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= psy5391
(157 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3J21|T Chain T, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 86
Score = 26.6 bits (57), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 37 NVVEFHVPLAMTNHDIKNYLEKIYNVTVKHV 67
N + F V T DIK +E+I+NV V+ V
Sbjct: 24 NKLTFIVDRRATKQDIKRAVEEIFNVKVEKV 54
>pdb|3TB9|A Chain A, Structure Of Yeast Ribonucleotide Reductase 1 Q288a With
Amppnp And Cdp
pdb|3TBA|A Chain A, Structure Of Yeast Ribonucleotide Reductase 1 Q288a With
Dgtp And Adp
Length = 888
Score = 26.2 bits (56), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 88 MTLQPTRTVSTSLFESYLSSGIITSAKRLMKCIKLQNGLFIKINPIGTKDLLVLGVW 144
+T+ P T STS Y + M ++ +G F +NP +DL+ LG+W
Sbjct: 601 LTMAPMPTASTSQILGY--NECFEPVTSNMYSRRVLSGEFQVVNPYLLRDLVDLGIW 655
>pdb|3S8A|A Chain A, Structure Of Yeast Ribonucleotide Reductase R293a With
Dgtp
pdb|3S8C|A Chain A, Structure Of Yeast Ribonucleotide Reductase 1 R293a With
Amppnp And Cdp
Length = 888
Score = 26.2 bits (56), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 88 MTLQPTRTVSTSLFESYLSSGIITSAKRLMKCIKLQNGLFIKINPIGTKDLLVLGVW 144
+T+ P T STS Y + M ++ +G F +NP +DL+ LG+W
Sbjct: 601 LTMAPMPTASTSQILGY--NECFEPVTSNMYSRRVLSGEFQVVNPYLLRDLVDLGIW 655
>pdb|1ZYZ|A Chain A, Structures Of Yeast Ribonucloetide Reductase I
pdb|1ZYZ|B Chain B, Structures Of Yeast Ribonucloetide Reductase I
pdb|1ZZD|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2CVS|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2CVT|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2CVU|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2CVV|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2CVW|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2CVX|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2CVY|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2EUD|A Chain A, Structures Of Yeast Ribonucleotide Reductase I Complexed
With Ligands And Subunit Peptides
pdb|2ZLF|A Chain A, The Structural Basis For Peptidomimetic Inhibition Of
Eukaryotic Ribonucleotide Reductase
pdb|2ZLG|A Chain A, The Structual Basis For Peptidomimetic Inhibition Of
Eukaryotic Ribonucleotide Reductase
pdb|3K8T|A Chain A, Structure Of Eukaryotic Rnr Large Subunit R1 Complexed
With Designed Adp Analog Compound
pdb|3PAW|A Chain A, Low Resolution X-Ray Crystal Structure Of Yeast Rnr1p With
Datp Bound In The A-Site
pdb|3PAW|B Chain B, Low Resolution X-Ray Crystal Structure Of Yeast Rnr1p With
Datp Bound In The A-Site
pdb|3PAW|C Chain C, Low Resolution X-Ray Crystal Structure Of Yeast Rnr1p With
Datp Bound In The A-Site
pdb|3PAW|D Chain D, Low Resolution X-Ray Crystal Structure Of Yeast Rnr1p With
Datp Bound In The A-Site
pdb|3S87|A Chain A, Structure Of Yeast Ribonucleotide Reductase 1 With Dgtp
And Adp
pdb|3S8B|A Chain A, Structure Of Yeast Ribonucleotide Reductase 1 With Amppnp
And Cdp
pdb|3RSR|A Chain A, Crystal Structure Of 5-Nitp Inhibition Of Yeast
Ribonucleotide Reductase
Length = 888
Score = 26.2 bits (56), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 88 MTLQPTRTVSTSLFESYLSSGIITSAKRLMKCIKLQNGLFIKINPIGTKDLLVLGVW 144
+T+ P T STS Y + M ++ +G F +NP +DL+ LG+W
Sbjct: 601 LTMAPMPTASTSQILGY--NECFEPVTSNMYSRRVLSGEFQVVNPYLLRDLVDLGIW 655
>pdb|1BVU|A Chain A, Glutamate Dehydrogenase From Thermococcus Litoralis
pdb|1BVU|B Chain B, Glutamate Dehydrogenase From Thermococcus Litoralis
pdb|1BVU|C Chain C, Glutamate Dehydrogenase From Thermococcus Litoralis
pdb|1BVU|D Chain D, Glutamate Dehydrogenase From Thermococcus Litoralis
pdb|1BVU|E Chain E, Glutamate Dehydrogenase From Thermococcus Litoralis
pdb|1BVU|F Chain F, Glutamate Dehydrogenase From Thermococcus Litoralis
Length = 418
Score = 26.2 bits (56), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 10/66 (15%)
Query: 35 PPNVVEFHVPLAMTNHDIK---------NYLEKIYNVTVK-HVESTLENATSMAEWVSWL 84
P +VE +P+ M + +K N+ ++ H E TL ++A W++W
Sbjct: 33 PQRIVEVSIPVEMDDGSVKVFTGFRVQYNWARGPTKGGIRWHPEETLSTVKALAAWMTWK 92
Query: 85 AFQMTL 90
M L
Sbjct: 93 TAVMDL 98
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 0.134 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,456,038
Number of Sequences: 62578
Number of extensions: 154986
Number of successful extensions: 397
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 392
Number of HSP's gapped (non-prelim): 9
length of query: 157
length of database: 14,973,337
effective HSP length: 91
effective length of query: 66
effective length of database: 9,278,739
effective search space: 612396774
effective search space used: 612396774
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: 47 (22.7 bits)