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= 026826
(232 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 49/91 (53%), Gaps = 14/91 (15%)
Query: 128 PPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSP 187
PP+ LF+ LP + + ++ +F F G+KEVRLV RH + FV+F +
Sbjct: 205 PPN--HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP--GRHD------IAFVEFDNE 254
Query: 188 AHAATAMDALQGYRFDEHDRDSVKLRLQFAR 218
A A DALQG++ +++ +++ FA+
Sbjct: 255 VQAGAARDALQGFKITQNN----AMKISFAK 281
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 49/91 (53%), Gaps = 14/91 (15%)
Query: 128 PPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSP 187
PP+ LF+ LP + + ++ +F F G+KEVRLV RH + FV+F +
Sbjct: 11 PPN--HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP--GRHD------IAFVEFDNE 60
Query: 188 AHAATAMDALQGYRFDEHDRDSVKLRLQFAR 218
A A DALQG++ +++ +++ FA+
Sbjct: 61 VQAGAARDALQGFKITQNN----AMKISFAK 87
>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 = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 10/74 (13%)
Query: 128 PPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSP 187
PP+ LF+ LP + + ++ +F F G+KEVRLV +RH + FV+F +
Sbjct: 6 PPN--QILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVP--NRHD------IAFVEFTTE 55
Query: 188 AHAATAMDALQGYR 201
+ A +ALQG++
Sbjct: 56 LQSNAAKEALQGFK 69
>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 = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 135 LFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSPAHAATAM 194
LF+ GLP C++ E+ I + K++RLV+ + P G L +V++ + + A+ A+
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG----LAYVEYENESQASQAV 75
Query: 195 DALQGYRFDEH 205
+ G E+
Sbjct: 76 MKMDGMTIKEN 86
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 39/89 (43%), Gaps = 11/89 (12%)
Query: 131 ASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSPAHA 190
+++ LFV P D E+ IF PF KEV++++ FV+F A
Sbjct: 30 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-----------FAFVEFEEAESA 78
Query: 191 ATAMDALQGYRFDEHDRDSVKLRLQFARY 219
A A++ + G F + V +L RY
Sbjct: 79 AKAIEEVHGKSFANQPLEVVYSKLPAKRY 107
>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 = 0.008, 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|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 35.4 bits (80), Expect = 0.025, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 11/72 (15%)
Query: 131 ASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSPAHA 190
+++ LFV P D E+ IF PF KEV++++ FV+F A
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-----------FAFVEFEEAESA 51
Query: 191 ATAMDALQGYRF 202
A A++ + G F
Sbjct: 52 AKAIEEVHGKSF 63
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 11/84 (13%)
Query: 135 LFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSPAHAATAM 194
++V LP D +++ +F + +++ L ++ GG P FV+F P A A+
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR----GGPPF--AFVEFEDPRDAEDAV 78
Query: 195 DALQGYRFDEHDRDSVKLRLQFAR 218
GY D D +LR++F R
Sbjct: 79 YGRDGY-----DYDGYRLRVEFPR 97
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 33/77 (42%)
Query: 132 SSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSPAHAA 191
SS LF++ L + + +F K + K+++ + FV++ P A
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 192 TAMDALQGYRFDEHDRD 208
A+ LQG+ D H +
Sbjct: 65 KALKQLQGHTVDGHKLE 81
>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 = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 36/86 (41%), Gaps = 5/86 (5%)
Query: 120 GGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRL-VSKESRHPGGDPLI 178
G E S TL+V L + ++ +F K++ + + K + G
Sbjct: 27 GDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG---- 82
Query: 179 LCFVDFVSPAHAATAMDALQGYRFDE 204
CFV++ S A A AM + G R D+
Sbjct: 83 FCFVEYYSRADAENAMRYINGTRLDD 108
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 29/97 (29%), Positives = 41/97 (42%), Gaps = 10/97 (10%)
Query: 129 PDASST-LFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSP 187
P AS+T L V LP D + RE+ +FR R+ + G FVDF S
Sbjct: 10 PRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRD---YKTGYSFGYAFVDFTSE 66
Query: 188 AHAATAMDALQGYRFDEHDRDSVKLRLQFARYPGARS 224
+ A+ L G +L++ +AR PG S
Sbjct: 67 XDSQRAIKVLNGITVRNK-----RLKVSYAR-PGGES 97
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 180 CFVDFVSPAHAATAMDALQGYRFDEHDRDSVKLRLQFARY 219
F+++ SPAHA A+ GY+ D+ V L F +Y
Sbjct: 64 IFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFDKY 103
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 31.6 bits (70), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 9/94 (9%)
Query: 131 ASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSPAHA 190
+++ L V LP D + RE+ +FR R++ + G FVDF S +
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRD---YKTGYSYGYAFVDFTSEMDS 58
Query: 191 ATAMDALQGYRFDEHDRDSVKLRLQFARYPGARS 224
A+ L G +L++ +AR PG S
Sbjct: 59 QRAIKVLNGITVRNK-----RLKVSYAR-PGGES 86
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 31.6 bits (70), Expect = 0.43, 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|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 31.2 bits (69), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 37/87 (42%), Gaps = 11/87 (12%)
Query: 132 SSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSPAHAA 191
S TLFV+GL D + + F G R+V+ G FVDF S A
Sbjct: 15 SKTLFVKGLSEDTTEETLKE---SFDGSVRARIVTD---RETGSSKGFGFVDFNSEEDAK 68
Query: 192 TAMDALQGYRFDEHDRDSVKLRLQFAR 218
A +A++ D + K+ L +A+
Sbjct: 69 AAKEAMEDGEIDGN-----KVTLDWAK 90
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 31.2 bits (69), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 9/94 (9%)
Query: 131 ASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSPAHA 190
+++ L V LP D + RE+ +FR R++ + G FVDF S +
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRD---YKTGYSYGYAFVDFTSEMDS 58
Query: 191 ATAMDALQGYRFDEHDRDSVKLRLQFARYPGARS 224
A+ L G +L++ +AR PG S
Sbjct: 59 QRAIKVLNGITVRNK-----RLKVSYAR-PGGES 86
>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 = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 35/85 (41%), Gaps = 4/85 (4%)
Query: 120 GGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLIL 179
G E S TL+V L + ++ +F K++ + + + G
Sbjct: 6 GDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACG----F 61
Query: 180 CFVDFVSPAHAATAMDALQGYRFDE 204
CFV++ S A A AM + G R D+
Sbjct: 62 CFVEYYSRADAENAMRYINGTRLDD 86
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 23/109 (21%), Positives = 49/109 (44%), Gaps = 18/109 (16%)
Query: 113 DRALGLGGGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRL-VSKESRH 171
+++G G + E P + LF+ LP + +++ +F PF ++ + K++
Sbjct: 10 QQSIGAAGSQKEGP----EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTN- 64
Query: 172 PGGDPLILC--FVDFVSPAHAATAMDALQGYRFDEHDRDSVKLRLQFAR 218
L C FV + +P A A+ ++ G++ +L++Q R
Sbjct: 65 -----LSKCFGFVSYDNPVSAQAAIQSMNGFQIGMK-----RLKVQLKR 103
>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 = 1.2, 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 = 2.5, 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|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 27.7 bits (60), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 21/84 (25%)
Query: 132 SSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVD-------- 183
++T+FV+GL + + VA F K++ ++ ++ G P+I + D
Sbjct: 7 NNTIFVQGLGENVTIESVADYF------KQIGII--KTNKKTGQPMINLYTDRETGKLKG 58
Query: 184 -----FVSPAHAATAMDALQGYRF 202
F P A A+D G F
Sbjct: 59 EATVSFDDPPSAKAAIDWFDGKEF 82
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 27.7 bits (60), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 180 CFVDFVSPAHAATAMDALQGYRFDEH 205
F+++ SPAHA A+ GY+ D+
Sbjct: 50 IFLEYASPAHAVDAVKNADGYKLDKQ 75
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
0.318 0.137 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,885,375
Number of Sequences: 62578
Number of extensions: 339352
Number of successful extensions: 579
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 563
Number of HSP's gapped (non-prelim): 26
length of query: 232
length of database: 14,973,337
effective HSP length: 96
effective length of query: 136
effective length of database: 8,965,849
effective search space: 1219355464
effective search space used: 1219355464
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)