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= psy9255
(127 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3J2K|6 Chain 6, Cryo-Em Structure Of The Mammalian Erf1-Erf3-Associated
Termination Complex
Length = 411
Score = 127 bits (319), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 58/75 (77%), Positives = 67/75 (89%)
Query: 41 IGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHL 100
IG+YFDEISQDTGKYCFGVEDTL+ALE+G+VE LI +ENLDI RYVL T E+++L+L
Sbjct: 278 IGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYL 337
Query: 101 TPEQEKDKSHFTDKE 115
TPEQEKDKSHFTDKE
Sbjct: 338 TPEQEKDKSHFTDKE 352
>pdb|3E1Y|A Chain A, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|B Chain B, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|C Chain C, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|D Chain D, Crystal Structure Of Human Erf1ERF3 COMPLEX
Length = 451
Score = 127 bits (319), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 58/75 (77%), Positives = 67/75 (89%)
Query: 41 IGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHL 100
IG+YFDEISQDTGKYCFGVEDTL+ALE+G+VE LI +ENLDI RYVL T E+++L+L
Sbjct: 301 IGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYL 360
Query: 101 TPEQEKDKSHFTDKE 115
TPEQEKDKSHFTDKE
Sbjct: 361 TPEQEKDKSHFTDKE 375
>pdb|1DT9|A Chain A, The Crystal Structure Of Human Eukaryotic Release Factor
Erf1-Mechanism Of Stop Codon Recognition And
Peptidyl-Trna Hydrolysis
Length = 437
Score = 127 bits (319), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 58/75 (77%), Positives = 67/75 (89%)
Query: 41 IGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHL 100
IG+YFDEISQDTGKYCFGVEDTL+ALE+G+VE LI +ENLDI RYVL T E+++L+L
Sbjct: 287 IGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYL 346
Query: 101 TPEQEKDKSHFTDKE 115
TPEQEKDKSHFTDKE
Sbjct: 347 TPEQEKDKSHFTDKE 361
>pdb|2KTU|A Chain A, Human Erf1 C-Domain, "closed" Conformer
pdb|2KTV|A Chain A, Human Erf1 C-Domain, "open" Conformer
Length = 170
Score = 125 bits (314), Expect = 5e-30, Method: Compositional matrix adjust.
Identities = 58/75 (77%), Positives = 67/75 (89%)
Query: 41 IGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHL 100
IG+YFDEISQDTGKYCFGVEDTL+ALE+G+VE LI +ENLDI RYVL T E+++L+L
Sbjct: 12 IGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYL 71
Query: 101 TPEQEKDKSHFTDKE 115
TPEQEKDKSHFTDKE
Sbjct: 72 TPEQEKDKSHFTDKE 86
>pdb|3E20|C Chain C, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|B Chain B, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|H Chain H, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|K Chain K, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
Length = 441
Score = 73.9 bits (180), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 36/69 (52%), Positives = 50/69 (72%), Gaps = 1/69 (1%)
Query: 41 IGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHL 100
I ++FDEIS D+GKYCFGV DT+ AL+ G+VETL+C+ +LD+ RY KN S + ++
Sbjct: 292 IQRFFDEISLDSGKYCFGVVDTMNALQEGAVETLLCFADLDMIRYEFKN-SEGNPVITYM 350
Query: 101 TPEQEKDKS 109
T EQE+ S
Sbjct: 351 TKEQEEKDS 359
>pdb|3AGK|A Chain A, Crystal Structure Of Archaeal Translation Termination
Factor, Arf1
pdb|3VMF|B Chain B, Archaeal Protein
Length = 373
Score = 32.3 bits (72), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 48 ISQDTGKYCFGVEDTLRALELGSVETLICWENL-DIQRYVLKNHSTSEDRVLHLTPEQEK 106
+++ TG +G +D ALE+G+V+TL+ E+ D++ +V K S+ + + PE
Sbjct: 293 LAKGTGMIVYGEKDVEAALEMGAVKTLLIHESREDLEEWVEKAKSSGAQVI--VVPESLA 350
Query: 107 DKSHF 111
+ F
Sbjct: 351 EAEWF 355
>pdb|3IR9|A Chain A, C-Terminal Domain Of Peptide Chain Release Factor From
Methanosarcina Mazei.
pdb|3IR9|B Chain B, C-Terminal Domain Of Peptide Chain Release Factor From
Methanosarcina Mazei
Length = 166
Score = 31.2 bits (69), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 39 NNIGKYFDEISQDTGKYCFGVEDTLRA-LELGSVETLICWENLDIQRYVLK 88
N + +F E+ D+GK +G E +RA LE+ SV+ L+ E+L +R K
Sbjct: 31 NAVRDFFKELIADSGKVAYG-ESQVRANLEINSVDVLLLSEDLRAERVTTK 80
>pdb|3J15|A Chain A, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 357
Score = 28.9 bits (63), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 20/91 (21%), Positives = 42/91 (46%), Gaps = 13/91 (14%)
Query: 3 KYFKDKHKYLGRYPAVQDL-----VGKYEILNY--------ERDMDLLFNNIGKYFDEIS 49
K+ K+K+ L + ++D G YE++ E + + K + I+
Sbjct: 216 KFLKEKYPELAKKVVIEDTSVTGRTGIYEVIKRGVVDRVYQENRVAKEVQLVEKVLENIA 275
Query: 50 QDTGKYCFGVEDTLRALELGSVETLICWENL 80
++ G +G+++ A+ G+VETL+ + L
Sbjct: 276 RNNGLVAYGLKEVEEAVNYGAVETLLVLDEL 306
>pdb|3MCA|B Chain B, Structure Of The Dom34-Hbs1 Complex And Implications For
Its Role In No-Go Decay
Length = 390
Score = 28.5 bits (62), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 25/40 (62%)
Query: 41 IGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENL 80
+ K++D +++D K +G L+A ELG++ L+ ++L
Sbjct: 278 LNKFYDVMNEDDRKAWYGPNHVLKAFELGAIGELLISDSL 317
>pdb|3OBW|A Chain A, Crystal Structure Of Two Archaeal Pelotas Reveal
Inter-Domain Structural Plasticity
Length = 364
Score = 27.3 bits (59), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 56 CFGVEDTLRALELGSVETLICWENL 80
+G+E A+E+G+VET++ E+L
Sbjct: 287 TYGLEQVKNAIEMGAVETVLVIEDL 311
>pdb|4F3T|A Chain A, Human Argonaute-2 - Mir-20a Complex
Length = 861
Score = 26.9 bits (58), Expect = 2.6, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 3 KYFKDKHKYLGRYP 16
+YFKD+HK + RYP
Sbjct: 312 QYFKDRHKLVLRYP 325
>pdb|4EI1|A Chain A, Crystal Structure Of Human Argonaute2
pdb|4EI3|A Chain A, Crystal Structure Of Human Argonaute2
Length = 859
Score = 26.9 bits (58), Expect = 2.7, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 3 KYFKDKHKYLGRYP 16
+YFKD+HK + RYP
Sbjct: 310 QYFKDRHKLVLRYP 323
>pdb|2BO1|A Chain A, Crystal Structure Of A Hybrid Ribosomal Protein L30e
With Surface Residues From T. Celer, And Core Residues
From Yeast
Length = 101
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 51 DTGKYCFGVEDTLRALELGSVETLICWEN 79
D+GKY G T+++L++G + +I N
Sbjct: 13 DSGKYTLGYRKTVQSLKMGGSKLIIIARN 41
>pdb|1GL4|A Chain A, Nidogen-1 G2PERLECAN IG3 COMPLEX
Length = 285
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 68 LGSVETLICWENLDIQRYVLKNHSTS 93
+GS + + +EN D+ YV+ NH S
Sbjct: 62 VGSSQVPVVFENTDLHSYVVMNHGRS 87
>pdb|1H4U|A Chain A, Domain G2 Of Mouse Nidogen-1
Length = 265
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 68 LGSVETLICWENLDIQRYVLKNHSTS 93
+GS + + +EN D+ YV+ NH S
Sbjct: 48 VGSSQVPVVFENTDLHSYVVMNHGRS 73
>pdb|1A2O|A Chain A, Structural Basis For Methylesterase Cheb Regulation By A
Phosphorylation-Activated Domain
pdb|1A2O|B Chain B, Structural Basis For Methylesterase Cheb Regulation By A
Phosphorylation-Activated Domain
Length = 349
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 18/25 (72%), Gaps = 3/25 (12%)
Query: 48 ISQDTGKYCFGVEDTLRALELGSVE 72
+S TGK G E TLRALELG+++
Sbjct: 82 VSSLTGK---GSEVTLRALELGAID 103
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
0.319 0.138 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,942,349
Number of Sequences: 62578
Number of extensions: 159340
Number of successful extensions: 447
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 432
Number of HSP's gapped (non-prelim): 20
length of query: 127
length of database: 14,973,337
effective HSP length: 87
effective length of query: 40
effective length of database: 9,529,051
effective search space: 381162040
effective search space used: 381162040
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)