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= psy8363
(536 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|VV Chain v, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 123
Score = 84.0 bits (206), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 53/119 (44%), Positives = 65/119 (54%), Gaps = 2/119 (1%)
Query: 307 VKVKCSELRTXXXXXXXXXXXXXXXXXANLRVAKVTGGAASKLSKIRVVRKAILRVYIVM 366
K+K +LR + LRVAKVTGGAASKLSKIRVVRK+I RV V+
Sbjct: 2 AKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTVI 61
Query: 367 HQKQKENMRNLIRKEHKKYKPLDXXXXXXXXXXXXXXXHERKLKTLKEIRRRQAFPPRK 425
+Q QKEN+R + KKYKPLD HE LKT K+ R+ + +P RK
Sbjct: 62 NQTQKENLRKFYK--GKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPLRK 118
>pdb|4A17|U Chain U, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|U Chain U, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|U Chain U, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|U Chain U, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 124
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 30/117 (25%), Positives = 55/117 (47%), Gaps = 2/117 (1%)
Query: 309 VKCSELRTXXXXXXXXXXXXXXXXXANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQ 368
V+ +LRT + LR+AK+ GG A+KL +I +VRKAI + ++++
Sbjct: 5 VRVFKLRTQTEEQLVGELGKLQTELSQLRIAKIAGGTANKLGRIGIVRKAIAKYLTIINE 64
Query: 369 KQKENMRNLIRKEHKKYKPLDXXXXXXXXXXXXXXXHERKLKTLKEIRRRQAFPPRK 425
K+++ +++ + K KPLD +R+ +K ++ F RK
Sbjct: 65 KRRQAVKDQFKG--KSLKPLDIRVKKTRAIRRKLTKKQREAVLVKTQKKLNNFGLRK 119
>pdb|2GO5|5 Chain 5, Structure Of Signal Recognition Particle Receptor (Sr) In
Complex With Signal Recognition Particle (Srp) And
Ribosome Nascent Chain Complex
pdb|2J37|5 Chain 5, Model Of Mammalian Srp Bound To 80s Rncs
pdb|3IZR|CC Chain c, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 124
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 3/84 (3%)
Query: 306 SVKVKCSELRTXXXXXXXXXXXXXXXXXANLRVAKVTGGAASKLSKIRVVRKAILRVYIV 365
S KVK EL LR+ KV + SKL++I +RK+I RV V
Sbjct: 3 SGKVKAGELWNKSKDDLTKQLAELKTELGQLRIQKV-ASSGSKLNRIHDIRKSIARVLTV 61
Query: 366 MHQKQKENMRNLIRKEHKKYKPLD 389
++ KQ+ +R + +KKY PLD
Sbjct: 62 INAKQRAQLRLFYK--NKKYAPLD 83
>pdb|1S1I|X Chain X, 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.
pdb|2WW9|N Chain N, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
To The Yeast 80s Ribosome
pdb|2WWA|N Chain N, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To The
Yeast 80s Ribosome
pdb|2WWB|N Chain N, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound To
The Actively Translating Wheat Germ 80s Ribosome
pdb|3IZS|CC Chain c, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|CC Chain c, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|CC Chain c, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|HH Chain h, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|HH Chain h, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|HH Chain h, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 120
Score = 38.1 bits (87), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 36/117 (30%), Positives = 54/117 (46%), Gaps = 5/117 (4%)
Query: 309 VKCSELRTXXXXXXXXXXXXXXXXXANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQ 368
VK ELRT A L+V K++ + L KI+ VRK+I V V+++
Sbjct: 4 VKAYELRTKSKEQLASQLVDLKKELAELKVQKLSRPS---LPKIKTVRKSIACVLTVINE 60
Query: 369 KQKENMRNLIRKEHKKYKPLDXXXXXXXXXXXXXXXHERKLKTLKEIRRRQAFPPRK 425
+Q+E +R L + KKY+P D E T K+ +++ AFP RK
Sbjct: 61 QQREAVRQLYK--GKKYQPKDLRAKKTRALRRALTKFEASQVTEKQRKKQIAFPQRK 115
>pdb|3ZF7|KK Chain k, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 127
Score = 37.7 bits (86), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 46/92 (50%), Gaps = 1/92 (1%)
Query: 334 ANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQKQKENMRNLIR-KEHKKYKPLDXXX 392
+ LRV++ A++L +IR +RK I R+ V+++ ++EN+R K+ + KP
Sbjct: 30 SQLRVSQQMNVGAARLGRIRTIRKGIARIMTVLNKNERENLRKFYSDKKLRSAKPKTLRA 89
Query: 393 XXXXXXXXXXXXHERKLKTLKEIRRRQAFPPR 424
+E+ KT +++R FP R
Sbjct: 90 KLTHRRRLALKANEKNRKTRRQLRMAHKFPRR 121
>pdb|3FAK|A Chain A, Structural And Functional Analysis Of A Hormone-Sensitive
Lipase Like Este5 From A Metagenome Library
pdb|3G9T|A Chain A, Crystal Structure Of Este5, Was Soaked By P-Nitrophenyl
Butyrate For 5sec
pdb|3G9U|A Chain A, Crystal Structure Of Este5, Was Soaked By P-nitrophenyl
Butyrate For 5min
pdb|3G9Z|A Chain A, Crystal Structure Of Este5, Was Soaked By P-Nitrophenyl
Caprylate
pdb|3H17|A Chain A, Crystal Structure Of Este5-Pmsf (I)
pdb|3H18|A Chain A, Crystal Structure Of Este5-pmsf (ii)
pdb|3H19|A Chain A, Crystal Structure Of Este5, Was Soaked By Methyl Alcohol
pdb|3H1A|A Chain A, Crystal Structure Of Este5, Was Soaked By Ethyl Alcohol
pdb|3H1B|A Chain A, Crystal Structure Of Este5, Was Soaked By Isopropyl
Alcohol
pdb|3L1H|A Chain A, Crystal Structure Of Este5, Was Soaked By Fecl3
pdb|3L1I|A Chain A, Crystal Structure Of Este5, Was Soaked By Cuso4
pdb|3L1J|A Chain A, Crystal Structure Of Este5, Was Soaked By Znso4
Length = 322
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 412 LKEIRRRQAFPPRKDLPLPVNRKRVE----EPADDV 443
LK+I R +A PP ++PL V RK +E + ADD+
Sbjct: 22 LKKILREKAVPPGTEVPLDVMRKGMEKVAFKAADDI 57
>pdb|3V9A|A Chain A, Crystal Structure Of EsteraseLIPASE FROM UNCULTURED
BACTERIUM
Length = 309
Score = 29.6 bits (65), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 412 LKEIRRRQAFPPRKDLPLPVNRKRVE----EPADDV 443
LK+I R +A PP ++PL V RK +E + ADD+
Sbjct: 9 LKKILREKAVPPGTEVPLDVMRKGMEKVAFKAADDI 44
>pdb|4B8J|A Chain A, Rimp_alpha1a
Length = 528
Score = 29.6 bits (65), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 34/127 (26%), Positives = 58/127 (45%), Gaps = 21/127 (16%)
Query: 64 LSKYIEPLRRMIARAANDD----IEKTTKMKKLLEILQSPNKRMPLETLLKCEHVLEKLD 119
+ K +E L MI +DD +E TT+ +KLL I +SP P+E +++ V +
Sbjct: 69 VDKKLESLPAMIGGVYSDDNNLQLEATTQFRKLLSIERSP----PIEEVIQSGVVPRFVQ 124
Query: 120 FKHSSLLRDHHPLLEAVSGALQSSNANHTLQRTFGPCLEILSGPLIKDLPLPVNRKRVEE 179
F L R+ P L+ + ++ A+ T + T +I +P+ K +
Sbjct: 125 F----LTREDFPQLQFEAAWALTNIASGTSENT---------KVVIDHGAVPIFVKLLGS 171
Query: 180 PADDVPE 186
+DDV E
Sbjct: 172 SSDDVRE 178
>pdb|2DI3|A Chain A, Crystal Structure Of The Transcriptional Factor Cgl2915
From Corynebacterium Glutamicum
pdb|2DI3|B Chain B, Crystal Structure Of The Transcriptional Factor Cgl2915
From Corynebacterium Glutamicum
Length = 239
Score = 28.9 bits (63), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 55/121 (45%), Gaps = 12/121 (9%)
Query: 33 SGSLNT--PGQAQPTSSPCPTQEDQVYRDKIRQLSKYIEPLRRMIARAANDDIEKTTKMK 90
SG++ T PGQA S +QV I + + +E + + A D + +
Sbjct: 68 SGTIITAAPGQALSLSVTLQLVTNQVGHHDIYETRQLLEGWAALHSSAERGDWDVA---E 124
Query: 91 KLLEILQSPNKRMPLETLLKCEHVLEKLDFKHSSLLRDHHPLLEAVSGALQSSNANHTLQ 150
LLE + P+ +PLE L+ + + K + +PL+ + AL+ S A+HT+
Sbjct: 125 ALLEKMDDPS--LPLEDFLRFDAEFHVVISKGA-----ENPLISTLMEALRLSVADHTVA 177
Query: 151 R 151
R
Sbjct: 178 R 178
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
0.317 0.132 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,092,730
Number of Sequences: 62578
Number of extensions: 526516
Number of successful extensions: 1416
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1406
Number of HSP's gapped (non-prelim): 12
length of query: 536
length of database: 14,973,337
effective HSP length: 103
effective length of query: 433
effective length of database: 8,527,803
effective search space: 3692538699
effective search space used: 3692538699
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)