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= 024507
(266 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 30.8 bits (68), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 5 RTVQVKNVSDLAHEREIHEFFSFSGDIERIEILREY-GQSKT-AFVTFKDAKALEIAL-L 61
RTV V N+ E ++E F +G + ++ I ++ G+ K+ FV FK +++ A+ L
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL 76
Query: 62 LSGATIVDQIVSIT 75
L+G + + ++++
Sbjct: 77 LNGIRLYGRPINVS 90
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 30.8 bits (68), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 3/48 (6%)
Query: 6 TVQVKNVSDLAHEREIHEFFSFSGDIERIEILRE--YGQSKT-AFVTF 50
T++V N+S+ E ++ E F G I RI + ++ GQSK AF++F
Sbjct: 17 TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 30.8 bits (68), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 6/77 (7%)
Query: 1 MQQTRTVQVKNVSDLAHEREIHEFFSFSGDIERIEILREYGQSKTA----FVTFKDAKAL 56
++++ T+ V N+S E +I+E FS SGDI++I I+ KTA FV +
Sbjct: 36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKI-IMGLDKMKKTACGFCFVEYYSRADA 94
Query: 57 EIAL-LLSGATIVDQIV 72
E A+ ++G + D+I+
Sbjct: 95 ENAMRYINGTRLDDRII 111
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 30.8 bits (68), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 9 VKNVSDLAHEREIHEFFSFSGDIERIEILREYGQSKT---AFVTFKDAKALEIALLLSGA 65
V + + E + ++F G IE IEI+ + G K AFVTF D +++ ++
Sbjct: 110 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 169
Query: 66 TI 67
T+
Sbjct: 170 TV 171
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 30.4 bits (67), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 24/34 (70%)
Query: 1 MQQTRTVQVKNVSDLAHEREIHEFFSFSGDIERI 34
++++ T+ V N+S E +I+E FS SGDI++I
Sbjct: 15 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKI 48
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 30.4 bits (67), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 9 VKNVSDLAHEREIHEFFSFSGDIERIEILREYGQSKT---AFVTFKDAKALEIALLLSGA 65
V + + E + ++F G IE IEI+ + G K AFVTF D +++ ++
Sbjct: 108 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 167
Query: 66 TI 67
T+
Sbjct: 168 TV 169
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 30.4 bits (67), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 9 VKNVSDLAHEREIHEFFSFSGDIERIEILREYGQSKT---AFVTFKDAKALEIALLLSGA 65
V + + E + ++F G IE IEI+ + G K AFVTF D +++ ++
Sbjct: 109 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 168
Query: 66 TI 67
T+
Sbjct: 169 TV 170
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 9 VKNVSDLAHEREIHEFFSFSGDIERIEILREYGQSKT---AFVTFKDAKALEIALLLSGA 65
V + + E + ++F G IE IEI+ + G K AFVTF D +++ ++
Sbjct: 109 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 168
Query: 66 TI 67
T+
Sbjct: 169 TV 170
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 5 RTVQVKNVSDLAHEREIHEFFSFSGDIERIEILREYGQSKT---AFVTFKDAKALEIALL 61
+ + V + + E + ++F G IE IEI+ + G K AFVTF D +++ ++
Sbjct: 103 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 162
Query: 62 LSGATI 67
T+
Sbjct: 163 QKYHTV 168
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 5 RTVQVKNVSDLAHEREIHEFFSFSGDIERIEILREYGQSKT---AFVTFKDAKALEIALL 61
+ + V + + E + ++F G IE IEI+ + G K AFVTF D +++ ++
Sbjct: 98 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 157
Query: 62 LSGATI 67
T+
Sbjct: 158 QKYHTV 163
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 7/69 (10%)
Query: 2 QQTRTVQVKNVSDLAHEREIHEFFSFSGDIERIEILREY-------GQSKTAFVTFKDAK 54
Q T + V+N+ A++REI E FS G+++ + + ++ G F+T +DAK
Sbjct: 13 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 72
Query: 55 ALEIALLLS 63
AL S
Sbjct: 73 KAFNALCHS 81
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 5/52 (9%)
Query: 1 MQQTRTVQVKNVSDLAHEREIHEFFSFSGDIERIEILREYGQSKTAFVTFKD 52
M + + + V+N++ E + + FS G +ER++ L++Y AFV F+D
Sbjct: 12 MAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDY-----AFVHFED 58
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/70 (21%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 2 QQTRTVQVKNVSDLAHEREIHEFFSFSGDIERIEILREYGQSKT---AFVTFKDAKALEI 58
+ RTV ++ R++ +FFS G + + I+ + ++ A+V F + +++ +
Sbjct: 23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 82
Query: 59 ALLLSGATIV 68
A+ L+G ++
Sbjct: 83 AIGLTGQRLL 92
>pdb|1S0U|A Chain A, Eif2gamma Apo
Length = 408
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 48 VTFKDAKALE--IALLLSGATIVDQIVSITPAENYVPKPESQE 88
V+F D+ E +A +LSGA+++D + + A P+P+++E
Sbjct: 83 VSFVDSPGHETLMATMLSGASLMDGAILVIAANEPCPQPQTKE 125
>pdb|2AHO|A Chain A, Structure Of The Archaeal Initiation Factor Eif2 Alpha-
Gamma Heterodimer From Sulfolobus Solfataricus Complexed
With Gdpnp
pdb|2PLF|A Chain A, The Structure Of Aif2gamma Subunit From The Archaeon
Sulfolobus Solfataricus In The Nucleotide-Free Form.
pdb|2QMU|A Chain A, Structure Of An Archaeal Heterotrimeric Initiation Factor
2 Reveals A Nucleotide State Between The Gtp And The Gdp
States
pdb|2QN6|A Chain A, Structure Of An Archaeal Heterotrimeric Initiation Factor
2 Reveals A Nucleotide State Between The Gtp And The Gdp
States
pdb|3V11|A Chain A, Structure Of The Ternary Initiation Complex
Aif2:gdpnp:methionylated Initiator Trna
Length = 414
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 48 VTFKDAKALEI--ALLLSGATIVDQIVSITPAENYVPKPESQE 88
++F DA E+ A +LSGA ++D + + A P+P+++E
Sbjct: 88 ISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTRE 130
>pdb|2PMD|A Chain A, The Structures Of Aif2gamma Subunit From The Archaeon
Sulfolobus Solfataricus In The Gdp-Bound Form.
pdb|2PMD|B Chain B, The Structures Of Aif2gamma Subunit From The Archaeon
Sulfolobus Solfataricus In The Gdp-Bound Form.
pdb|3CW2|A Chain A, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|B Chain B, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|E Chain E, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|F Chain F, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3I1F|A Chain A, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus In Complex With Gpp(Ch2)p
pdb|3I1F|B Chain B, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus In Complex With Gpp(Ch2)p
pdb|3P3M|A Chain A, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus Complexed With Gtp
pdb|3P3M|B Chain B, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus Complexed With Gtp
pdb|3P3M|C Chain C, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus Complexed With Gtp
pdb|3P3M|D Chain D, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus Complexed With Gtp
pdb|3P3M|E Chain E, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus Complexed With Gtp
pdb|3P3M|F Chain F, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus Complexed With Gtp
pdb|3QSY|A Chain A, Recognition Of The Methionylated Initiator Trna By The
Translation Initiation Factor 2 In Archaea
Length = 415
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 48 VTFKDAKALEI--ALLLSGATIVDQIVSITPAENYVPKPESQE 88
++F DA E+ A +LSGA ++D + + A P+P+++E
Sbjct: 89 ISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTRE 131
>pdb|3SJZ|A Chain A, The Structure Of Aif2gamma Subunit Delta 41-45 From
Archaeon Sulfolobus Solfataricus Complexed With Gdp And
Gdpnp
Length = 409
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 48 VTFKDAKALEI--ALLLSGATIVDQIVSITPAENYVPKPESQE 88
++F DA E+ A +LSGA ++D + + A P+P+++E
Sbjct: 83 ISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTRE 125
>pdb|3PEN|A Chain A, Structure Of Archaeal Initiation Factor Aif2gamma Subunit
Delta 37-47 From Sulfolobus Solfataricus In The
Gdp-Bound Form.
pdb|3SJY|A Chain A, The Structure Of Initiation Factor Aif2 Gamma Subunit
Delta 37-47 From Archaeon Sulfolobus Solfataricus
Complexed With Gdpcp
Length = 403
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 48 VTFKDAKALEI--ALLLSGATIVDQIVSITPAENYVPKPESQE 88
++F DA E+ A +LSGA ++D + + A P+P+++E
Sbjct: 77 ISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTRE 119
>pdb|1KJZ|A Chain A, Structure Of The Large Gamma Subunit Of Initiation Factor
Eif2 From Pyrococcus Abyssi-G235d Mutant
pdb|1KK1|A Chain A, Structure Of The Large Gamma Subunit Of Initiation Factor
Eif2 From Pyrococcus Abyssi-G235d Mutant Complexed With
Gdpnp-Mg2+
pdb|1KK2|A Chain A, Structure Of The Large Gamma Subunit Of Initiation Factor
Eif2 From Pyrococcus Abyssi-G235d Mutant Complexed With
Gdp-Mg2+
Length = 410
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 5/64 (7%)
Query: 40 YGQSKTAFV---TFKDAKALEIAL--LLSGATIVDQIVSITPAENYVPKPESQEVTVVVN 94
Y +T FV +F DA E + +L+GA+++D + + A P+P+++E + +
Sbjct: 74 YCGHETEFVRRVSFIDAPGHEALMTTMLAGASLMDGAILVIAANEPCPRPQTREHLMALQ 133
Query: 95 AVSE 98
+ +
Sbjct: 134 IIGQ 137
>pdb|1KK3|A Chain A, Structure Of The Wild-Type Large Gamma Subunit Of
Initiation Factor Eif2 From Pyrococcus Abyssi Complexed
With Gdp-Mg2+
Length = 410
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 5/64 (7%)
Query: 40 YGQSKTAFV---TFKDAKALEIAL--LLSGATIVDQIVSITPAENYVPKPESQEVTVVVN 94
Y +T FV +F DA E + +L+GA+++D + + A P+P+++E + +
Sbjct: 74 YCGHETEFVRRVSFIDAPGHEALMTTMLAGASLMDGAILVIAANEPCPRPQTREHLMALQ 133
Query: 95 AVSE 98
+ +
Sbjct: 134 IIGQ 137
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 28.1 bits (61), Expect = 5.8, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 10/74 (13%)
Query: 18 EREIHEFFSFSGDIERIEILREYGQSKTAFVTFKDAKALEIALLLSGATIVDQIVSI--- 74
E E+ EFFS GD+ + I + + AFVTF D +IA L G ++ + +S+
Sbjct: 19 EDELREFFSQYGDVMDVFIPKPF--RAFAFVTFADD---QIAQSLCGEDLIIKGISVHIS 73
Query: 75 --TPAENYVPKPES 86
P N P S
Sbjct: 74 NAEPKHNSNSGPSS 87
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
0.312 0.125 0.328
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,479,724
Number of Sequences: 62578
Number of extensions: 233599
Number of successful extensions: 550
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 542
Number of HSP's gapped (non-prelim): 25
length of query: 266
length of database: 14,973,337
effective HSP length: 97
effective length of query: 169
effective length of database: 8,903,271
effective search space: 1504652799
effective search space used: 1504652799
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)