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= 013150
(448 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 109 bits (272), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 58/117 (49%), Positives = 75/117 (64%), Gaps = 1/117 (0%)
Query: 236 GKKLEPESNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQT 295
G + +S VL +EN+ Y VTLDVLH +FS FG V KI F KN QAL+QY D +
Sbjct: 37 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS 96
Query: 296 AVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLPSTPMVNSQPSI 352
A AK +L+G IY+ C L I +S+ T L++K NND+SRDYT P P +SQPS+
Sbjct: 97 AQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSL 152
Score = 87.8 bits (216), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 50/112 (44%), Positives = 69/112 (61%), Gaps = 9/112 (8%)
Query: 125 VSIDVLHLVFSAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPEN 184
V++DVLH +FS FG V KI TF K FQAL+Q++D +A AK +LDG++I
Sbjct: 58 VTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN------ 111
Query: 185 MGPCTLRITYSAHTDLSVKFQSHRSRDYTNPYLPVAPS--AIDASGQLSVGL 234
CTLRI +S T L+VK+ + +SRDYT P LP S ++D + + GL
Sbjct: 112 -ACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSLDQTMAAAFGL 162
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 108 bits (270), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 58/117 (49%), Positives = 75/117 (64%), Gaps = 1/117 (0%)
Query: 236 GKKLEPESNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQT 295
G + +S VL +EN+ Y VTLDVLH +FS FG V KI F KN QAL+QY D +
Sbjct: 24 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS 83
Query: 296 AVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLPSTPMVNSQPSI 352
A AK +L+G IY+ C L I +S+ T L++K NND+SRDYT P P +SQPS+
Sbjct: 84 AQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSL 139
Score = 86.7 bits (213), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 47/98 (47%), Positives = 62/98 (63%), Gaps = 7/98 (7%)
Query: 125 VSIDVLHLVFSAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPEN 184
V++DVLH +FS FG V KI TF K FQAL+Q++D +A AK +LDG++I
Sbjct: 45 VTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN------ 98
Query: 185 MGPCTLRITYSAHTDLSVKFQSHRSRDYTNPYLPVAPS 222
CTLRI +S T L+VK+ + +SRDYT P LP S
Sbjct: 99 -ACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDS 135
>pdb|3ZZY|A Chain A, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZY|B Chain B, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|A Chain A, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|B Chain B, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
Length = 130
Score = 102 bits (253), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 54/109 (49%), Positives = 69/109 (63%), Gaps = 1/109 (0%)
Query: 236 GKKLEPESNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQT 295
G + +S VL +EN+ Y VTLDVLH +FS FG V KI F KN QAL+QY D +
Sbjct: 19 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS 78
Query: 296 AVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLPSTP 344
A AK +L+G IY+ C L I +S+ T L++K NND+SRDYT P P
Sbjct: 79 AQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLP 126
Score = 87.0 bits (214), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 47/98 (47%), Positives = 62/98 (63%), Gaps = 7/98 (7%)
Query: 125 VSIDVLHLVFSAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPEN 184
V++DVLH +FS FG V KI TF K FQAL+Q++D +A AK +LDG++I
Sbjct: 40 VTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN------ 93
Query: 185 MGPCTLRITYSAHTDLSVKFQSHRSRDYTNPYLPVAPS 222
CTLRI +S T L+VK+ + +SRDYT P LP S
Sbjct: 94 -ACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDS 130
>pdb|2E5I|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Heterogeneous Nuclear Ribonucleoprotein L-Like
Length = 124
Score = 77.0 bits (188), Expect = 2e-14, Method: Composition-based stats.
Identities = 49/120 (40%), Positives = 69/120 (57%), Gaps = 11/120 (9%)
Query: 231 SVGLDGKKLEPESN---------VLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKN 281
S G GK++ N VLL SI+N Y +T+DVL+ V + G VQ+I +F +N
Sbjct: 2 SSGSSGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN 61
Query: 282 GGLQALIQYPDVQTAVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLP 341
G+QA++++ V A AK AL G IY G C L I Y+R T L++ N++ S DYT P
Sbjct: 62 -GIQAMVEFESVLCAQKAKAALNGADIY-AGCCTLKIEYARPTRLNVIRNDNDSWDYTKP 119
Score = 60.5 bits (145), Expect = 2e-09, Method: Composition-based stats.
Identities = 45/126 (35%), Positives = 66/126 (52%), Gaps = 11/126 (8%)
Query: 94 SNRQEIVNNKTTADVAG--NVLLVTIEGTDARLVSIDVLHLVFSAFGFVHKITTFEKTAG 151
S+ + I T D +G VLL++I+ +++DVL+ V + G V +I F++ G
Sbjct: 5 SSGKRITRPGNTDDPSGGNKVLLLSIQNP-LYPITVDVLYTVCNPVGKVQRIVIFKRN-G 62
Query: 152 FQALVQFSDTETASSAKNALDGRSIPRYLLPENMGPCTLRITYSAHTDLSVKFQSHRSRD 211
QA+V+F A AK AL+G I G CTL+I Y+ T L+V + S D
Sbjct: 63 IQAMVEFESVLCAQKAKAALNGADI-------YAGCCTLKIEYARPTRLNVIRNDNDSWD 115
Query: 212 YTNPYL 217
YT PYL
Sbjct: 116 YTKPYL 121
>pdb|2CQ1|A Chain A, Solution Structure Of Rna Binding Domain In Ptb-Like
Protein L
Length = 101
Score = 65.1 bits (157), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 38/95 (40%), Positives = 52/95 (54%), Gaps = 7/95 (7%)
Query: 16 PSKVLHLRNLPWECTEEELIELGKPFGKVVNTKCNVGANRNQAFIEFADLNQXXXXXXXX 75
PS+VLH+R LP E TE E+I LG PFGKV N G +NQAF+E A +
Sbjct: 14 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG--KNQAFLELA--TEEAAITMVN 69
Query: 76 XXXXEPAQVRGKTVYLQYSNRQEIVNNKTTADVAG 110
+R + +Y+QYSN +E+ KT+ +G
Sbjct: 70 YYSAVTPHLRNQPIYIQYSNHKEL---KTSGPSSG 101
>pdb|2AD9|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd1 Complexed With Cucucu Rna
Length = 119
Score = 62.8 bits (151), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 34/84 (40%), Positives = 49/84 (58%), Gaps = 4/84 (4%)
Query: 16 PSKVLHLRNLPWECTEEELIELGKPFGKVVNTKCNVGANRNQAFIEFADLNQXXXXXXXX 75
PS+V+H+R LP + TE E+I LG PFGKV N G +NQAFIE + +
Sbjct: 30 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG--KNQAFIEM-NTEEAANTMVNY 86
Query: 76 XXXXEPAQVRGKTVYLQYSNRQEI 99
P +RG+ +Y+Q+SN +E+
Sbjct: 87 YTSVTPV-LRGQPIYIQFSNHKEL 109
>pdb|1SJQ|A Chain A, Nmr Structure Of Rrm1 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 105
Score = 62.0 bits (149), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 34/84 (40%), Positives = 49/84 (58%), Gaps = 4/84 (4%)
Query: 16 PSKVLHLRNLPWECTEEELIELGKPFGKVVNTKCNVGANRNQAFIEFADLNQXXXXXXXX 75
PS+V+H+R LP + TE E+I LG PFGKV N G +NQAFIE + +
Sbjct: 15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG--KNQAFIEM-NTEEAANTMVNY 71
Query: 76 XXXXEPAQVRGKTVYLQYSNRQEI 99
P +RG+ +Y+Q+SN +E+
Sbjct: 72 YTSVTPV-LRGQPIYIQFSNHKEL 94
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 36/55 (65%), Gaps = 4/55 (7%)
Query: 15 PPSKVLHLRNLPWECTEEELIELGKPFGKVVNTKC----NVGANRNQAFIEFADL 65
PPS+V++L ++P++ TEE++++L G V+N K G ++ AFIEF DL
Sbjct: 2 PPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDL 56
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/54 (38%), Positives = 35/54 (64%), Gaps = 4/54 (7%)
Query: 16 PSKVLHLRNLPWECTEEELIELGKPFGKVVNTKC----NVGANRNQAFIEFADL 65
PS+V++L ++P++ TEE++++L G V+N K G ++ AFIEF DL
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDL 54
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/54 (38%), Positives = 35/54 (64%), Gaps = 4/54 (7%)
Query: 16 PSKVLHLRNLPWECTEEELIELGKPFGKVVNTKC----NVGANRNQAFIEFADL 65
PS+V++L ++P++ TEE++++L G V+N K G ++ AFIEF DL
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDL 55
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 55/217 (25%), Positives = 92/217 (42%), Gaps = 21/217 (9%)
Query: 109 AGNVLLVTIEGTDARLVSIDVLHLVFSAFGFVHKITT-FEKTAGFQALVQFSDTETASSA 167
AGN +L+ + + V+ L ++F +G V ++ F K ALVQ +D A A
Sbjct: 32 AGNSVLL-VSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE--NALVQMADGNQAQLA 88
Query: 168 KNALDGRSIPRYLLPENMGPCTLRITYSAHTDLSVKFQSHRSRDYTNPYLPVAPSAIDAS 227
+ L+G + +RIT S H ++ + + + T Y
Sbjct: 89 MSHLNGHKLH---------GKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKP 139
Query: 228 GQLSVGLDGKKLEPESNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQAL 287
G + + + P S L + N+ +V+ + L ++FS+ G V K F + AL
Sbjct: 140 GSKNF----QNIFPPSATL--HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMAL 193
Query: 288 IQYPDVQTAVVAKEALEGHCIYDGGFCKLHISYSRHT 324
IQ V+ AV A L H + G L +S+S+ T
Sbjct: 194 IQMGSVEEAVQALIDLHNHDL--GENHHLRVSFSKST 228
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 27/58 (46%)
Query: 10 FRYTQPPSKVLHLRNLPWECTEEELIELGKPFGKVVNTKCNVGANRNQAFIEFADLNQ 67
F+ PPS LHL N+P +EE+L L G VV +R A I+ + +
Sbjct: 144 FQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEE 201
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 37.0 bits (84), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 54/216 (25%), Positives = 91/216 (42%), Gaps = 21/216 (9%)
Query: 110 GNVLLVTIEGTDARLVSIDVLHLVFSAFGFVHKITT-FEKTAGFQALVQFSDTETASSAK 168
GN +L+ + + V+ L ++F +G V ++ F K ALVQ +D A A
Sbjct: 2 GNSVLL-VSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE--NALVQMADGNQAQLAM 58
Query: 169 NALDGRSIPRYLLPENMGPCTLRITYSAHTDLSVKFQSHRSRDYTNPYLPVAPSAIDASG 228
+ L+G + +RIT S H ++ + + + T Y G
Sbjct: 59 SHLNGHK---------LHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPG 109
Query: 229 QLSVGLDGKKLEPESNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALI 288
+ + + P S L + N+ +V+ + L ++FS+ G V K F + ALI
Sbjct: 110 SKNF----QNIFPPSATL--HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALI 163
Query: 289 QYPDVQTAVVAKEALEGHCIYDGGFCKLHISYSRHT 324
Q V+ AV A L H + G L +S+S+ T
Sbjct: 164 QMGSVEEAVQALIDLHNHDL--GENHHLRVSFSKST 197
Score = 32.0 bits (71), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 27/58 (46%)
Query: 10 FRYTQPPSKVLHLRNLPWECTEEELIELGKPFGKVVNTKCNVGANRNQAFIEFADLNQ 67
F+ PPS LHL N+P +EE+L L G VV +R A I+ + +
Sbjct: 113 FQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEE 170
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 35.4 bits (80), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 31/50 (62%), Gaps = 4/50 (8%)
Query: 17 SKVLHLRNLPWECTEEELIELGKPFGKVVNTKCNVGANRNQ----AFIEF 62
S L++R L T+++L++L +P+GK+V+TK + N+ F++F
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 54
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 35.0 bits (79), Expect = 0.082, Method: Composition-based stats.
Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 8 PQFRYTQP--PSKVLHLRNLPWECTEEELIELGKPF----GKVVNTKCNVGANRNQAFIE 61
P F P P+KVL+L+NL TE +L+ L F G + + G R QAFI
Sbjct: 14 PMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFIT 73
Query: 62 FAD 64
F +
Sbjct: 74 FPN 76
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 15 PP--SKVLHLRNLPWECTEEELIELGKPFGKVVNTKC-NVGANRNQAFIEFADL 65
PP +++L++RNLP++ T EE+ ++ +G + + N R A++ + D+
Sbjct: 8 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDI 61
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 34.3 bits (77), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 9/60 (15%)
Query: 12 YTQPPSKV-----LHLRNLPWECTEEELIELGKPFGKVVNTKCNV----GANRNQAFIEF 62
Y +P S+V L++ LP T++++ ++ FG+++N++ V G +R AFI F
Sbjct: 78 YARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRF 137
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 9/60 (15%)
Query: 12 YTQPPSKV-----LHLRNLPWECTEEELIELGKPFGKVVNTKCNV----GANRNQAFIEF 62
Y +P S+V L++ LP T++++ ++ FG+++N++ V G +R AFI F
Sbjct: 78 YARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRF 137
>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 = 33.5 bits (75), Expect = 0.23, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 15 PP--SKVLHLRNLPWECTEEELIELGKPFGKVVNTKC-NVGANRNQAFIEFADL 65
PP +++L++RNLP++ T EE+ ++ +G + + N R A++ + D+
Sbjct: 14 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDI 67
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 15 PP--SKVLHLRNLPWECTEEELIELGKPFGKVVNTKC-NVGANRNQAFIEFADL 65
PP +++L++RNLP++ T EE+ ++ +G + + N R A++ + D+
Sbjct: 4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDI 57
>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 = 33.1 bits (74), Expect = 0.30, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 2 ASVSSQPQFRYTQPPSK-VLHLRNLPWECTEEELIELGKPFGKVVNTKC---NVGANRNQ 57
S S FRY+ K L + LP+ CT+EEL E+ K G V + + G +
Sbjct: 1 GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGL 60
Query: 58 AFIEFADLNQ 67
A++E+ + +Q
Sbjct: 61 AYVEYENESQ 70
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 33.1 bits (74), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 3/43 (6%)
Query: 20 LHLRNLPWECTEEELIELGKPFGKVVNTKC---NVGANRNQAF 59
L++ NLP E+EL + KPFG+V++T+ + G +R F
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGF 70
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 32.3 bits (72), Expect = 0.58, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 2 ASVSSQPQFRYTQPPSKVLHLRNLPWECTEEELIELGKPFGKVVNTK-----CNVGANRN 56
S S Q Q SK+L +RN+P++ + E+ EL FG++ + GA+R
Sbjct: 1 GSSGSSGQVPKKQTTSKIL-VRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 59
Query: 57 QAFIEF 62
F++F
Sbjct: 60 FGFVDF 65
>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 = 32.3 bits (72), Expect = 0.58, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 15 PP--SKVLHLRNLPWECTEEELIELGKPFGKVVNTKC-NVGANRNQAFIEFADL 65
PP +++L +RNLP++ T EE+ ++ +G + + N R A++ + D+
Sbjct: 14 PPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDI 67
>pdb|3R27|A Chain A, Crystal Structure Of The First Rrm Domain Of
Heterogeneous Nuclear Ribonucleoprotein L (Hnrnp L)
pdb|3R27|B Chain B, Crystal Structure Of The First Rrm Domain Of
Heterogeneous Nuclear Ribonucleoprotein L (Hnrnp L)
Length = 100
Score = 31.6 bits (70), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 12 YTQPPSKVLHLRNLPWECTEEELIELGKPFGKVVNTKCNVGANRNQAFIEFADL 65
+ P S V+H+R L E +L+E + FG + + V + QA +EF D+
Sbjct: 16 HKTPASPVVHIRGLIDGVVEADLVEALQEFGPI--SYVVVMPKKRQALVEFEDV 67
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 3/62 (4%)
Query: 250 IENMQYAVTLDVLHMVFSAFGPVQKIA-MFDKNGG--LQALIQYPDVQTAVVAKEALEGH 306
+ N+ A+T D+L F GP+ I M DKN A ++Y A +A + L G
Sbjct: 5 VGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGK 64
Query: 307 CI 308
I
Sbjct: 65 QI 66
>pdb|3TO8|A Chain A, Crystal Structure Of The Two C-Terminal Rrm Domains Of
Heterogeneous Nuclear Ribonucleoprotein L (Hnrnp L)
Length = 218
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 15/29 (51%)
Query: 14 QPPSKVLHLRNLPWECTEEELIELGKPFG 42
Q PS VLH N P E TEE E+ G
Sbjct: 126 QHPSNVLHFFNAPLEVTEENFFEICDELG 154
>pdb|3TYT|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein L (Hnrpl) From Mus Musculus At 1.60 A
Resolution
Length = 205
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 15/29 (51%)
Query: 14 QPPSKVLHLRNLPWECTEEELIELGKPFG 42
Q PS VLH N P E TEE E+ G
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELG 148
>pdb|3S01|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein L (Hnrpl) From Mus Musculus At 2.15 A
Resolution
Length = 212
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 15/29 (51%)
Query: 14 QPPSKVLHLRNLPWECTEEELIELGKPFG 42
Q PS VLH N P E TEE E+ G
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELG 148
>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 = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 15 PPSKVLHLRNLPWECTEEELIELGKPFGKVVNTKCNVGANRN 56
P L + +LP E +++L+++ PFG VV+ K + N
Sbjct: 23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTN 64
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 28.9 bits (63), Expect = 5.3, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 11 RYTQPPSKVLHLRNLPWECTEEELIELGKPFGKV----VNTKCNVGANRNQAFIEFAD 64
R Q S ++ L LPW+ TE++L E FG+V V G ++ F+ F +
Sbjct: 10 RAVQKTSDLIVL-GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE 66
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 28.9 bits (63), Expect = 6.8, Method: Composition-based stats.
Identities = 16/45 (35%), Positives = 27/45 (60%), Gaps = 4/45 (8%)
Query: 20 LHLRNLPWECTEEELIELGKPFGKVVNTKCNVGANRNQAFIEFAD 64
L + NLP E TE+E+ L + +GKV+ +C++ +N F+ D
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVL--ECDI--IKNYGFVHIED 51
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.5 bits (62), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 249 SIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQTAVVAKEALEGHCI 308
+++N+ V+ ++L FS FGPV+K + + G + + A++ALE C
Sbjct: 100 TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALE-RC- 157
Query: 309 YDGGF 313
DG F
Sbjct: 158 GDGAF 162
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 28.1 bits (61), Expect = 9.1, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 19/40 (47%)
Query: 135 SAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGR 174
S FG + K+ F++ A V F D E A LDGR
Sbjct: 48 SKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGR 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
0.317 0.132 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,320,700
Number of Sequences: 62578
Number of extensions: 420257
Number of successful extensions: 963
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 908
Number of HSP's gapped (non-prelim): 52
length of query: 448
length of database: 14,973,337
effective HSP length: 102
effective length of query: 346
effective length of database: 8,590,381
effective search space: 2972271826
effective search space used: 2972271826
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: 53 (25.0 bits)