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= psy14161
(91 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MCA|B Chain B, Structure Of The Dom34-Hbs1 Complex And Implications For
Its Role In No-Go Decay
Length = 390
Score = 80.5 bits (197), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 40/86 (46%), Positives = 55/86 (63%), Gaps = 1/86 (1%)
Query: 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLITEGDSVRASTIRKVQXXXXXXXXXXX 60
MKL+ KNI +K+ SG + + PEE EDMWH YN++ GD ++AST+R+V
Sbjct: 1 MKLIQKNI-EKNGSGWITMCPEEPEDMWHLYNILQVGDQLKASTVRRVVKVGATGSTSGS 59
Query: 61 RVRTMLTISVESIDFDTQACVLRLKG 86
RV L I VE++DFDT+A L +KG
Sbjct: 60 RVVMKLRILVENMDFDTKAAQLHIKG 85
>pdb|3OBY|A Chain A, Crystal Structure Of Archaeoglobus Fulgidus Pelota
Reveals Inter- Domain Structural Plasticity
pdb|3OBY|B Chain B, Crystal Structure Of Archaeoglobus Fulgidus Pelota
Reveals Inter- Domain Structural Plasticity
Length = 352
Score = 47.8 bits (112), Expect = 2e-06, Method: Composition-based stats.
Identities = 29/86 (33%), Positives = 44/86 (51%), Gaps = 3/86 (3%)
Query: 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLITEGDSVRASTIRKVQXXXXXXXXXXX 60
M++V +N+ +D G + L+PE +D+WH +I +GD V A+T R Q
Sbjct: 1 MQIVEENL--RDNEGEIKLIPETLDDLWHLRFIIEKGDVVFATTKRASQSSDKLRSDKEM 58
Query: 61 RVRTMLTISVESIDFDTQACVLRLKG 86
V L I VE ++F A LR+ G
Sbjct: 59 -VTVRLGIEVEKVEFHRFANRLRVSG 83
>pdb|3J15|A Chain A, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 357
Score = 42.4 bits (98), Expect = 8e-05, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 8 INDKDKSGVVALVPEESEDMWHAYNLITEGDSVRASTIRK-VQXXXXXXXXXXXRVRTML 66
+ +K K G V + E +D+WH Y++I GD V A T+RK Q + L
Sbjct: 4 LEEKPKEGKVKVKAETLDDLWHLYHIIDPGDIVYAKTLRKQAQRADSLRAEKVEVIPVFL 63
Query: 67 TISVESIDFDTQACVLRLKG 86
+ E I+F A +R+ G
Sbjct: 64 GVQAEKINFHKFANQVRVTG 83
>pdb|2QI2|A Chain A, Crystal Structure Of The Thermoplasma Acidophilum Pelota
Protein
Length = 347
Score = 36.6 bits (83), Expect = 0.004, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 22 EESEDMWHAYNLITEGDSVRASTIRKVQXXX-XXXXXXXXRVRTMLTISVESIDFDTQAC 80
E +D+W+ N+++EGD V A T R+V+ R+ + + VE I+F
Sbjct: 18 ESLDDLWYLRNILSEGDEVSAITFRRVEESADVQRSRERERIPITIRLKVEKIEFQDFDN 77
Query: 81 VLRLKG 86
LR+ G
Sbjct: 78 RLRILG 83
>pdb|3AGJ|B Chain B, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|D Chain D, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|F Chain F, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|H Chain H, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
Length = 358
Score = 35.0 bits (79), Expect = 0.010, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 33/75 (44%), Gaps = 4/75 (5%)
Query: 12 DKSGVVALVPEESEDMWHAYNLITEGDSVRASTIRKVQXXXXXXXXXXXRVRTMLTISVE 71
+K +V L PE ED+W + GD VR T R V RV L I ++
Sbjct: 10 NKRRIVRLRPESEEDLWLLRITLRPGDVVRKRTSRDVP----VGSGRKERVVMTLRIRLD 65
Query: 72 SIDFDTQACVLRLKG 86
SI+F LR+ G
Sbjct: 66 SIEFQPFTGKLRISG 80
>pdb|2VGM|A Chain A, Structure Of Yeast Dom34 : A Protein Related To
Translation Termination Factor Erf1 And Involved In
No-Go Decay.
pdb|3IZQ|0 Chain 0, Structure Of The Dom34-Hbs1-Gdpnp Complex Bound To A
Translating Ribosome
pdb|3J16|A Chain A, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 386
Score = 30.0 bits (66), Expect = 0.36, Method: Composition-based stats.
Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 1 MKLVHKNINDKDKSG-VVALVPEESEDMWHAYNLITEGDSVRASTIRKVQXXXXXXXXXX 59
MK++ + +K G V+ L+PE+ ED++ Y ++ + D + +K
Sbjct: 1 MKVISLKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDELIFK--KKFTSKLDEAGKKK 58
Query: 60 XRVRTMLTISVESIDFDTQACVLRLKG 86
L I V S DFD + L+ KG
Sbjct: 59 STDLVKLKIKVISEDFDMKDEYLKYKG 85
>pdb|2VGN|A Chain A, Structure Of Yeast Dom34 : A Protein Related To
Translation Termination Factor Erf1 And Involved In
No-go Decay.
pdb|2VGN|B Chain B, Structure Of Yeast Dom34 : A Protein Related To
Translation Termination Factor Erf1 And Involved In
No-go Decay
Length = 386
Score = 28.5 bits (62), Expect = 1.1, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 2/72 (2%)
Query: 15 GVVALVPEESEDMWHAYNLITEGDSVRASTIRKVQXXXXXXXXXXXRVRTMLTISVESID 74
V+ L+PE+ ED++ Y ++ + D + +K L I V S D
Sbjct: 16 AVITLLPEDKEDLFTVYQIVDKDDELIFK--KKFTSKLDEAGKKKSTDLVKLKIKVISED 73
Query: 75 FDTQACVLRLKG 86
FD + L+ KG
Sbjct: 74 FDXKDEYLKYKG 85
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
0.318 0.132 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,143,077
Number of Sequences: 62578
Number of extensions: 52543
Number of successful extensions: 77
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 70
Number of HSP's gapped (non-prelim): 7
length of query: 91
length of database: 14,973,337
effective HSP length: 58
effective length of query: 33
effective length of database: 11,343,813
effective search space: 374345829
effective search space used: 374345829
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)