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= 006173
(658 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4HB5|A Chain A, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or267.
pdb|4HB5|B Chain B, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or267
Length = 169
Score = 35.8 bits (81), Expect = 0.073, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 40/87 (45%), Gaps = 17/87 (19%)
Query: 101 NFARDEGSEYMEYAVSTGKLNLITTLMGYNEELPNIKVEKKDDPNIKDEEKDDLLPVHMA 160
N + +G + YA G ++E+ + + K DPN KD D P+H A
Sbjct: 31 NASDSDGRTPLHYAAENG-----------HKEIVKLLLSKGADPNAKDS--DGRTPLHYA 77
Query: 161 AKAGKRDAVRHLLPKTREP----LDGR 183
A+ G ++ V+ LL K +P DGR
Sbjct: 78 AENGHKEIVKLLLSKGADPNAKDSDGR 104
Score = 35.0 bits (79), Expect = 0.12, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 17/87 (19%)
Query: 101 NFARDEGSEYMEYAVSTGKLNLITTLMGYNEELPNIKVEKKDDPNIKDEEKDDLLPVHMA 160
N +G + YA G ++E+ + + K DPN KD D P+H A
Sbjct: 64 NAKDSDGRTPLHYAAENG-----------HKEIVKLLLSKGADPNAKDS--DGRTPLHYA 110
Query: 161 AKAGKRDAVRHLLPKTREP----LDGR 183
A+ G ++ V+ LL K +P DGR
Sbjct: 111 AENGHKEIVKLLLSKGADPNTSDSDGR 137
>pdb|3BK7|A Chain A, Structure Of The Complete Abce1RNAASE-L Inhibitor Protein
From Pyrococcus Abysii
Length = 607
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 27/122 (22%), Positives = 56/122 (45%), Gaps = 13/122 (10%)
Query: 268 GGDLEKQLSVTSKIQLKKFFLQKIPSAFGSLRQKLKFVLWNNLMELAPSIKSIRDAKIIH 327
GG+L++ + ++ F+ PS++ +RQ+LK + + LA K++ ++
Sbjct: 231 GGELQRVAIAAALLRKAHFYFFDEPSSYLDIRQRLK--VARVIRRLANEGKAV----LVV 284
Query: 328 EQTLEILRIMCAGAVDILNTHEEAQNVFKKPMFKAARLGIYEIVMGIMNS----YFPWSL 383
E L +L + + + ++ +F KP K R GI E + G + + P+ +
Sbjct: 285 EHDLAVLDYL-SDVIHVVYGEPGVYGIFSKP--KGTRNGINEFLQGYLKDENVRFRPYEI 341
Query: 384 EF 385
F
Sbjct: 342 RF 343
>pdb|3J15|B Chain B, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 593
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 27/122 (22%), Positives = 56/122 (45%), Gaps = 13/122 (10%)
Query: 268 GGDLEKQLSVTSKIQLKKFFLQKIPSAFGSLRQKLKFVLWNNLMELAPSIKSIRDAKIIH 327
GG+L++ + ++ F+ PS++ +RQ+LK + + LA K++ ++
Sbjct: 217 GGELQRVAIAAALLRKAHFYFFDEPSSYLDIRQRLK--VARVIRRLANEGKAV----LVV 270
Query: 328 EQTLEILRIMCAGAVDILNTHEEAQNVFKKPMFKAARLGIYEIVMGIMNS----YFPWSL 383
E L +L + + + ++ +F KP K R GI E + G + + P+ +
Sbjct: 271 EHDLAVLDYL-SDVIHVVYGEPGVYGIFSKP--KGTRNGINEFLQGYLKDENVRFRPYEI 327
Query: 384 EF 385
F
Sbjct: 328 RF 329
>pdb|4HQD|A Chain A, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or265.
pdb|4HQD|B Chain B, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or265
Length = 169
Score = 30.8 bits (68), Expect = 2.7, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 13/75 (17%)
Query: 101 NFARDEGSEYMEYAVSTGKLNLITTLMGYNEELPNIKVEKKDDPNIKDEEKDDLLPVHMA 160
N + +G + YA G ++E+ + + K D N KD D P+H A
Sbjct: 31 NASDSDGRTPLHYAAKEG-----------HKEIVKLLISKGADVNAKDS--DGRTPLHYA 77
Query: 161 AKAGKRDAVRHLLPK 175
AK G ++ V+ L+ K
Sbjct: 78 AKEGHKEIVKLLISK 92
Score = 30.4 bits (67), Expect = 3.6, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 12/62 (19%)
Query: 130 NEELPNIKVEKKDDPNIKDEEKDDLLPVHMAAKAGKRDAVRHLLPK----------TREP 179
++E+ + + K D N KD D P+H AAK G ++ V+ L+ K R P
Sbjct: 82 HKEIVKLLISKGADVNAKDS--DGRTPLHYAAKEGHKEIVKLLISKGADVNTSDSDGRTP 139
Query: 180 LD 181
LD
Sbjct: 140 LD 141
>pdb|1MX4|A Chain A, Structure Of P18ink4c (F82q)
pdb|1MX4|B Chain B, Structure Of P18ink4c (F82q)
Length = 168
Score = 30.8 bits (68), Expect = 2.8, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 13/63 (20%)
Query: 114 AVSTGKLNLITTLMGYNEELPNIKVEKKDDPNIKDEEKDDLLPVHMAAKAGKRDAVRHLL 173
A G+L+ + TL+ E + D NI+D E + LP+H+AAK G V L+
Sbjct: 77 AARAGQLDTLQTLL-----------EFQADVNIEDNEGN--LPLHLAAKEGHLRVVEFLV 123
Query: 174 PKT 176
T
Sbjct: 124 KHT 126
>pdb|1MX6|A Chain A, Structure Of P18ink4c (F92n)
pdb|1MX6|B Chain B, Structure Of P18ink4c (F92n)
Length = 168
Score = 30.4 bits (67), Expect = 3.7, Method: Composition-based stats.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 138 VEKKDDPNIKDEEKDDLLPVHMAAKAGKRDAVRHLLPKT 176
+E + D NI+D E + LP+H+AAK G V L+ T
Sbjct: 90 LENQADVNIEDNEGN--LPLHLAAKEGHLRVVEFLVKHT 126
>pdb|1S70|B Chain B, Complex Between Protein Ser/thr Phosphatase-1 (delta) And
The Myosin Phosphatase Targeting Subunit 1 (mypt1)
Length = 299
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 111 MEYAVSTGKLNLITTLMGYNEELPNIKVEKKDDPNIKDEEKDDLLPVHMAAKAGKRDAVR 170
+ +A S G + GY E L + ++ + D NIKD D P+H AA GK +A R
Sbjct: 193 VRHAKSGGTALHVAAAKGYTEVLK-LLIQARYDVNIKD--YDGWTPLHAAAHWGKEEACR 249
Query: 171 HLL 173
L+
Sbjct: 250 ILV 252
>pdb|2PK9|A Chain A, Structure Of The Pho85-pho80 Cdk-cyclin Complex Of The
Phosphate-responsive Signal Transduction Pathway
pdb|2PK9|C Chain C, Structure Of The Pho85-pho80 Cdk-cyclin Complex Of The
Phosphate-responsive Signal Transduction Pathway
pdb|2PMI|A Chain A, Structure Of The Pho85-Pho80 Cdk-Cyclin Complex Of The
Phosphate- Responsive Signal Transduction Pathway With
Bound Atp-Gamma-S
pdb|2PMI|C Chain C, Structure Of The Pho85-Pho80 Cdk-Cyclin Complex Of The
Phosphate- Responsive Signal Transduction Pathway With
Bound Atp-Gamma-S
Length = 317
Score = 29.6 bits (65), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 30/93 (32%), Positives = 39/93 (41%), Gaps = 29/93 (31%)
Query: 119 KLNLITTLMGY-NEEL-PNIKVEKKDDPNIKDEEKDDLLPVHMAAKAGKRDAVRHLLPKT 176
+L LI +MG NE L P++ K +PNI+ DL V L P T
Sbjct: 217 QLKLIFDIMGTPNESLWPSVTKLPKYNPNIQQRPPRDLRQV--------------LQPHT 262
Query: 177 REPLDGRQGFVLLKFLIDSNLFDMALALLKCHP 209
+EPLDG NL D LL+ +P
Sbjct: 263 KEPLDG-------------NLMDFLHGLLQLNP 282
>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 = 29.3 bits (64), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 33/131 (25%), Positives = 58/131 (44%), Gaps = 27/131 (20%)
Query: 142 DDPNIKDEEKDDLLPVHMAAKAGKRDAVRHLLPKTREPLDGRQGFVLLK--------FLI 193
DDP +K+ K + + +A +++ RHLLPK +P+D R V ++ L
Sbjct: 66 DDPELKEMAKAEREALLARKEALEKELERHLLPK--DPMDERDAIVEIRAGTGGEEAALF 123
Query: 194 DSNLFDMAL----------ALLKCHPMIARADIGETGKILESLSKRPKAFASGSRLGSWK 243
+LF+M L +L HP D+G K++ + + P A+ +
Sbjct: 124 ARDLFNMYLRFAEEMGFETEVLDSHP----TDLGGFSKVVFEV-RGPGAYGTFKYESGVH 178
Query: 244 RLLYQWIPIQE 254
R+ Q +P+ E
Sbjct: 179 RV--QRVPVTE 187
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 0.137 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,419,736
Number of Sequences: 62578
Number of extensions: 740525
Number of successful extensions: 1571
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1564
Number of HSP's gapped (non-prelim): 13
length of query: 658
length of database: 14,973,337
effective HSP length: 105
effective length of query: 553
effective length of database: 8,402,647
effective search space: 4646663791
effective search space used: 4646663791
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: 55 (25.8 bits)