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= 016679
(384 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KVN|X Chain X, Crystal Structure Of The Full-Length Autotransporter Esta
From Pseudomonas Aeruginosa
pdb|3KVN|A Chain A, Crystal Structure Of The Full-Length Autotransporter Esta
From Pseudomonas Aeruginosa
Length = 632
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 82/349 (23%), Positives = 129/349 (36%), Gaps = 72/349 (20%)
Query: 35 PRPFNKIYAFGDSFTDTGNTKTATGPSGFGHVSTSPYGSTY------FHHPTNRYSDGRL 88
P P++ + FGDS +D G GP+G T+ G TY PT G
Sbjct: 12 PSPYSTLVVFGDSLSDAGQFPDPAGPAGSTSRFTNRVGPTYQNGSGEIFGPTAPMLLGN- 70
Query: 89 VIDFVTQSLSLPFLPPYLHNKDNATYGVNFAVGG---------ATAINHAFFVKNNLSLD 139
+ L+ P ++ + G N+AVGG TA N + ++N
Sbjct: 71 QLGIAPGDLAASTSP--VNAQQGIADGNNWAVGGYRTDQIYDSITAANGSLIERDN---- 124
Query: 140 ITPQSIQTQLIWFNKFLESKGCKAAESSVPQCQAAFDDALFWVGEIGVNDYAYTLGSSVT 199
T L + +L + Q A +AL+++ G ND+ L +
Sbjct: 125 -------TLLRSRDGYLVDR--------ARQGLGADPNALYYI-TGGGNDF---LQGRIL 165
Query: 200 SDTIRKLAIPSFTNFLQALLKRGAKYVVVQGLPTTGCLPLAMYLAPEDDRDGIGCVKSVN 259
+D + A + +QAL + GA+Y+VV LP G P A + P +
Sbjct: 166 NDVQAQQAAGRLVDSVQALQQAGARYIVVWLLPDLGLTP-ATFGGP--------LQPFAS 216
Query: 260 NQSYTHNLVLQAQLQNLRQQFPQAVIVYADYWNAFRMVMKNPGKYGF--KEPFKACCGSG 317
S T N L AQL A ++ + + M NP +G + C SG
Sbjct: 217 QLSGTFNAELTAQLSQ-----AGANVIPLNIPLLLKEGMANPASFGLAADQNLIGTCFSG 271
Query: 318 -----EPPYNFNVFATCGSPSAKACPNPYQYINWDGVHLTEAMYKVMSD 361
P Y N + P+P + + D VH T ++++D
Sbjct: 272 NGCTMNPTYGIN----------GSTPDPSKLLFNDSVHPTITGQRLIAD 310
>pdb|3JYW|E Chain E, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 237
Score = 34.7 bits (78), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 30/112 (26%), Positives = 42/112 (37%), Gaps = 13/112 (11%)
Query: 35 PRPFNKIYAFGDSFTDTGNTKTATGPSGFGHVSTSPYGSTYFHHPTNRYSDGRLVIDFVT 94
PRPF F D G +T TG FG + + G Y H NR+ DF T
Sbjct: 129 PRPFK-------VFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPG----WDFET 177
Query: 95 QSLSLPFLPPYLHNKDNATYGVNFAVGGATAINHAFFVKNNLSLDITPQSIQ 146
+ + L Y+ + Y A + F K L+ DI S++
Sbjct: 178 EEIDPELLRSYIFGGHVSQYMEELADDDEERFSELF--KGYLADDIDADSLE 227
>pdb|3IZS|Q Chain Q, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|E Chain E, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|E Chain E, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit
Length = 297
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 30/112 (26%), Positives = 42/112 (37%), Gaps = 13/112 (11%)
Query: 35 PRPFNKIYAFGDSFTDTGNTKTATGPSGFGHVSTSPYGSTYFHHPTNRYSDGRLVIDFVT 94
PRPF F D G +T TG FG + + G Y H NR+ DF T
Sbjct: 139 PRPFK-------VFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPG----WDFET 187
Query: 95 QSLSLPFLPPYLHNKDNATYGVNFAVGGATAINHAFFVKNNLSLDITPQSIQ 146
+ + L Y+ + Y A + F K L+ DI S++
Sbjct: 188 EEIDPELLRSYIFGGHVSQYMEELADDDEERFSELF--KGYLADDIDADSLE 237
>pdb|3U5E|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|D Chain D, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 297
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 30/112 (26%), Positives = 42/112 (37%), Gaps = 13/112 (11%)
Query: 35 PRPFNKIYAFGDSFTDTGNTKTATGPSGFGHVSTSPYGSTYFHHPTNRYSDGRLVIDFVT 94
PRPF F D G +T TG FG + + G Y H NR+ DF T
Sbjct: 139 PRPFK-------VFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPG----WDFET 187
Query: 95 QSLSLPFLPPYLHNKDNATYGVNFAVGGATAINHAFFVKNNLSLDITPQSIQ 146
+ + L Y+ + Y A + F K L+ DI S++
Sbjct: 188 EEIDPELLRSYIFGGHVSQYMEELADDDEERFSELF--KGYLADDIDADSLE 237
>pdb|1S1I|E Chain E, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h
Length = 222
Score = 32.0 bits (71), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 29/106 (27%), Positives = 39/106 (36%), Gaps = 13/106 (12%)
Query: 35 PRPFNKIYAFGDSFTDTGNTKTATGPSGFGHVSTSPYGSTYFHHPTNRYSDGRLVIDFVT 94
PRPF F D G +T TG FG + + G Y H NR+ DF T
Sbjct: 129 PRPFK-------VFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPG----WDFET 177
Query: 95 QSLSLPFLPPYLHNKDNATYGVNFAVGGATAINHAFFVKNNLSLDI 140
+ + L Y+ + Y A + F K L+ DI
Sbjct: 178 EEIDPELLRSYIFGGHVSQYMEELADDDEERFSELF--KGYLADDI 221
>pdb|1XAS|A Chain A, Crystal Structure, At 2.6 Angstroms Resolution, Of The
Streptomyces Lividans Xylanase A, A Member Of The F
Family Of Beta-1,4-D-Glycanses
Length = 299
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 327 ATCGSPSAKACPNPYQYINWDGVHLTEAMYKVMSDMFLSG 366
A PSAK C N Y NW T+AMY ++ D G
Sbjct: 158 ARAADPSAKLCYNDYNVENWTWAK-TQAMYNMVRDFKQRG 196
>pdb|1E0W|A Chain A, Xylanase 10a From Sreptomyces Lividans. Native Structure
At 1.2 Angstrom Resolution
pdb|1E0X|A Chain A, Xylanase 10a From Sreptomyces Lividans. Xylobiosyl-Enzyme
Intermediate At 1.65 A
pdb|1E0X|B Chain B, Xylanase 10a From Sreptomyces Lividans. Xylobiosyl-Enzyme
Intermediate At 1.65 A
pdb|1OD8|A Chain A, Xylanase Xyn10a From Streptomyces Lividans In Complex With
Xylobio-Isofagomine Lactam
pdb|1V0K|A Chain A, Xylanase Xyn10a From Streptomyces Lividans In Complex With
Xylobio-Deoxynojirimycin At Ph 5.8
pdb|1V0L|A Chain A, Xylanase Xyn10a From Streptomyces Lividans In Complex With
Xylobio-isofagomine At Ph 5.8
pdb|1V0M|A Chain A, Xylanase Xyn10a From Streptomyces Lividans In Complex With
Xylobio-deoxynojirimycin At Ph 7.5
pdb|1V0N|A Chain A, Xylanase Xyn10a From Streptomyces Lividans In Complex With
Xylobio-Isofagomine At Ph 7.5
Length = 313
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 327 ATCGSPSAKACPNPYQYINWDGVHLTEAMYKVMSDMFLSG 366
A PSAK C N Y NW T+AMY ++ D G
Sbjct: 158 ARAADPSAKLCYNDYNVENWTWAK-TQAMYNMVRDFKQRG 196
>pdb|1E0V|A Chain A, Xylanase 10a From Sreptomyces Lividans. Cellobiosyl-Enzyme
Intermediate At 1.7 A
Length = 313
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 327 ATCGSPSAKACPNPYQYINWDGVHLTEAMYKVMSDMFLSG 366
A PSAK C N Y NW T+AMY ++ D G
Sbjct: 158 ARAADPSAKLCYNDYNVENWTWAK-TQAMYNMVRDFKQRG 196
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 0.136 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,939,033
Number of Sequences: 62578
Number of extensions: 510892
Number of successful extensions: 1027
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1025
Number of HSP's gapped (non-prelim): 9
length of query: 384
length of database: 14,973,337
effective HSP length: 101
effective length of query: 283
effective length of database: 8,652,959
effective search space: 2448787397
effective search space used: 2448787397
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: 52 (24.6 bits)