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= 028098
(214 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 7/81 (8%)
Query: 135 LFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSPAHAATA- 193
LF+ GLP C++ E+ I + K++RLV+ + P G L +V++ + + A+ A
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG----LAYVEYENESQASQAV 75
Query: 194 --MDALQVQSKVVAPNQYQSG 212
MD + ++ ++ SG
Sbjct: 76 MKMDGMTIKENIIKVAISNSG 96
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 10/71 (14%)
Query: 128 PPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSP 187
PP+ LF+ LP + + ++ +F F G+KEVRLV RH + FV+F +
Sbjct: 205 PPN--HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP--GRHD------IAFVEFDNE 254
Query: 188 AHAATAMDALQ 198
A A DALQ
Sbjct: 255 VQAGAARDALQ 265
>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
pdb|2AYM|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
Length = 83
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 10/71 (14%)
Query: 128 PPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSP 187
PP+ LF+ LP + + ++ +F F G+KEVRLV +RH + FV+F +
Sbjct: 6 PPN--QILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVP--NRHD------IAFVEFTTE 55
Query: 188 AHAATAMDALQ 198
+ A +ALQ
Sbjct: 56 LQSNAAKEALQ 66
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 10/71 (14%)
Query: 128 PPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSP 187
PP+ LF+ LP + + ++ +F F G+KEVRLV RH + FV+F +
Sbjct: 11 PPN--HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP--GRHD------IAFVEFDNE 60
Query: 188 AHAATAMDALQ 198
A A DALQ
Sbjct: 61 VQAGAARDALQ 71
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 38/84 (45%), Gaps = 9/84 (10%)
Query: 117 GLGGGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKES---RHPG 173
G G +VP +S + V +P ++RE+ +F F K VRL K + H G
Sbjct: 1 GSSGSSGQVP-KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 59
Query: 174 GDPLILCFVDFVSPAHAATAMDAL 197
FVDF++ A A +AL
Sbjct: 60 -----FGFVDFITKQDAKKAFNAL 78
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 11/71 (15%)
Query: 131 ASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSPAHA 190
+++ LFV P D E+ IF PF KEV++++ FV+F A
Sbjct: 30 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-----------FAFVEFEEAESA 78
Query: 191 ATAMDALQVQS 201
A A++ + +S
Sbjct: 79 AKAIEEVHGKS 89
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 12/44 (27%), Positives = 25/44 (56%)
Query: 121 GRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRL 164
GR+ + LPP+ + L++ LP + E+ IF + +++R+
Sbjct: 1 GRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV 44
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 30.4 bits (67), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 11/68 (16%)
Query: 131 ASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSPAHA 190
+++ LFV P D E+ IF PF KEV++++ FV+F A
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-----------FAFVEFEEAESA 51
Query: 191 ATAMDALQ 198
A A++ +
Sbjct: 52 AKAIEEVH 59
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 30.0 bits (66), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 11/46 (23%), Positives = 24/46 (52%)
Query: 119 GGGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRL 164
R+ + LPP+ + L++ LP + E+ IF + +++R+
Sbjct: 5 AAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV 50
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 11/46 (23%), Positives = 23/46 (50%)
Query: 119 GGGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRL 164
R+ + LPP+ + L + LP + E+ IF + +++R+
Sbjct: 5 AAKRANIRLPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRV 50
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 26.9 bits (58), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 133 STLFVEGLPSDCSRREVAHIFRPFVGYKEVRLV-SKESRHPGGDPLI 178
+ +FV G+P +C E+ F+ F EV ++ E + P G I
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFI 57
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
0.316 0.134 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,031,685
Number of Sequences: 62578
Number of extensions: 304381
Number of successful extensions: 526
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 514
Number of HSP's gapped (non-prelim): 13
length of query: 214
length of database: 14,973,337
effective HSP length: 95
effective length of query: 119
effective length of database: 9,028,427
effective search space: 1074382813
effective search space used: 1074382813
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: 49 (23.5 bits)