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= psy14481
(179 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1G9L|A Chain A, Solution Structure Of The Pabc Domain Of Human Poly(A)
Binding Protein
Length = 144
Score = 126 bits (316), Expect = 7e-30, Method: Compositional matrix adjust.
Identities = 61/74 (82%), Positives = 69/74 (93%)
Query: 88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
AVHVQGQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct: 44 AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 103
Query: 148 MLEHNESLKSKVEE 161
MLE ESL+SKV+E
Sbjct: 104 MLESPESLRSKVDE 117
>pdb|2RQG|B Chain B, Structure Of Gspt1ERF3A-Pabc
pdb|2RQH|B Chain B, Structure Of Gspt1ERF3A-Pabc
Length = 83
Score = 114 bits (286), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 56/69 (81%), Positives = 64/69 (92%)
Query: 93 GQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHN 152
GQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE
Sbjct: 1 GQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESP 60
Query: 153 ESLKSKVEE 161
ESL+SKV+E
Sbjct: 61 ESLRSKVDE 69
>pdb|3PTH|A Chain A, The Pabc1 Mlle Domain Bound To The Variant Pam2 Motif Of
Larp4b
Length = 82
Score = 110 bits (274), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 54/67 (80%), Positives = 62/67 (92%)
Query: 95 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNES 154
EPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE ES
Sbjct: 4 EPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPES 63
Query: 155 LKSKVEE 161
L+SKV+E
Sbjct: 64 LRSKVDE 70
>pdb|1JGN|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of Human
Poly(A)-Binding Protein In Complex With The Peptide From
Paip2
pdb|1JH4|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of Human
Poly(A)-Binding Protein In Complex With The Peptide From
Paip1
Length = 98
Score = 109 bits (273), Expect = 7e-25, Method: Compositional matrix adjust.
Identities = 53/66 (80%), Positives = 61/66 (92%)
Query: 96 PLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESL 155
PLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE ESL
Sbjct: 6 PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESL 65
Query: 156 KSKVEE 161
+SKV+E
Sbjct: 66 RSKVDE 71
>pdb|3KUS|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUS|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUT|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(a)-binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUT|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(a)-binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KTP|A Chain A, Structural Basis Of Gw182 Recognition By Poly(a)-binding
Protein
pdb|3KTR|A Chain A, Structural Basis Of Ataxin-2 Recognition By
Poly(A)-Binding
pdb|3KUI|A Chain A, Crystal Structure Of C-Terminal Domain Of Pabpc1 In
Complex Binding Region Of Erf3a
pdb|3KUJ|A Chain A, Crystal Structure Of C-Terminal Domain Of Pabpc1 In
Complex With Binding Region Of Erf3a
pdb|3PKN|A Chain A, Crystal Structure Of Mlle Domain Of Poly(A) Binding
Protein In Complex With Pam2 Motif Of La-Related Protein
4 (Larp4)
Length = 88
Score = 108 bits (271), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 53/66 (80%), Positives = 61/66 (92%)
Query: 96 PLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESL 155
PLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE ESL
Sbjct: 6 PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESL 65
Query: 156 KSKVEE 161
+SKV+E
Sbjct: 66 RSKVDE 71
>pdb|3KUR|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|C Chain C, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|D Chain D, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|E Chain E, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|F Chain F, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|G Chain G, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|H Chain H, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
Length = 79
Score = 108 bits (269), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 53/66 (80%), Positives = 61/66 (92%)
Query: 96 PLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESL 155
PLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE ESL
Sbjct: 6 PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESL 65
Query: 156 KSKVEE 161
+SKV+E
Sbjct: 66 RSKVDE 71
>pdb|2X04|A Chain A, Crystal Structure Of The Pabc-Tnrc6c Complex
pdb|2X04|B Chain B, Crystal Structure Of The Pabc-Tnrc6c Complex
Length = 80
Score = 105 bits (263), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 52/65 (80%), Positives = 60/65 (92%)
Query: 97 LTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLK 156
LT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE ESL+
Sbjct: 6 LTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLR 65
Query: 157 SKVEE 161
SKV+E
Sbjct: 66 SKVDE 70
>pdb|4IVE|A Chain A, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
pdb|4IVE|B Chain B, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
pdb|4IVE|C Chain C, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
pdb|4IVE|D Chain D, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
Length = 98
Score = 102 bits (254), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 51/70 (72%), Positives = 59/70 (84%)
Query: 92 QGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEH 151
QGQE LT++ LA+A PQ+QKQ LGERLFPLIQ +P LAGKITG LLEIDN+ELLY LE
Sbjct: 2 QGQETLTASRLASAPPQKQKQXLGERLFPLIQAXHPTLAGKITGXLLEIDNSELLYXLES 61
Query: 152 NESLKSKVEE 161
ESL+SKV+E
Sbjct: 62 PESLRSKVDE 71
>pdb|2DYD|A Chain A, Solution Structure Of The Pabc Domain From Triticum
Aevestium Poly(A)-Binding Protein
Length = 85
Score = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 29/63 (46%), Positives = 47/63 (74%)
Query: 99 STMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSK 158
++ LA + P+ Q+ MLGE L+PL+ ++ + A K+TGMLLE+D E+L++LE ++LK+K
Sbjct: 11 ASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLESPDALKAK 70
Query: 159 VEE 161
V E
Sbjct: 71 VAE 73
>pdb|1NMR|A Chain A, Solution Structure Of C-Terminal Domain From Trypanosoma
Cruzi Poly(A)-Binding Protein
Length = 85
Score = 61.6 bits (148), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 34/70 (48%), Positives = 47/70 (67%), Gaps = 2/70 (2%)
Query: 92 QGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEH 151
QGQ ST+LA P++QK +LGERL+ I + P A K+TGMLLE+DN E+L +L+
Sbjct: 7 QGQN--LSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDT 64
Query: 152 NESLKSKVEE 161
L +KV+E
Sbjct: 65 PGLLDAKVQE 74
>pdb|3NTW|A Chain A, Structure Of The Mlle Domain Of Edd In Complex With A Pam2
Peptide From Paip1
pdb|3NTW|C Chain C, Structure Of The Mlle Domain Of Edd In Complex With A Pam2
Peptide From Paip1
Length = 65
Score = 53.1 bits (126), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 28/52 (53%), Positives = 38/52 (73%)
Query: 110 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 161
+Q LGERL+P +Q M P A KITGMLLE+ A+LL +L +SL+++VEE
Sbjct: 6 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVEE 57
>pdb|1I2T|A Chain A, X-Ray Structure Of The Human Hyperplastic Discs Protein:
An Ortholog Of The C-Terminal Domain Of Poly(A)-Binding
Protein
Length = 61
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/52 (51%), Positives = 38/52 (73%)
Query: 110 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 161
+Q LGERL+P +Q M P A KITGMLLE+ A+LL +L +SL+++V+E
Sbjct: 1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDE 52
>pdb|1IFW|A Chain A, Solution Structure Of C-Terminal Domain Of Poly(A) Binding
Protein From Saccharomyces Cerevisiae
Length = 92
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 108 QEQKQMLGERLFPLI--QRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 161
Q+Q+Q LGE+L+ + + E AGKITGM+L++ E+ +LE +E + +E
Sbjct: 18 QKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKE 73
>pdb|2H1Y|A Chain A, Crystal Structure Of Malonyl-Coa:acyl Carrier Protein
Transacylase (Mcat) From Helicobacter Pylori
pdb|2H1Y|B Chain B, Crystal Structure Of Malonyl-Coa:acyl Carrier Protein
Transacylase (Mcat) From Helicobacter Pylori
Length = 321
Score = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 26/51 (50%)
Query: 28 GGVNVAMISGISFGALALVTLFGAVSFIMYRRYRWNKPQTLSDKCSNPDSS 78
GG+ G S G ++ V+L GA+ F + + + + + C+N D+S
Sbjct: 93 GGLKPVFALGHSLGEVSAVSLSGALDFEKALKLTHQRGKMMQEACANKDAS 143
>pdb|3MCQ|A Chain A, Crystal Structure Of Thiamine-Monophosphate Kinase
(Mfla_0573) From Methylobacillus Flagellatus Kt At 1.91
A Resolution
Length = 319
Score = 26.6 bits (57), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 42/81 (51%), Gaps = 15/81 (18%)
Query: 78 SGYIDDSTLRAVHVQGQEPLTSTMLAAA-----QPQEQKQMLGERLFPLIQRMYPELAGK 132
SG + D+ L +QG+ PL+ T LAA QPQ + +LG+ L R A
Sbjct: 155 SGPLGDAALALAAIQGRYPLSDTELAACGKALHQPQP-RVVLGQAL-----RGLAHSALD 208
Query: 133 ITGMLLEIDNAELLYMLEHNE 153
I+ LL A+L ++LEH++
Sbjct: 209 ISDGLL----ADLGHILEHSQ 225
>pdb|4IQ1|A Chain A, Crystal Structure Of Glutathione S-transferase Mha_0454
(target Efi- 507015) From Mannheimia Haemolytica,
Substrate-free
pdb|4IQ1|B Chain B, Crystal Structure Of Glutathione S-transferase Mha_0454
(target Efi- 507015) From Mannheimia Haemolytica,
Substrate-free
pdb|4IQ1|C Chain C, Crystal Structure Of Glutathione S-transferase Mha_0454
(target Efi- 507015) From Mannheimia Haemolytica,
Substrate-free
pdb|4IW9|A Chain A, Crystal Structure Of Glutathione S-transferase Mha_0454
(target Efi- 507015) From Mannheimia Haemolytica, Gsh
Complex
pdb|4IW9|B Chain B, Crystal Structure Of Glutathione S-transferase Mha_0454
(target Efi- 507015) From Mannheimia Haemolytica, Gsh
Complex
pdb|4IW9|C Chain C, Crystal Structure Of Glutathione S-transferase Mha_0454
(target Efi- 507015) From Mannheimia Haemolytica, Gsh
Complex
Length = 231
Score = 26.6 bits (57), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 37/92 (40%), Gaps = 9/92 (9%)
Query: 38 ISFGALALVTLFGAVSFIMYRRYRWNKPQTLSDKCSNPDSSGYIDDSTLRAVHVQGQEP- 96
+ F ++ L L GA SF+ + W K + D S +I + A++ +G P
Sbjct: 18 LYFQSMKLYGLTGACSFVPHVALEWVKLRANQDYAFQAVSREFIKSAEYLALNPRGNVPL 77
Query: 97 LTSTMLAAAQPQEQKQMLGERLFPLIQRMYPE 128
L LA Q Q L E +YPE
Sbjct: 78 LVDGDLALTQNQAIVHYLDE--------LYPE 101
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
0.315 0.131 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,627,457
Number of Sequences: 62578
Number of extensions: 168666
Number of successful extensions: 402
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 387
Number of HSP's gapped (non-prelim): 19
length of query: 179
length of database: 14,973,337
effective HSP length: 93
effective length of query: 86
effective length of database: 9,153,583
effective search space: 787208138
effective search space used: 787208138
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)