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= 016026
(396 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1S31|A Chain A, Crystal Structure Analysis Of The Human Tub Protein
(isoform A) Spanning Residues 289 Through 561
Length = 273
Score = 149 bits (376), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 106/315 (33%), Positives = 145/315 (46%), Gaps = 100/315 (31%)
Query: 117 QPGPRDGTIQCFIKRDKSNL------TYHLFL--------------------------CL 144
+P P+ TI+C I RDK + TY L L +
Sbjct: 24 RPAPQGITIKCRITRDKKGMDRGMFPTYFLHLDREDGKKVFLLAGRKRKKSKTSNYLISV 83
Query: 145 SPDNISRSSSTYIGKLRSNFLGTKFIIYD--TQPPYNSAQLSPPGRSRRFYSKKVSPKVP 202
P ++SR +YIGKLRSN +GTKF +YD P S+ G R+
Sbjct: 84 DPTDLSRGGDSYIGKLRSNLMGTKFTVYDNGVNPQKASSSTLESGTLRQ----------- 132
Query: 203 TGSYNIAQVSYELNVLGTRGPRRMHCTMHSIPASALEPG-GSVPGQAELNPRSLEDSFRN 261
+A V YE NVLG +GPR+M S + PG V + + PR+ ++
Sbjct: 133 ----ELAAVCYETNVLGFKGPRKM---------SVIVPGMNMVHERVSIRPRNEHETLL- 178
Query: 262 FSKSIDVSTEFSSSRFSDIVGPRDEEDEGKDRPLILRNKAPRWHEQLQCWCLNFRGRVTV 321
+R+ +++ + + L+NK P W++ Q + LNF GRVT
Sbjct: 179 -------------ARW---------QNKNTESIIELQNKTPVWNDDTQSYVLNFHGRVTQ 216
Query: 322 ASVKNFQLIXXXXXXXXXXXXXXXXXXXXXDHDKIILQFGKVGKDMFTMDYRYPLSAFQA 381
ASVKNFQ+I D D I++QFG+V +D+FTMDY YPL A QA
Sbjct: 217 ASVKNFQIIHGN------------------DPDYIVMQFGRVAEDVFTMDYNYPLCALQA 258
Query: 382 FAICLSSFDTKLACE 396
FAI LSSFD+KLACE
Sbjct: 259 FAIALSSFDSKLACE 273
>pdb|1C8Z|A Chain A, C-Terminal Domain Of Mouse Brain Tubby Protein
Length = 265
Score = 147 bits (372), Expect = 7e-36, Method: Compositional matrix adjust.
Identities = 106/315 (33%), Positives = 145/315 (46%), Gaps = 100/315 (31%)
Query: 117 QPGPRDGTIQCFIKRDKSNL------TYHLFL--------------------------CL 144
+P P+ TI+C I RDK + TY L L +
Sbjct: 16 RPAPQGITIKCRITRDKKGMDRGMFPTYFLHLDREDGKKVFLLAGRKRKKSKTSNYLISV 75
Query: 145 SPDNISRSSSTYIGKLRSNFLGTKFIIYD--TQPPYNSAQLSPPGRSRRFYSKKVSPKVP 202
P ++SR +YIGKLRSN +GTKF +YD P S+ G R+
Sbjct: 76 DPTDLSRGGDSYIGKLRSNLMGTKFTVYDNGVNPQKASSSTLESGTLRQ----------- 124
Query: 203 TGSYNIAQVSYELNVLGTRGPRRMHCTMHSIPASALEPG-GSVPGQAELNPRSLEDSFRN 261
+A V YE NVLG +GPR+M S + PG V + + PR+ ++
Sbjct: 125 ----ELAAVCYETNVLGFKGPRKM---------SVIVPGMNMVHERVCIRPRNEHETLL- 170
Query: 262 FSKSIDVSTEFSSSRFSDIVGPRDEEDEGKDRPLILRNKAPRWHEQLQCWCLNFRGRVTV 321
+R+ +++ + + L+NK P W++ Q + LNF GRVT
Sbjct: 171 -------------ARW---------QNKNTESIIELQNKTPVWNDDTQSYVLNFHGRVTQ 208
Query: 322 ASVKNFQLIXXXXXXXXXXXXXXXXXXXXXDHDKIILQFGKVGKDMFTMDYRYPLSAFQA 381
ASVKNFQ+I D D I++QFG+V +D+FTMDY YPL A QA
Sbjct: 209 ASVKNFQIIHGN------------------DPDYIVMQFGRVAEDVFTMDYNYPLCALQA 250
Query: 382 FAICLSSFDTKLACE 396
FAI LSSFD+KLACE
Sbjct: 251 FAIALSSFDSKLACE 265
>pdb|1I7E|A Chain A, C-Terminal Domain Of Mouse Brain Tubby Protein Bound To
Phosphatidylinositol 4,5-Bis-Phosphate
Length = 265
Score = 146 bits (369), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 105/315 (33%), Positives = 145/315 (46%), Gaps = 100/315 (31%)
Query: 117 QPGPRDGTIQCFIKRDKSNL------TYHLFL--------------------------CL 144
+P P+ TI+C I RDK + TY L L +
Sbjct: 16 RPAPQGITIKCRITRDKKGMDRGMFPTYFLHLDREDGKKVFLLAGRKRKKSKTSNYLISV 75
Query: 145 SPDNISRSSSTYIGKLRSNFLGTKFIIYD--TQPPYNSAQLSPPGRSRRFYSKKVSPKVP 202
P ++SR +YIGKLRSN +GTKF +YD P S+ G R+
Sbjct: 76 DPTDLSRGGDSYIGKLRSNLMGTKFTVYDNGVNPQKASSSTLESGTLRQ----------- 124
Query: 203 TGSYNIAQVSYELNVLGTRGPRRMHCTMHSIPASALEPG-GSVPGQAELNPRSLEDSFRN 261
+A V YE NVLG +GPR+M S + PG V + + PR+ ++
Sbjct: 125 ----ELAAVCYETNVLGFKGPRKM---------SVIVPGMNMVHERVCIRPRNEHETLL- 170
Query: 262 FSKSIDVSTEFSSSRFSDIVGPRDEEDEGKDRPLILRNKAPRWHEQLQCWCLNFRGRVTV 321
+R+ +++ + + L+NK P W++ + + LNF GRVT
Sbjct: 171 -------------ARW---------QNKNTESIIELQNKTPVWNDDTESYVLNFHGRVTQ 208
Query: 322 ASVKNFQLIXXXXXXXXXXXXXXXXXXXXXDHDKIILQFGKVGKDMFTMDYRYPLSAFQA 381
ASVKNFQ+I D D I++QFG+V +D+FTMDY YPL A QA
Sbjct: 209 ASVKNFQIIHGN------------------DPDYIVMQFGRVAEDVFTMDYNYPLCALQA 250
Query: 382 FAICLSSFDTKLACE 396
FAI LSSFD+KLACE
Sbjct: 251 FAIALSSFDSKLACE 265
>pdb|2FIM|A Chain A, Structure Of The C-Terminal Domain Of Human Tubby-Like
Protein 1
pdb|2FIM|B Chain B, Structure Of The C-Terminal Domain Of Human Tubby-Like
Protein 1
Length = 276
Score = 143 bits (360), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 104/314 (33%), Positives = 141/314 (44%), Gaps = 102/314 (32%)
Query: 117 QPGPRDGTIQCFIKRDKSNL------------------------------TYHLFLCLSP 146
+P P+ T++C + RDK + T + + + P
Sbjct: 31 RPAPQGRTVRCRLTRDKKGMDRGMYPSYFLHLDTEKKVFLLAGRKRKRSKTANYLISIDP 90
Query: 147 DNISRSSSTYIGKLRSNFLGTKFIIYDT-QPPYNSAQLSPPGRSRRFYSKKVSPKVPTGS 205
N+SR +IGKLRSN LG +F ++D Q P +R YS V+ +
Sbjct: 91 TNLSRGGENFIGKLRSNLLGNRFTVFDNGQNP------------QRGYSTNVA----SLR 134
Query: 206 YNIAQVSYELNVLGTRGPRRMHCTMHSIPASALEPGGSVPGQ-AELNPRSLEDSF--RNF 262
+A V YE NVLG RGPRRM + + PG S + + PR+ D R
Sbjct: 135 QELAAVIYETNVLGFRGPRRM---------TVIIPGMSAENERVPIRPRNASDGLLVRWQ 185
Query: 263 SKSIDVSTEFSSSRFSDIVGPRDEEDEGKDRPLILRNKAPRWHEQLQCWCLNFRGRVTVA 322
+K+++ E L NK P W++ + LNF+GRVT A
Sbjct: 186 NKTLESLIE-------------------------LHNKPPVWNDDSGSYTLNFQGRVTQA 220
Query: 323 SVKNFQLIXXXXXXXXXXXXXXXXXXXXXDHDKIILQFGKVGKDMFTMDYRYPLSAFQAF 382
SVKNFQ++ D D I+LQFG+V +D FT+DYRYPL A QAF
Sbjct: 221 SVKNFQIVHAD------------------DPDYIVLQFGRVAEDAFTLDYRYPLCALQAF 262
Query: 383 AICLSSFDTKLACE 396
AI LSSFD KLACE
Sbjct: 263 AIALSSFDGKLACE 276
>pdb|3C5N|A Chain A, Structure Of Human Tulp1 In Complex With Ip3
pdb|3C5N|B Chain B, Structure Of Human Tulp1 In Complex With Ip3
Length = 246
Score = 132 bits (333), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 99/308 (32%), Positives = 136/308 (44%), Gaps = 102/308 (33%)
Query: 117 QPGPRDGTIQCFIKRDKSNL------------------------------TYHLFLCLSP 146
+P P+ T++C + RDK + T + + + P
Sbjct: 7 RPAPQGRTVRCRLTRDKKGMDRGMYPSYFLHLDTEKKVFLLAGRKRKRSKTANYLISIDP 66
Query: 147 DNISRSSSTYIGKLRSNFLGTKFIIYDT-QPPYNSAQLSPPGRSRRFYSKKVSPKVPTGS 205
N+SR +IGKLRSN LG +F ++D Q P +R YS V+ +
Sbjct: 67 TNLSRGGENFIGKLRSNLLGNRFTVFDNGQNP------------QRGYSTNVA----SLR 110
Query: 206 YNIAQVSYELNVLGTRGPRRMHCTMHSIPASALEPGGSVPGQ-AELNPRSLEDSF--RNF 262
+A V YE NVLG RGPRRM + + PG S + + PR+ D R
Sbjct: 111 QELAAVIYETNVLGFRGPRRM---------TVIIPGMSAENERVPIRPRNASDGLLVRWQ 161
Query: 263 SKSIDVSTEFSSSRFSDIVGPRDEEDEGKDRPLILRNKAPRWHEQLQCWCLNFRGRVTVA 322
+K+++ E L NK P W++ + LNF+GRVT A
Sbjct: 162 NKTLESLIE-------------------------LHNKPPVWNDDSGSYTLNFQGRVTQA 196
Query: 323 SVKNFQLIXXXXXXXXXXXXXXXXXXXXXDHDKIILQFGKVGKDMFTMDYRYPLSAFQAF 382
SVKNFQ++ D D I+LQFG+V +D FT+DYRYPL A QAF
Sbjct: 197 SVKNFQIVHAD------------------DPDYIVLQFGRVAEDAFTLDYRYPLCALQAF 238
Query: 383 AICLSSFD 390
AI LSSFD
Sbjct: 239 AIALSSFD 246
>pdb|2B64|Y Chain Y, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf1
From A Crystal Structure Of The Whole Ribosomal Complex.
This File Contains The 30s Subunit, Trnas, Mrna And
Release Factor Rf1 From A Crystal Structure Of The Whole
Ribosomal Complex". The Entire Crystal Structure
Contains One 70s Ribosome, Trnas, Mrna And Release
Factor Rf1 And Is Described In Remark 400.
pdb|3D5A|X Chain X, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of One 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes As Described In Remark 400.
pdb|3D5C|X Chain X, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400.
pdb|3MR8|V Chain V, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3mr8 Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 3ms1.
Molecule B In The Same Asymmetric Unit Is Deposited As
3mrz (50s) And 3ms0 (30s).
pdb|3MS0|V Chain V, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3ms0 Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 3mrz.
Molecule A In The Same Asymmetric Unit Is Deposited As
3mr8 (30s) And 3ms1 (50s)
Length = 354
Score = 28.5 bits (62), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 1 MSFRSIVRDVR-DGFGSLSRRSFEVRLPGHHGRGKSHGSVHELHDQPVVIQNSR 53
M F + V D G S+ FEVR PG +G K VH + PV R
Sbjct: 138 MGFETEVLDSHPTDLGGFSKVVFEVRGPGAYGTFKYESGVHRVQRVPVTETQGR 191
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: 11,701,531
Number of Sequences: 62578
Number of extensions: 465114
Number of successful extensions: 850
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 824
Number of HSP's gapped (non-prelim): 17
length of query: 396
length of database: 14,973,337
effective HSP length: 101
effective length of query: 295
effective length of database: 8,652,959
effective search space: 2552622905
effective search space used: 2552622905
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)