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= 029074
(199 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WEX|A Chain A, Solution Structure Of Rrm Domain In Protein Bab28521
Length = 104
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 15 KVKRTVYLDNLSPQVTEPVIRTALDQFGNVKNVQFIPNYTEFRNIPHCALVEMENLKQAK 74
V V++ L V E + AL++FG + V +P + ALVE EN+ AK
Sbjct: 13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQ-------ALVEFENIDSAK 65
Query: 75 DVVTSLHEFPFMMSG 89
+ VT + P ++G
Sbjct: 66 ECVTFAADVPVYIAG 80
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 35.4 bits (80), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 9/66 (13%)
Query: 20 VYLDNLSPQVTEPVIRTALDQFGNVKNVQFIPNYTEFRNIPHCALVEMENLKQAKDVVTS 79
+++ NL + TE IR+ +Q+G V I NY V +E+ A+D + +
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKNY---------GFVHIEDKTAAEDAIRN 61
Query: 80 LHEFPF 85
LH +
Sbjct: 62 LHHYKL 67
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 34.7 bits (78), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 18 RTVYLDNLSPQVTEPVIRTALDQFGNVKNVQFIPNYTEFRNIPHC 62
RT+Y+ NLS VTE +I Q G K+ + I +T N P+C
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYC 58
>pdb|2DGX|A Chain A, Solution Structure Of The Rna Recognition Motif In
Kiaa0430 Protein
Length = 96
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 36/61 (59%), Gaps = 4/61 (6%)
Query: 25 LSPQVTEPVIRTALDQFGNVKNVQFIPNYTEFRNIPHCALVEMENLKQAKDVVTSLHEFP 84
LS + + +++ A + G VK+V+ P +T+++ A+V+MENL+ A V SLH +
Sbjct: 21 LSRKELQQLLQEAFARHGKVKSVELSP-HTDYQ---LKAVVQMENLQDAIGAVNSLHRYK 76
Query: 85 F 85
Sbjct: 77 I 77
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 31/129 (24%), Positives = 52/129 (40%), Gaps = 16/129 (12%)
Query: 20 VYLDNLSPQVTEPVIRTALDQFGNVKNVQFIPNYTEFRNIPHCALVEMENLKQAKDVVTS 79
+ + NLSP V+ ++ A QFG V+ + + + VE A+ +
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD--DRGRATGKGFVEFAAKPPARKALER 156
Query: 80 LHEFPFMMSGMPRPVRARAAEVEMFDDHPAKPGQRIQF------------QWLDPNDPDF 127
+ F+++ PRPV +E FDD P + +Q ++ P +F
Sbjct: 157 CGDGAFLLTTTPRPVIVEP--MEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEF 214
Query: 128 EVAQRLKRL 136
E A R K L
Sbjct: 215 EYASRWKAL 223
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 31.2 bits (69), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 23/37 (62%)
Query: 18 RTVYLDNLSPQVTEPVIRTALDQFGNVKNVQFIPNYT 54
+ +++ NL+ VTE ++ A QFG ++ V+ + +Y
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYA 48
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 2 GSTTEAEYAAFLEKVKRTVYLDNLSPQVTEPVIRTALDQFGNVKNVQFIPNY 53
GS+ + + KVK +++ NL+ VTE ++ + +FG ++ V+ + +Y
Sbjct: 1 GSSGSSGDPEVMAKVK-VLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDY 51
>pdb|1ZA0|A Chain A, X-Ray Structure Of Putative Acyl-Acp Desaturase Desa2 From
Mycobacterium Tuberculosis H37rv
Length = 275
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 9 YAAFLEKVKRTVYLDNLSPQVTEPVIRTALDQFG--NVKNVQFIPNYTEFRNIPHC 62
Y AF E+ V+ NL+ Q+ EP++ +D+ V++ +F N + HC
Sbjct: 154 YMAFYERCG-AVFCRNLAAQIEEPILAGLIDRIARDEVRHEEFFANL-----VTHC 203
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 28.1 bits (61), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 18 RTVYLDNLSPQVTEPVIRTALDQFGNVKNVQFI 50
R +Y+ NL T ++ QFG V NV+ I
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLI 34
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 28.1 bits (61), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 9/71 (12%)
Query: 15 KVKRTVYLDNLSPQVTEPVIRTALDQFGNVKNVQFIPNYTEFRNIPHCALVEMENLKQAK 74
K +++ N+SP T +R +++G V + +Y A V ME + A
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY---------AFVHMERAEDAV 58
Query: 75 DVVTSLHEFPF 85
+ + L F
Sbjct: 59 EAIRGLDNTEF 69
>pdb|4GLM|A Chain A, Crystal Structure Of The Sh3 Domain Of Dnmbp Protein [homo
Sapiens]
pdb|4GLM|B Chain B, Crystal Structure Of The Sh3 Domain Of Dnmbp Protein [homo
Sapiens]
pdb|4GLM|C Chain C, Crystal Structure Of The Sh3 Domain Of Dnmbp Protein [homo
Sapiens]
pdb|4GLM|D Chain D, Crystal Structure Of The Sh3 Domain Of Dnmbp Protein [homo
Sapiens]
Length = 72
Score = 27.7 bits (60), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 17/22 (77%)
Query: 116 QFQWLDPNDPDFEVAQRLKRLA 137
+FQ L+PN+ DFEV +++ LA
Sbjct: 21 RFQALEPNELDFEVGDKIRILA 42
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 27.3 bits (59), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 18 RTVYLDNLSPQVTEPVIRTALDQFGNVKNVQFI 50
+TV++ NLS E + L QFG++K V+ +
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVV 48
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 27.3 bits (59), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 30/131 (22%), Positives = 52/131 (39%), Gaps = 18/131 (13%)
Query: 19 TVYLDNLSPQVTEPVIRTALDQFGNVKNVQFIPNYTEFRNIPHC-ALVEMENLKQAKDVV 77
++ + NL V+ ++ A FG V+ I + R P +VE A+ +
Sbjct: 98 SLTVRNLPQYVSNELLEEAFSVFGQVERAVVI---VDDRGRPSGKGIVEFSGKPAARKAL 154
Query: 78 TSLHEFPFMMSGMPRPVRARAAEVEMFDDHPAKPGQRI----QF--------QWLDPNDP 125
E F+++ PRPV ++ DD P + + QF ++ P
Sbjct: 155 DRCSEGSFLLTTFPRPVTVEP--MDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSF 212
Query: 126 DFEVAQRLKRL 136
++E A R K L
Sbjct: 213 EYEYAMRWKAL 223
>pdb|1UD9|A Chain A, Crystal Structure Of Proliferating Cell Nuclear Antigen
(Pcna) Homolog From Sulfolobus Tokodaii
pdb|1UD9|B Chain B, Crystal Structure Of Proliferating Cell Nuclear Antigen
(Pcna) Homolog From Sulfolobus Tokodaii
pdb|1UD9|C Chain C, Crystal Structure Of Proliferating Cell Nuclear Antigen
(Pcna) Homolog From Sulfolobus Tokodaii
pdb|1UD9|D Chain D, Crystal Structure Of Proliferating Cell Nuclear Antigen
(Pcna) Homolog From Sulfolobus Tokodaii
Length = 245
Score = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 15 KVKRTVYLDNLSPQVTEPVIRTALDQFGNVKNVQFIP 51
K K + +D SP+V + + AL++ NV N++ +P
Sbjct: 82 KRKEEIIIDADSPEVVKLTLSGALNRVFNVNNIEVLP 118
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
0.320 0.134 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,245,254
Number of Sequences: 62578
Number of extensions: 177773
Number of successful extensions: 570
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 561
Number of HSP's gapped (non-prelim): 16
length of query: 199
length of database: 14,973,337
effective HSP length: 94
effective length of query: 105
effective length of database: 9,091,005
effective search space: 954555525
effective search space used: 954555525
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)