF 254
EI + + + KK K I YV + YY++ A ++++A P G+ +++
Sbjct: 65 AEIHKKLEEIKKETKKPI-YVSMGSMAASGGYYISTAADKIFATPETLTGSLGVIMESVN 123
Query: 255 LGGVLEKVGIEPQVQRIGKYKSAGDQLTRKTMSEENCEMLTALLDNIYGNWLDKVSSTKG 314
+ +K+GI + + G + A + M++E ++ +++DN Y ++D +S +G
Sbjct: 124 YSKLADKLGISFETIKSGAH--ADIMSPSREMTKEEKNIMQSMVDNSYEGFVDVISKGRG 181
Query: 315 KRKEDIERFINDGVYKVERLKEEGFITNV-LYDDEVISMLKERLGVQKD-KNLPMVDYRK 372
K ++++ + VY + K+ + + YDD + +M K+ KD KN ++ Y +
Sbjct: 182 MPKAEVKKIADGRVYDGRQAKKLNLVDELGFYDDTITAMKKD----HKDLKNASVISYEE 237
Query: 373 YSG 375
G
Sbjct: 238 SFG 240
>pdb|4GIZ|C Chain C, Crystal Structure Of Full-length Human Papillomavirus
Oncoprotein E6 In Complex With Lxxll Peptide Of
Ubiquitin Ligase E6ap At 2.55 A Resolution
pdb|4GIZ|D Chain D, Crystal Structure Of Full-length Human Papillomavirus
Oncoprotein E6 In Complex With Lxxll Peptide Of
Ubiquitin Ligase E6ap At 2.55 A Resolution
Length = 142
Score = 29.6 bits (65), Expect = 5.3, Method: Composition-based stats.
Identities = 27/96 (28%), Positives = 41/96 (42%), Gaps = 20/96 (20%)
Query: 164 LPQICENFVKAAYDPRIVGIYLHIEPLSCGWGKVEEIRRHVVDFKKSGKFIIGYVPVCGE 223
LPQ+C +D I+ L C + K + +RR V DF + I V +
Sbjct: 11 LPQLCTELQTTIHD--II--------LECVYCKQQLLRREVYDFARRDLCI-----VYRD 55
Query: 224 KEYYLAC-ACEELYAPPSAY----FSLYGLTVQASF 254
Y C C + Y+ S Y +SLYG T++ +
Sbjct: 56 GNPYAVCDKCLKFYSKISEYRHYSYSLYGTTLEQQY 91
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
0.318 0.135 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,811,018
Number of Sequences: 62578
Number of extensions: 744556
Number of successful extensions: 1653
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1640
Number of HSP's gapped (non-prelim): 9
length of query: 690
length of database: 14,973,337
effective HSP length: 106
effective length of query: 584
effective length of database: 8,340,069
effective search space: 4870600296
effective search space used: 4870600296
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)