RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17274
(184 letters)
>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA,
spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1
d.58.7.1
Length = 198
Score = 197 bits (501), Expect = 7e-65
Identities = 120/178 (67%), Positives = 145/178 (81%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+F L GVYGDV RVKIL+NKK++AL+QMA+ +QA LAM H++ ++ GK +R+ +SKHQ
Sbjct: 21 LFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN 80
Query: 61 VQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEA 120
VQLP+EGQ D GLTKDY SPLHRFKKPGSKNFQNI+PPS TLHLSNIP SV+E++LK
Sbjct: 81 VQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVL 140
Query: 121 FTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKSNI 178
F+ G VKGFKFF KDRKMAL+Q+ S+EEA+ ALI +HNH L E HLRVSFSKS I
Sbjct: 141 FSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 198
Score = 47.2 bits (112), Expect = 3e-07
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 100 SPTLHLSNI-PASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQM 158
+ L +SN+ P VT L F G V+ K ++ AL+Q+ +A A+ +
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYG-DVQRVKILFNKKENALVQMADGNQAQLAMSHL 61
Query: 159 HNHQLSEQSHLRVSFSKSN 177
+ H+L + +R++ SK
Sbjct: 62 NGHKLHGKP-IRITLSKHQ 79
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 193 bits (492), Expect = 5e-63
Identities = 120/178 (67%), Positives = 145/178 (81%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+F L GVYGDV RVKIL+NKK++AL+QMA+ +QA LAM H++ ++ GK +R+ +SKHQ
Sbjct: 52 LFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN 111
Query: 61 VQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEA 120
VQLP+EGQ D GLTKDY SPLHRFKKPGSKNFQNI+PPS TLHLSNIP SV+E++LK
Sbjct: 112 VQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVL 171
Query: 121 FTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKSNI 178
F+ G VKGFKFF KDRKMAL+Q+ S+EEA+ ALI +HNH L E HLRVSFSKS I
Sbjct: 172 FSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 229
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A
Length = 205
Score = 145 bits (367), Expect = 1e-44
Identities = 51/184 (27%), Positives = 92/184 (50%), Gaps = 11/184 (5%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+F++ +YG+V +VK + +K +A+++MA+ + A+ H++ +FG++M V +SK A
Sbjct: 22 VFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPA 81
Query: 61 VQLPKEGQPDAG--LTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELK 118
+ + + G KD++ S +RF P I PS LH N P VTE+
Sbjct: 82 IMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFF 141
Query: 119 EAFTEKGF----TVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQS-----HL 169
E E G +VK F + LL+ DS +A+ L ++++Q+ + L
Sbjct: 142 EICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTL 201
Query: 170 RVSF 173
++ F
Sbjct: 202 KLCF 205
Score = 50.5 bits (120), Expect = 3e-08
Identities = 16/88 (18%), Positives = 33/88 (37%), Gaps = 3/88 (3%)
Query: 98 PPSPTLHLSNI-PASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALI 156
SP L + + + + D + F G V+ KF A++++ A+
Sbjct: 2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYG-NVEKVKFMKSKPGAAMVEMADGYAVDRAIT 60
Query: 157 QMHNHQLSEQSHLRVSFSKSNIQDIRDN 184
++N+ + Q + V SK +
Sbjct: 61 HLNNNFMFGQK-MNVCVSKQPAIMPGQS 87
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 72.9 bits (179), Expect = 1e-17
Identities = 22/98 (22%), Positives = 40/98 (40%), Gaps = 4/98 (4%)
Query: 80 SPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK 139
H + P SP +H+ + V E +L EA E G + P ++
Sbjct: 2 GHHHHHHMENYDDPHKT-PASPVVHIRGLIDGVVEADLVEALQEFG-PISYVVVMP-KKR 58
Query: 140 MALLQLDSIEEAITALIQMHNHQLSEQSH-LRVSFSKS 176
AL++ + + A A+ ++Q+ H V++S S
Sbjct: 59 QALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTS 96
Score = 32.8 bits (75), Expect = 0.014
Identities = 11/54 (20%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAM--MHMDKLRVFGKQMRVMISKHQ 59
+G + V ++ K+ AL++ + A A+ +++ + G V S Q
Sbjct: 45 FGPISYVVVMPKKRQ-ALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQ 97
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 68.7 bits (168), Expect = 6e-16
Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 3/91 (3%)
Query: 88 PGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDS 147
GS + SP +H+ + SV E +L EA + G T+ P ++ AL++ ++
Sbjct: 3 SGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFG-TICYVMMMP-FKRQALVEFEN 60
Query: 148 IEEAITALIQMHNHQLSEQSH-LRVSFSKSN 177
I+ A + + + ++S S
Sbjct: 61 IDSAKECVTFAADVPVYIAGQQAFFNYSTSK 91
Score = 42.1 bits (99), Expect = 8e-06
Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 3/67 (4%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAM--MHMDKLRVFGKQMRVMISKHQAVQLPK 65
+G + V ++ K+ AL++ A + + + G+Q S + + P
Sbjct: 39 FGTICYVMMMPFKR-QALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPG 97
Query: 66 EGQPDAG 72
P +G
Sbjct: 98 NSGPSSG 104
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 61.8 bits (150), Expect = 3e-13
Identities = 21/89 (23%), Positives = 34/89 (38%), Gaps = 3/89 (3%)
Query: 89 GSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSI 148
GS + PS LH+ +P VTE E+ G V + A L+L +
Sbjct: 4 GSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFG-KVTNILMLK-GKNQAFLELATE 61
Query: 149 EEAITALIQMHNHQLSEQSH-LRVSFSKS 176
E AIT + ++ + + +S
Sbjct: 62 EAAITMVNYYSAVTPHLRNQPIYIQYSNH 90
Score = 34.4 bits (79), Expect = 0.004
Identities = 9/63 (14%), Positives = 23/63 (36%), Gaps = 3/63 (4%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAM--MHMDKLRVFGKQMRVMISKHQAVQLPK 65
+G V + +L K A +++A A + + + + + S H+ ++
Sbjct: 39 FGKVTNILMLKGKNQ-AFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKTSG 97
Query: 66 EGQ 68
Sbjct: 98 PSS 100
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 60.3 bits (146), Expect = 2e-12
Identities = 18/104 (17%), Positives = 38/104 (36%), Gaps = 3/104 (2%)
Query: 74 TKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKF 133
+ S + + ++ PS +H+ +P VTE E+ G V
Sbjct: 5 HHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFG-KVTNLLM 63
Query: 134 FPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSH-LRVSFSKS 176
K + A +++++ E A T + + + + + FS
Sbjct: 64 L-KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 59.1 bits (143), Expect = 3e-12
Identities = 17/92 (18%), Positives = 34/92 (36%), Gaps = 3/92 (3%)
Query: 86 KKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQL 145
+ + PS +H+ +P VTE E+ G V K + A +++
Sbjct: 2 RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFG-KVTNLL-MLKGKNQAFIEM 59
Query: 146 DSIEEAITALIQMHNHQLSEQSH-LRVSFSKS 176
++ E A T + + + + + FS
Sbjct: 60 NTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 91
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 58.4 bits (142), Expect = 4e-12
Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 3/81 (3%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQ 157
P+ L + + + + L F G +++ K A +Q +S++ A A +
Sbjct: 15 NPTTRLWVGGLGPNTSLAALAREFDRFG-SIRTID-HVKGDSFAYIQYESLDAAQAACAK 72
Query: 158 MHNHQLSEQSH-LRVSFSKSN 177
M L LRV F+KS
Sbjct: 73 MRGFPLGGPDRRLRVDFAKSG 93
Score = 33.4 bits (77), Expect = 0.010
Identities = 9/49 (18%), Positives = 16/49 (32%), Gaps = 1/49 (2%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMIS 56
+G + + + A IQ A A M + G R+ +
Sbjct: 41 FGSIRTIDHVKGDS-FAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD 88
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing,
transcription, RNA binding protein, mRNA processing; NMR
{Homo sapiens} PDB: 2yh1_A
Length = 198
Score = 57.7 bits (140), Expect = 6e-11
Identities = 28/187 (14%), Positives = 65/187 (34%), Gaps = 32/187 (17%)
Query: 1 MFSLTGVYGDV--LRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
F+ G + + + + A ++ + AM D + G+ +++
Sbjct: 24 FFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKI 82
Query: 54 MISKHQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVT 113
+ P + QP G++++ + + ++ + +P +
Sbjct: 83 --------RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLF-------IGGLPNYLN 127
Query: 114 EDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEAITALIQMHNHQLSEQS 167
+D++KE T G +K F KD A + I A+ ++ QL ++
Sbjct: 128 DDQVKELLTSFG-PLKAFN-LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK- 184
Query: 168 HLRVSFS 174
L V +
Sbjct: 185 KLLVQRA 191
Score = 41.9 bits (99), Expect = 3e-05
Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 13/84 (15%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFP----------KDRKMALLQLDSIEEA 151
L++ NIP +TE+ + + F + + G P +D+ A L+ S++E
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQM-RLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 152 ITALIQMHNHQLSEQSHLRVSFSK 175
A + QS L++
Sbjct: 65 TQA-MAFDGIIFQGQS-LKIRRPH 86
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A
Length = 282
Score = 58.0 bits (139), Expect = 1e-10
Identities = 20/114 (17%), Positives = 44/114 (38%), Gaps = 1/114 (0%)
Query: 62 QLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAF 121
+P G + + + PP+ L L+N+P E L F
Sbjct: 169 MIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLF 228
Query: 122 TEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSK 175
+ K + P +A ++ D+ +A A + ++++ + +++SF+K
Sbjct: 229 NQFP-GFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK 281
Score = 42.6 bits (99), Expect = 2e-05
Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 6/85 (7%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTE--KGF-TVKGFKFF--PKDRKMALLQLDSIEEAI 152
P+ T++++N+ + +DELK++ F + K R A + + A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 153 TALIQMHNHQLSEQSHLRVSFSKSN 177
AL M + +R+ ++K++
Sbjct: 67 NALRSMQGFPFYD-KPMRIQYAKTD 90
Score = 36.8 bits (84), Expect = 0.002
Identities = 15/96 (15%), Positives = 32/96 (33%), Gaps = 2/96 (2%)
Query: 8 YGDVLRVKILYNK--KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQLPK 65
+G +L + + + + A + E A A+ M + K MR+ +K + + K
Sbjct: 37 FGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 96
Query: 66 EGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSP 101
+ + P +K +P
Sbjct: 97 MKGTFVERDRKREKRKPKSQETPATKKAVQGGGATP 132
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 55.8 bits (135), Expect = 4e-10
Identities = 27/185 (14%), Positives = 64/185 (34%), Gaps = 52/185 (28%)
Query: 8 YGDVLRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQ 62
+G + + + ++ A ++ A LA+ M+ + + G+ ++V +
Sbjct: 52 FGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVG--RPSN-- 107
Query: 63 LPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFT 122
+ QP ++ F IY ++++ +++D++K F
Sbjct: 108 -IGQAQPII------------DQLAEEARAFNRIY-------VASVHQDLSDDDIKSVFE 147
Query: 123 EKGFTV-------------KGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHL 169
G KG+ F ++ + + + A+ M+ L Q L
Sbjct: 148 AFGKIKSATLARDPTTGKHKGYGF---------IEYEKAQSSQDAVSSMNLFDLGGQY-L 197
Query: 170 RVSFS 174
RV +
Sbjct: 198 RVGKA 202
Score = 30.4 bits (69), Expect = 0.26
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 107 NIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------ALLQLDSIEEAITALIQMHN 160
+I + ED +++AF G +K D A ++ + E A AL QM++
Sbjct: 35 SIYYELGEDTIRQAFAPFG-PIKSID-MSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS 92
Query: 161 HQL 163
L
Sbjct: 93 VML 95
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 53.5 bits (128), Expect = 8e-10
Identities = 24/90 (26%), Positives = 39/90 (43%), Gaps = 3/90 (3%)
Query: 98 PPSPTLHLS--NIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITAL 155
SP L + N+ VT D L + F++ G +K F ++ ALLQ A A
Sbjct: 24 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAK 83
Query: 156 IQMHNHQLSEQSH-LRVSFSKSNIQDIRDN 184
+ + + LR+ FSK +++ N
Sbjct: 84 LSLDGQNIYNACCTLRIDFSKLTSLNVKYN 113
>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related
protein, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 52.7 bits (127), Expect = 1e-09
Identities = 12/91 (13%), Positives = 41/91 (45%), Gaps = 7/91 (7%)
Query: 91 KNFQNIYPPSP----TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLD 146
F+++ S T++ I + +T+ +++ F+ G + + ++ + ++
Sbjct: 12 LRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFG-QIMEIR-VFPEKGYSFVRFS 69
Query: 147 SIEEAITALIQMHNHQLSEQSHLRVSFSKSN 177
+ E A A++ ++ + E ++ + K +
Sbjct: 70 THESAAHAIVSVNGTTI-EGHVVKCYWGKES 99
Score = 40.4 bits (95), Expect = 3e-05
Identities = 8/65 (12%), Positives = 28/65 (43%), Gaps = 4/65 (6%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEG 67
+G ++ +++ + +K + ++ + A A++ ++ + G ++ K
Sbjct: 49 FGQIMEIRV-FPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP---DMTS 104
Query: 68 QPDAG 72
P +G
Sbjct: 105 GPSSG 109
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 51.2 bits (123), Expect = 3e-09
Identities = 20/90 (22%), Positives = 39/90 (43%), Gaps = 7/90 (7%)
Query: 91 KNFQNIYPPSP----TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLD 146
+ +I +P T ++ NIP TE +L F G + FK ++ ++ D
Sbjct: 14 QAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFG-FILDFK-HYPEKGCCFIKYD 71
Query: 147 SIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
+ E+A ++ + N ++ LR + K
Sbjct: 72 THEQAAVCIVALANFPFQGRN-LRTGWGKE 100
Score = 37.3 bits (87), Expect = 3e-04
Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 1/52 (1%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQ 59
+G +L K K I+ QA + ++ + G+ +R K +
Sbjct: 51 FGFILDFKHYPEKG-CCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER 101
>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; 2.00A {Homo sapiens} PDB:
2ek6_A
Length = 95
Score = 50.8 bits (122), Expect = 4e-09
Identities = 18/94 (19%), Positives = 40/94 (42%), Gaps = 7/94 (7%)
Query: 88 PGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-----MAL 142
GS + P + + N+P +V+ DE+ + F + K A+
Sbjct: 3 SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVC-LKYNEKGMPTGEAM 61
Query: 143 LQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
+ +S +EA A+I +++ + + +++S S
Sbjct: 62 VAFESRDEATAAVIDLNDRPIGSR-KVKLSGPSS 94
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 51.6 bits (123), Expect = 6e-09
Identities = 24/90 (26%), Positives = 39/90 (43%), Gaps = 3/90 (3%)
Query: 98 PPSPTLHLS--NIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITAL 155
SP L + N+ VT D L + F++ G +K F ++ ALLQ A A
Sbjct: 42 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAK 101
Query: 156 IQMHNHQLSEQSH-LRVSFSKSNIQDIRDN 184
+ + + LR+ FSK +++ N
Sbjct: 102 LSLDGQNIYNACCTLRIDFSKLTSLNVKYN 131
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 49.6 bits (119), Expect = 7e-09
Identities = 14/74 (18%), Positives = 33/74 (44%), Gaps = 2/74 (2%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNH 161
TL++ + ++TE +L+ F + G ++ ++ A +Q + + A A + N
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFG-EIRTITVVQ-RQQCAFIQFATRQAAEVAAEKSFNK 71
Query: 162 QLSEQSHLRVSFSK 175
+ L V + +
Sbjct: 72 LIVNGRRLNVKWGR 85
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 50.5 bits (120), Expect = 1e-08
Identities = 12/86 (13%), Positives = 33/86 (38%), Gaps = 6/86 (6%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGK--QMRVMISKH 58
++++ G V R+ I A+++ A A ++ ++ +++ ++
Sbjct: 42 LYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP 101
Query: 59 QAVQLPKEGQPDAGLTKDYTASPLHR 84
+ + + + DYT L R
Sbjct: 102 TRLNVIRNDND----SWDYTKPYLGR 123
Score = 45.8 bits (108), Expect = 4e-07
Identities = 20/109 (18%), Positives = 44/109 (40%), Gaps = 6/109 (5%)
Query: 79 ASPLHRFKKPGSKNFQNIYPPSPTLHLS--NIPASVTEDELKEAFTEKGFTVKGFKFFPK 136
S R +PG+ + + + L LS N +T D L G V+ F +
Sbjct: 4 GSSGKRITRPGNTDDPS--GGNKVLLLSIQNPLYPITVDVLYTVCNPVGK-VQRIVIFKR 60
Query: 137 DRKMALLQLDSIEEAITALIQMHNHQLSEQSH-LRVSFSKSNIQDIRDN 184
+ A+++ +S+ A A ++ + L++ +++ ++ N
Sbjct: 61 NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLNVIRN 109
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition
motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 99
Score = 49.6 bits (119), Expect = 1e-08
Identities = 22/89 (24%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 88 PGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDS 147
GS + + L + N+P +TE+E+++ F + G + F KD+ ++L++
Sbjct: 3 SGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGE--VFIHKDKGFGFIRLET 60
Query: 148 IEEAITALIQMHNHQLSEQSHLRVSFSKS 176
A A +++ N L + LRV F+
Sbjct: 61 RTLAEIAKVELDNMPLRGKQ-LRVRFACH 88
Score = 32.6 bits (75), Expect = 0.016
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 4/65 (6%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEG 67
YG V I +K I++ A +A + +D + + GKQ+RV + H A
Sbjct: 39 YGKAGEVFIHKDKG-FGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA---SLTS 94
Query: 68 QPDAG 72
P +G
Sbjct: 95 GPSSG 99
>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding
domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 98
Score = 49.2 bits (118), Expect = 1e-08
Identities = 16/94 (17%), Positives = 38/94 (40%), Gaps = 7/94 (7%)
Query: 88 PGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-----MAL 142
GS + P + + N+P +V+ DE+ + F + K A+
Sbjct: 3 SGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVC-LKYNEKGMPTGEAM 61
Query: 143 LQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
+ +S +EA A+I +++ + + +++
Sbjct: 62 VAFESRDEATAAVIDLNDRPIGSR-KVKLVLGSG 94
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 48.7 bits (116), Expect = 3e-08
Identities = 18/79 (22%), Positives = 34/79 (43%), Gaps = 2/79 (2%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQ 157
P + +++ N+P +LK A E G +V + R+ A L A A+
Sbjct: 17 PLAADVYVGNLPRDARVSDLKRALRELG-SVPLRLTWQGPRRRAFLHYPDSAAAQQAVSC 75
Query: 158 MHNHQLSEQSHLRVSFSKS 176
+ +L + LRV+ ++
Sbjct: 76 LQGLRLGTDT-LRVALARQ 93
>1b7f_A Protein (SXL-lethal protein), RNA
(5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing
regulation, RNP domain, RNA complex; 2.60A {Drosophila
melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A*
1sxl_A 2sxl_A
Length = 168
Score = 49.9 bits (120), Expect = 3e-08
Identities = 31/192 (16%), Positives = 63/192 (32%), Gaps = 66/192 (34%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMI 55
+F G + +I+ + K A + + A+ ++ + V K+++V
Sbjct: 23 LFR---AIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSY 79
Query: 56 SKHQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTED 115
+ + E D N+Y ++N+P ++T+D
Sbjct: 80 A-----RPGGESIKDT-----------------------NLY-------VTNLPRTITDD 104
Query: 116 ELKEAFTEKGFTV-------------KGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQ 162
+L F + G V +G F ++ + EEA A+ ++N
Sbjct: 105 QLDTIFGKYGSIVQKNILRDKLTGRPRGVAF---------VRYNKREEAQEAISALNNVI 155
Query: 163 LSEQSH-LRVSF 173
S L V
Sbjct: 156 PEGGSQPLSVRL 167
Score = 36.8 bits (86), Expect = 0.001
Identities = 17/89 (19%), Positives = 39/89 (43%), Gaps = 9/89 (10%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------ALLQLDSIEEAITAL 155
L ++ +P +T+ EL F G + + +D K A + S ++ A+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIG-PINTCR-IMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 156 IQMHNHQLSEQSHLRVSFSKSNIQDIRDN 184
++ + + L+VS+++ + I+D
Sbjct: 63 KVLNGITVRNKR-LKVSYARPGGESIKDT 90
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 48.0 bits (115), Expect = 4e-08
Identities = 23/96 (23%), Positives = 44/96 (45%), Gaps = 9/96 (9%)
Query: 87 KPGSKNFQNIYPPSP-TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-----M 140
S F+ L +S +P S T++EL+E G TVK + +R +
Sbjct: 3 SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHG-TVKDLR-LVTNRAGKPKGL 60
Query: 141 ALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
A ++ ++ +A A+++M + E ++V+ S S
Sbjct: 61 AYVEYENESQASQAVMKMDGMTIKENI-IKVAISNS 95
Score = 34.2 bits (79), Expect = 0.005
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 8 YGDVLRVKILYNK----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
+G V ++++ N+ K A ++ QA A+M MD + + ++V IS
Sbjct: 41 HGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISN 94
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 47.8 bits (114), Expect = 4e-08
Identities = 12/78 (15%), Positives = 31/78 (39%), Gaps = 4/78 (5%)
Query: 100 SPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMH 159
S + + N+P E+ + + + ++++ A + L + E+A A+ H
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYDLKY---CYVDRNKRTAFVTLLNGEQAQNAIQMFH 61
Query: 160 NHQLSEQSHLRVSFSKSN 177
+ + L V ++
Sbjct: 62 QYSFRGK-DLIVQLQPTD 78
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 48.0 bits (115), Expect = 4e-08
Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 9/85 (10%)
Query: 97 YPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEE 150
L ++ + TE+++ + F E G +K DR+ L++ ++ +E
Sbjct: 20 SVEGWILFVTGVHEEATEEDIHDKFAEYG-EIKNIH-LNLDRRTGYLKGYTLVEYETYKE 77
Query: 151 AITALIQMHNHQLSEQSHLRVSFSK 175
A A+ ++ L Q + V +
Sbjct: 78 AQAAMEGLNGQDLMGQP-ISVDWCF 101
Score = 31.5 bits (72), Expect = 0.051
Identities = 9/51 (17%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
YG++ + + ++ K L++ +A AM ++ + G+ + V
Sbjct: 47 YGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 97
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA
splicing, mRNA transport, nonsense-mediated mRNA decay,
nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*
Length = 126
Score = 48.5 bits (116), Expect = 4e-08
Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 9/85 (10%)
Query: 97 YPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEE 150
L ++ + TE+++ + F E G +K DR+ L++ ++ +E
Sbjct: 19 SVEGWILFVTGVHEEATEEDIHDKFAEYG-EIKNIH-LNLDRRTGYLKGYTLVEYETYKE 76
Query: 151 AITALIQMHNHQLSEQSHLRVSFSK 175
A A+ ++ L Q + V +
Sbjct: 77 AQAAMEGLNGQDLMGQP-ISVDWCF 100
Score = 29.6 bits (67), Expect = 0.26
Identities = 9/51 (17%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
YG++ + + ++ K L++ +A AM ++ + G+ + V
Sbjct: 46 YGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 96
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 112
Score = 48.0 bits (114), Expect = 5e-08
Identities = 17/101 (16%), Positives = 41/101 (40%), Gaps = 4/101 (3%)
Query: 78 TASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPAS-VTEDELKEAFTEKGFTVKGFKFFPK 136
+ S + + + F +HLSN+P S ++ + + G +K +
Sbjct: 3 SGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYG-KIKNYILMRM 61
Query: 137 DRKMALLQLDSIEEAITALIQMHNHQLSEQSH-LRVSFSKS 176
+ A +++++ E+A+ + L Q ++V S+
Sbjct: 62 -KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK 101
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein
complex, EXON junct complex, signaling protein; 1.85A
{Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B*
2j0s_D* 2xb2_D*
Length = 110
Score = 46.5 bits (111), Expect = 2e-07
Identities = 17/85 (20%), Positives = 40/85 (47%), Gaps = 9/85 (10%)
Query: 97 YPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEE 150
L +++I EDE++E F + G +K DR+ AL++ ++ ++
Sbjct: 23 SVEGWILFVTSIHEEAQEDEIQEKFCDYG-EIKNIH-LNLDRRTGFSKGYALVEYETHKQ 80
Query: 151 AITALIQMHNHQLSEQSHLRVSFSK 175
A+ A ++ ++ Q+ ++V +
Sbjct: 81 ALAAKEALNGAEIMGQT-IQVDWCF 104
Score = 32.3 bits (74), Expect = 0.023
Identities = 10/51 (19%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
YG++ + + ++ K AL++ QA A ++ + G+ ++V
Sbjct: 50 YGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 100
>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex,
AU-rich element, transcription/RNA complex; 1.80A {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H
1d8z_A 1d9a_A 3hi9_A
Length = 167
Score = 47.6 bits (114), Expect = 2e-07
Identities = 29/192 (15%), Positives = 65/192 (33%), Gaps = 66/192 (34%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMI 55
+F G++ K++ +K + + A A+ ++ LR+ K ++V
Sbjct: 22 LFG---SIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSY 78
Query: 56 SKHQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTED 115
++ P N+Y +S +P ++T+
Sbjct: 79 AR------PSSASIRDA----------------------NLY-------VSGLPKTMTQK 103
Query: 116 ELKEAFTEKGFTV-------------KGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQ 162
EL++ F++ G + +G F ++ D EA A+ ++ +
Sbjct: 104 ELEQLFSQYGRIITSRILVDQVTGVSRGVGF---------IRFDKRIEAEEAIKGLNGQK 154
Query: 163 LSEQSH-LRVSF 173
S + + V F
Sbjct: 155 PSGATEPITVKF 166
Score = 36.0 bits (84), Expect = 0.002
Identities = 15/83 (18%), Positives = 40/83 (48%), Gaps = 9/83 (10%)
Query: 107 NIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------ALLQLDSIEEAITALIQMHN 160
+P ++T++E + F G ++ K +D+ + ++A A+ ++
Sbjct: 9 YLPQNMTQEEFRSLFGSIG-EIESCK-LVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG 66
Query: 161 HQLSEQSHLRVSFSKSNIQDIRD 183
+L ++ ++VS+++ + IRD
Sbjct: 67 LRLQTKT-IKVSYARPSSASIRD 88
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 45.9 bits (109), Expect = 2e-07
Identities = 17/78 (21%), Positives = 33/78 (42%), Gaps = 4/78 (5%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDR--KMALLQLDSIEEAITALIQMH 159
L + NIP + + L + G V+ + D + + S ++A AL +++
Sbjct: 17 KLQIRNIPPHLQWEVLDSLLVQYG-VVESCEQVNTDSETAVVNVTYSSKDQARQALDKLN 75
Query: 160 NHQLSEQSHLRVSFSKSN 177
QL E L+V++
Sbjct: 76 GFQL-ENFTLKVAYIPDE 92
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 46.3 bits (110), Expect = 2e-07
Identities = 12/81 (14%), Positives = 28/81 (34%), Gaps = 7/81 (8%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEAITAL 155
L + IP +E+ E + V + A ++ +S A A
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 156 IQMHNHQLSEQSH-LRVSFSK 175
++ ++ H + V +++
Sbjct: 70 RKLMPGRIQLWGHQIAVDWAE 90
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain,
RNA-protein complex, nucleolus, structural protein/RNA
complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1
d.58.7.1 PDB: 1rkj_A 2krr_A
Length = 175
Score = 47.2 bits (113), Expect = 3e-07
Identities = 21/181 (11%), Positives = 55/181 (30%), Gaps = 58/181 (32%)
Query: 8 YGDVLRVKILYNKKDS----ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQL 63
+ ++ + + + + A+ + L+VFG ++++ K
Sbjct: 37 LFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPK------ 89
Query: 64 PKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTE 123
+ + + N+ ++TEDELKE F +
Sbjct: 90 --------------------GRDSKKVRAARTLL-------AKNLSFNITEDELKEVFED 122
Query: 124 KGFTV---------KGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFS 174
+ KG + ++ S +A L + ++ +S + + ++
Sbjct: 123 AL-EIRLVSQDGKSKGIAY---------IEFKSEADAEKNLEEKQGAEIDGRS-VSLYYT 171
Query: 175 K 175
Sbjct: 172 G 172
Score = 33.7 bits (78), Expect = 0.017
Identities = 13/83 (15%), Positives = 29/83 (34%), Gaps = 7/83 (8%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKD----RKMALLQLDSIEEAIT 153
L + N+ + + ELK A +E RK + +S E+
Sbjct: 11 TTPFNLFIGNLNPNKSVAELKVAISELF-AKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69
Query: 154 ALIQMHNHQLSEQSHLRVSFSKS 176
A +++ ++ +++ K
Sbjct: 70 A-LELTGLKVFGN-EIKLEKPKG 90
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 45.7 bits (108), Expect = 4e-07
Identities = 10/79 (12%), Positives = 30/79 (37%), Gaps = 6/79 (7%)
Query: 99 PSPTLHL----SNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITA 154
T L + V+ ++L + G V P ++ + + + EE+ A
Sbjct: 22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCG-LVDALLMPP-NKPYSFARYRTTEESKRA 79
Query: 155 LIQMHNHQLSEQSHLRVSF 173
+ ++ ++ + +++
Sbjct: 80 YVTLNGKEVVDDLGQKITL 98
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 45.6 bits (108), Expect = 5e-07
Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 3/77 (3%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNH 161
+ N+PA E++E F+ G ++ P+ A+++ EA A +
Sbjct: 12 VILAKNLPAGTLAAEIQETFSRFG-SLGRVL-LPEGGITAIVEFLEPLEARKAFRHLAYS 69
Query: 162 QLSEQSHLRVSFSKSNI 178
+ L + ++ +
Sbjct: 70 KF-HHVPLYLEWAPIGV 85
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 45.0 bits (107), Expect = 5e-07
Identities = 19/89 (21%), Positives = 32/89 (35%), Gaps = 11/89 (12%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKG-FTVKGFKFFPKDRK------MALLQLDSIEE 150
T+ L NI D + A + V + KD++ A +QL S +
Sbjct: 7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIR-LIKDKQTQQNRGFAFVQLSSAMD 65
Query: 151 AITALIQMHNHQLSEQ---SHLRVSFSKS 176
A L + + + + V F+KS
Sbjct: 66 ASQLLQILQSLHPPLKIDGKTIGVDFAKS 94
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear
ribonucleoprotein, R binding domain, RNA binding
protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1
PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A*
3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P*
3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A*
...
Length = 97
Score = 44.9 bits (107), Expect = 6e-07
Identities = 18/87 (20%), Positives = 41/87 (47%), Gaps = 10/87 (11%)
Query: 98 PPSPTLHLSNIPASVTEDELKEA----FTEKGFTVKGFKFFPKDRKM---ALLQLDSIEE 150
P+ T++++N+ + +DELK++ F+ G + + KM A + +
Sbjct: 6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFG-QILDIL-VSRSLKMRGQAFVIFKEVSS 63
Query: 151 AITALIQMHNHQLSEQSHLRVSFSKSN 177
A AL M ++ +R+ ++K++
Sbjct: 64 ATNALRSMQGFPFYDK-PMRIQYAKTD 89
Score = 36.1 bits (84), Expect = 0.001
Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 2/59 (3%)
Query: 1 MFSLTGVYGDVLRVKILYNK--KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
+ ++ +G +L + + + + A + E A A+ M + K MR+ +K
Sbjct: 29 LHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK 87
>4a8x_A RNA-binding protein with serine-rich domain 1; transcription,
splicing, RNA processing, nonsense mediated D NMD, HDAC,
histone deacetylation; 1.90A {Homo sapiens}
Length = 88
Score = 44.5 bits (106), Expect = 6e-07
Identities = 18/85 (21%), Positives = 35/85 (41%), Gaps = 10/85 (11%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-------MALLQLDSIEE 150
+H+ + +VT+D + E F+ G +K P +R A ++ ++ +E
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYG-KIKMID-MPVERMHPHLSKGYAYVEFENPDE 59
Query: 151 AITALIQMHNHQLSEQSHLRVSFSK 175
A AL M Q+ Q + +
Sbjct: 60 AEKALKHMDGGQIDGQE-ITATAVL 83
Score = 34.1 bits (79), Expect = 0.004
Identities = 9/54 (16%), Positives = 22/54 (40%), Gaps = 6/54 (11%)
Query: 6 GVYGDVLRVKILYNKKDS------ALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
YG + + + + A ++ +A A+ HMD ++ G+++
Sbjct: 26 STYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITA 79
>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 115
Score = 45.4 bits (108), Expect = 6e-07
Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 10/97 (10%)
Query: 86 KKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDR---KM-- 140
K P ++ P+ L+L N+ VTE +L F KG +M
Sbjct: 12 KIPMFSSYNPG-EPNKVLYLKNLSPRVTERDLVSLFARFQ-EKKGPP-IQFRMMTGRMRG 68
Query: 141 -ALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
A + + E A AL ++ ++L + L + F K+
Sbjct: 69 QAFITFPNKEIAWQALHLVNGYKLYGKI-LVIEFGKN 104
Score = 31.5 bits (72), Expect = 0.052
Identities = 10/72 (13%), Positives = 25/72 (34%), Gaps = 8/72 (11%)
Query: 6 GVYGDVLRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+ + I + A I A A+ ++ +++GK + + K++
Sbjct: 47 ARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK 106
Query: 61 VQLPKEGQPDAG 72
+ P +G
Sbjct: 107 ---QRSSGPSSG 115
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 45.0 bits (107), Expect = 7e-07
Identities = 14/86 (16%), Positives = 32/86 (37%), Gaps = 9/86 (10%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM-------ALLQLDSIEE 150
+ + + NIP + E++E F+ G +K + PK + + ++
Sbjct: 13 QTTSKILVRNIPFQANQREIRELFSTFG-ELKTVR-LPKKMTGTGAHRGFGFVDFITKQD 70
Query: 151 AITALIQMHNHQLSEQSHLRVSFSKS 176
A A + + L + ++ S
Sbjct: 71 AKKAFNALCHSTHLYGRRLVLEWADS 96
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA
recognition, alternative conformation binding protein;
HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A
Length = 87
Score = 44.3 bits (105), Expect = 7e-07
Identities = 15/74 (20%), Positives = 28/74 (37%), Gaps = 13/74 (17%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKG---------FKFFPKDRKMALLQLDSIEEAIT 153
L++ NIP +TE+ + + F + +D+ A L+ S++E
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 154 AL----IQMHNHQL 163
A+ I L
Sbjct: 69 AMAFDGIIFQGQSL 82
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif,
U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein;
2.50A {Homo sapiens}
Length = 143
Score = 45.6 bits (108), Expect = 7e-07
Identities = 20/107 (18%), Positives = 43/107 (40%), Gaps = 11/107 (10%)
Query: 79 ASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKG-FTVKGFKFFPKD 137
S ++++ P+ +++ N+ V E +LK F F+ + +
Sbjct: 25 ISREEMETLSVFRSYEPG-EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDI 83
Query: 138 RKM--------ALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
R M A + L + + A AL + + + L + + V F++S
Sbjct: 84 RLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK-PMVVQFARS 129
Score = 27.1 bits (60), Expect = 2.0
Identities = 10/37 (27%), Positives = 16/37 (43%)
Query: 21 KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
K A I + A A+ + +FGK M V ++
Sbjct: 92 KGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFAR 128
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 45.1 bits (107), Expect = 7e-07
Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 7/81 (8%)
Query: 88 PGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-----MAL 142
GS ++ H++NIP S+T+ ++ + + D AL
Sbjct: 3 SGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIP-VDENAVHVLVDNNGQGLGQAL 61
Query: 143 LQLDSIEEAITALIQMHNHQL 163
+Q + ++A + ++H +L
Sbjct: 62 VQFKNEDDARKSE-RLHRKKL 81
>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP,
RBD, poly(U) binding, tandem, acetylation, cytopla
nucleus; 2.70A {Saccharomyces cerevisiae}
Length = 166
Score = 46.0 bits (110), Expect = 8e-07
Identities = 25/190 (13%), Positives = 69/190 (36%), Gaps = 60/190 (31%)
Query: 2 FSLTGVYGDVLRVKILYNKKDSAL----IQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
V G + +KI+ +K + + ++ +SH A++A+ ++ ++ +++ +
Sbjct: 18 KQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWA- 76
Query: 58 HQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDEL 117
+ D T N++ + ++ +V ++ L
Sbjct: 77 ----------FQSQQSSSDDTF---------------NLF-------VGDLNVNVDDETL 104
Query: 118 KEAFTEKGFTV-------------KGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLS 164
+ AF + + +G+ F + S ++A A+ M L+
Sbjct: 105 RNAFKDFPSYLSGHVMWDMQTGSSRGYGF---------VSFTSQDDAQNAMDSMQGQDLN 155
Query: 165 EQSHLRVSFS 174
+ LR++++
Sbjct: 156 GRP-LRINWA 164
Score = 35.2 bits (82), Expect = 0.005
Identities = 18/88 (20%), Positives = 40/88 (45%), Gaps = 8/88 (9%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM-----ALLQLDSIEEAITALI 156
L++ N+ ++TED LK+ F G + K D+ A ++ +A AL
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGG-PIANIK-IMIDKNNKNVNYAFVEYHQSHDANIALQ 59
Query: 157 QMHNHQLSEQSHLRVSFSKSNIQDIRDN 184
++ Q+ ++++++ + Q D+
Sbjct: 60 TLNGKQIENNI-VKINWAFQSQQSSSDD 86
>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 99
Score = 44.6 bits (106), Expect = 8e-07
Identities = 17/88 (19%), Positives = 39/88 (44%), Gaps = 3/88 (3%)
Query: 88 PGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDS 147
GS ++ L++ N+ S +E+ +++ F + K R A + +
Sbjct: 3 SGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIK-PGAVER-VKKIRDYAFVHFSN 60
Query: 148 IEEAITALIQMHNHQLSEQSHLRVSFSK 175
E+A+ A+ ++ L + S + V+ +K
Sbjct: 61 REDAVEAMKALNGKVL-DGSPIEVTLAK 87
Score = 31.9 bits (73), Expect = 0.027
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 9 GDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
G V RVK + +D A + + A AM ++ + G + V ++K
Sbjct: 42 GAVERVKKI---RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK 87
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 44.5 bits (106), Expect = 8e-07
Identities = 18/83 (21%), Positives = 39/83 (46%), Gaps = 9/83 (10%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------ALLQLDSIEEAI 152
PS ++L +IP TE+++ + + G V K D + A ++ +E +
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVG-PVINLK-MMFDPQTGRSKGYAFIEFRDLESSA 58
Query: 153 TALIQMHNHQLSEQSHLRVSFSK 175
+A+ ++ +QL + L+ +S
Sbjct: 59 SAVRNLNGYQLGSRF-LKCGYSS 80
Score = 27.6 bits (62), Expect = 0.86
Identities = 7/51 (13%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
G V+ +K++++ K A I+ + + A+ +++ ++ + ++
Sbjct: 26 VGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC 76
>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA
binding domain, RNA recognition motif, SP factor, snRNP,
spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP:
d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A
Length = 292
Score = 46.9 bits (112), Expect = 9e-07
Identities = 26/181 (14%), Positives = 61/181 (33%), Gaps = 43/181 (23%)
Query: 8 YGDVLRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQ 62
V L + + + A I + A + ++ L++ G + +S
Sbjct: 141 INVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN----- 195
Query: 63 LPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVT-EDELKEAF 121
PL + K+ S + + + N+ + E+ L+E+F
Sbjct: 196 ------------------PLEKSKRTDSATLE-----GREIMIRNLSTELLDENLLRESF 232
Query: 122 TEKGFTVKGFKFFPKDRKM------ALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSK 175
G +++ ++ A + ++ + A A +QM+ L + + VS +
Sbjct: 233 EGFG-SIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA-LQMNRSLLGNRE-ISVSLAD 289
Query: 176 S 176
Sbjct: 290 K 290
Score = 43.4 bits (103), Expect = 1e-05
Identities = 24/176 (13%), Positives = 52/176 (29%), Gaps = 53/176 (30%)
Query: 8 YGDVLRVKILYNKKDS---ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQLP 64
G ++ V + + K + A I+ A A A+ K V ++ V
Sbjct: 65 CGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK-VVGQNEIIV----------- 112
Query: 65 KEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEK 124
++ ++N P S T+ +++ +
Sbjct: 113 ------------------------SHLTECTLW-------MTNFPPSYTQRNIRDLLQDI 141
Query: 125 GFTVKGFKFFPKDRKM-----ALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSK 175
V P R A + + S E+A + +++ ++ + L S
Sbjct: 142 N-VVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYT-LVTKVSN 195
Score = 32.7 bits (75), Expect = 0.046
Identities = 11/62 (17%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFP---KDRKMALLQLDSIEEAITALIQM 158
T+ + N+P S ++++ + F G + K+ + A ++ + A+ A+ +
Sbjct: 43 TVLVKNLPKSYNQNKVYKYFKHCG-PIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 101
Query: 159 HN 160
H
Sbjct: 102 HK 103
>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar
mRNA localization, translation; 1.90A {Drosophila
melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A
Length = 165
Score = 45.2 bits (107), Expect = 1e-06
Identities = 17/86 (19%), Positives = 40/86 (46%), Gaps = 9/86 (10%)
Query: 97 YPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------ALLQLDSIEE 150
L +++I EDE++E F + G +K DR+ AL++ ++ ++
Sbjct: 69 SVEGWILFVTSIHEEAQEDEIQEKFCDYG-EIKNIH-LNLDRRTGFSKGYALVEYETHKQ 126
Query: 151 AITALIQMHNHQLSEQSHLRVSFSKS 176
A+ A ++ ++ Q+ ++V +
Sbjct: 127 ALAAKEALNGAEIMGQT-IQVDWCFV 151
Score = 34.4 bits (79), Expect = 0.008
Identities = 11/67 (16%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQ 62
YG++ + + ++ K AL++ QA A ++ + G+ ++V + +
Sbjct: 96 YGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK 155
Query: 63 LPKEGQP 69
K+ +
Sbjct: 156 RVKKSEK 162
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1;
RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 94
Score = 43.4 bits (103), Expect = 2e-06
Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 9/93 (9%)
Query: 88 PGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MA 141
S + P T+++SN+P S+T ++L F++ G V KD+ +A
Sbjct: 4 GSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYG-KVVKVT-IMKDKDTRKSKGVA 61
Query: 142 LLQLDSIEEAITALIQMHNHQLSEQSHLRVSFS 174
+ + A ++N QL + ++ S +
Sbjct: 62 FILFLDKDSAQNCTRAINNKQLFGRV-IKASIA 93
Score = 32.6 bits (75), Expect = 0.014
Identities = 12/51 (23%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
YG V++V I+ +K K A I + A ++ ++FG+ ++
Sbjct: 40 YGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKA 90
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 43.6 bits (103), Expect = 2e-06
Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 9/71 (12%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-----MALLQLDSIEEAI 152
P + + +P S E+++++ F G V KD L++ S ++
Sbjct: 14 PDDLYVSVHGMPFSAMENDVRDFF--HGLRVDAVH-LLKDHVGRNNGNGLVKFLSPQDTF 70
Query: 153 TALIQMHNHQL 163
AL + + +
Sbjct: 71 EAL-KRNRMLM 80
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 101
Score = 43.4 bits (103), Expect = 2e-06
Identities = 25/96 (26%), Positives = 38/96 (39%), Gaps = 19/96 (19%)
Query: 89 GSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTV---------KGFKFFPKDRK 139
GS S TL LSN+ S TE+ L+E F + F KG+ F
Sbjct: 4 GSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAF------ 57
Query: 140 MALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSK 175
++ S E+A AL + ++ E +R+
Sbjct: 58 ---IEFASFEDAKEALNSCNKREI-EGRAIRLELQG 89
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 43.7 bits (103), Expect = 3e-06
Identities = 14/105 (13%), Positives = 34/105 (32%), Gaps = 8/105 (7%)
Query: 78 TASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEA----FTEKG--FTVKGF 131
P + PS + ++NI V +++L+ + +G +
Sbjct: 7 AKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD 66
Query: 132 KFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
+ A + + E A + + L ++FS++
Sbjct: 67 L-SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGN-PLVITFSET 109
Score = 41.0 bits (96), Expect = 3e-05
Identities = 11/65 (16%), Positives = 23/65 (35%), Gaps = 2/65 (3%)
Query: 8 YGDVLRVKILYNKK--DSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQLPK 65
GD+L + + + A I A A + G + + S+ Q+ +
Sbjct: 57 QGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAE 116
Query: 66 EGQPD 70
+G +
Sbjct: 117 DGSLE 121
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM
domain, riken structural genomics/proteomics initiative,
RSGI; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 42.8 bits (101), Expect = 4e-06
Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 5/70 (7%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM----ALLQLDSIEEAIT 153
+ L +P +++E+ + F+ G + A +Q S E A
Sbjct: 13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEK 72
Query: 154 ALIQMHNHQL 163
AL + H ++
Sbjct: 73 AL-KKHKERI 81
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif,
C-terminal helix, N-terminal helix, RNA binding protein;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 43.0 bits (102), Expect = 4e-06
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 9/87 (10%)
Query: 96 IYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIE 149
+ ++ + NIP TE++LK+ F+E G V F+ DR+ + E
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVG-PVVSFR-LVYDRETGKPKGYGFCEYQDQE 61
Query: 150 EAITALIQMHNHQLSEQSHLRVSFSKS 176
A++A+ ++ + S ++ LRV + S
Sbjct: 62 TALSAMRNLNGREFSGRA-LRVDNAAS 87
Score = 28.0 bits (63), Expect = 0.73
Identities = 10/51 (19%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
G V+ +++Y++ K + + A AM +++ G+ +RV
Sbjct: 32 VGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRV 82
>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA
processing, mRNA splicing, transport, nucleus,
RNA-binding, spliceosome, transport; NMR {Mus musculus}
Length = 124
Score = 43.1 bits (102), Expect = 4e-06
Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 8/85 (9%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-----MALLQLDSIEEAI 152
L +SN+ V++ +++E F E G T+K DR A + + +A+
Sbjct: 33 ETGAKLLVSNLDFGVSDADIQELFAEFG-TLKKAA-VDYDRSGRSLGTADVHFERRADAL 90
Query: 153 TALIQMHNHQLSEQSHLRVSFSKSN 177
A+ Q L + + + S
Sbjct: 91 KAMKQYKGVPLDGRP-MDIQLVASQ 114
Score = 32.7 bits (75), Expect = 0.020
Identities = 8/50 (16%), Positives = 20/50 (40%), Gaps = 4/50 (8%)
Query: 8 YGDVLRVKILYNK----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+G + + + Y++ +A + A AM + + G+ M +
Sbjct: 59 FGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI 108
>2bz2_A Negative elongation factor E; NELF E, RNA recognition motif,
alternative splicing, nuclear protein, phosphorylation,
repeat, repressor; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2jx2_A
Length = 121
Score = 43.2 bits (102), Expect = 4e-06
Identities = 19/101 (18%), Positives = 40/101 (39%), Gaps = 9/101 (8%)
Query: 81 PLHRFKKPGSKNFQNIYPPSP----TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPK 136
P P ++ +P TL++ +T L+ AF+ G +
Sbjct: 16 PRGSHMGPFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFG-NIIDLSM-DP 71
Query: 137 DRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKSN 177
R A + + +E A A+ +++ Q+ E L+V+ ++
Sbjct: 72 PRNCAFVTYEKMESADQAVAELNGTQV-ESVQLKVNIARKQ 111
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural
genomi center for structural genomics, JCSG, protein
structure INI PSI-biology; 2.54A {Homo sapiens} PDB:
1no8_A
Length = 107
Score = 42.7 bits (101), Expect = 5e-06
Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 8/84 (9%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-----MALLQLDSIEEAI 152
L +SN+ V++ +++E F E G T+K DR A + + +A+
Sbjct: 27 ETGGKLLVSNLDFGVSDADIQELFAEFG-TLKKAA-VHYDRSGRSLGTADVHFERKADAL 84
Query: 153 TALIQMHNHQLSEQSHLRVSFSKS 176
A+ Q + L + + + S
Sbjct: 85 KAMKQYNGVPLDGRP-MNIQLVTS 107
Score = 33.0 bits (76), Expect = 0.016
Identities = 8/50 (16%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 8 YGDVLRVKILYNK----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+G + + + Y++ +A + A AM + + + G+ M +
Sbjct: 53 FGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 102
>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 99
Score = 41.8 bits (99), Expect = 9e-06
Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 9/84 (10%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEA 151
S L + N+ + +E++L++ F+ G + +P D A + E A
Sbjct: 6 SGSGRLFVRNLSYTSSEEDLEKLFSAYG-PLSELH-YPIDSLTKKPKGFAFVTFMFPEHA 63
Query: 152 ITALIQMHNHQLSEQSHLRVSFSK 175
+ A ++ + L V S
Sbjct: 64 VKAYAEVDGQVFQGRM-LHVLPST 86
Score = 30.3 bits (69), Expect = 0.099
Identities = 12/70 (17%), Positives = 22/70 (31%), Gaps = 11/70 (15%)
Query: 8 YGDVLRVKILYNK--KDS---ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQ 62
YG + + + K A + A A +D G+ + V+ S
Sbjct: 32 YGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST----- 86
Query: 63 LPKEGQPDAG 72
K+ +G
Sbjct: 87 -IKKEASQSG 95
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 96
Score = 41.5 bits (98), Expect = 9e-06
Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 18/87 (20%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTV--------KGFKFFPKDRKMALLQLDSIE 149
+ TL N+ ++TEDELKE F + KG + ++ S
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAY---------IEFKSEA 64
Query: 150 EAITALIQMHNHQLSEQSHLRVSFSKS 176
+A L + ++ +S + + ++
Sbjct: 65 DAEKNLEEKQGAEIDGRS-VSLYYTGE 90
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 43.4 bits (103), Expect = 1e-05
Identities = 25/185 (13%), Positives = 54/185 (29%), Gaps = 47/185 (25%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMI 55
+ +G + R ++Y+++ + + A A + + + + V
Sbjct: 115 LVR---PFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW 171
Query: 56 SKHQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTED 115
+ + P S L + +P +
Sbjct: 172 TD------AGQLTPAL--------------------------LHSRCLCVDRLPPGFNDV 199
Query: 116 E-LKEAFTEKGFTVKGFKFFP----KDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLR 170
+ L A + + + + + A+L+ ++ E A A Q L HLR
Sbjct: 200 DALCRALSAVH-SPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGS-HLR 257
Query: 171 VSFSK 175
VSF
Sbjct: 258 VSFCA 262
Score = 42.7 bits (101), Expect = 2e-05
Identities = 21/182 (11%), Positives = 54/182 (29%), Gaps = 53/182 (29%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+ S + + K +A + + QA A+ + R+ +++ V + A
Sbjct: 42 LLSDYEL----KYCFVDKYKG-TAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDA 96
Query: 61 VQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEA 120
+ ++N+P S+T+ + +E
Sbjct: 97 ----------------------------------LLC-------VANLPPSLTQQQFEEL 115
Query: 121 FTEKGFTVKGFKFFPKDRKM-----ALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSK 175
G +++ +R + + A A + L ++ L V ++
Sbjct: 116 VRPFG-SLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRT-LYVHWTD 173
Query: 176 SN 177
+
Sbjct: 174 AG 175
Score = 40.7 bits (96), Expect = 9e-05
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 4/71 (5%)
Query: 107 NIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQ 166
+P VT E+ + ++ F K + A + L + E+A A+ H +L E+
Sbjct: 29 GLPGDVTNQEVHDLLSDYELKY---CFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRER 85
Query: 167 SHLRVSFSKSN 177
L V ++
Sbjct: 86 -ELSVQLQPTD 95
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 42.9 bits (101), Expect = 1e-05
Identities = 21/108 (19%), Positives = 40/108 (37%), Gaps = 9/108 (8%)
Query: 75 KDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFF 134
K H G + + + L +SN+ V++ +++E F E G T+K
Sbjct: 64 KPLPDKWQHDLFDSGCGGGEGVETGA-KLLVSNLDFGVSDADIQELFAEFG-TLKKAA-V 120
Query: 135 PKDRK-----MALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKSN 177
DR A + + +A+ A+ Q L + + + S
Sbjct: 121 DYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRP-MDIQLVASQ 167
Score = 34.4 bits (79), Expect = 0.009
Identities = 8/50 (16%), Positives = 20/50 (40%), Gaps = 4/50 (8%)
Query: 8 YGDVLRVKILYNK----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+G + + + Y++ +A + A AM + + G+ M +
Sbjct: 112 FGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI 161
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 41.0 bits (97), Expect = 1e-05
Identities = 19/94 (20%), Positives = 41/94 (43%), Gaps = 9/94 (9%)
Query: 89 GSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------AL 142
GS + P+ L + + TE +L+E F++ G + D++ A
Sbjct: 4 GSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYG-PIADVS-IVYDQQSRRSRGFAF 61
Query: 143 LQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
+ +++++A A + + +L + +RVS S
Sbjct: 62 VYFENVDDAKEAKERANGMELDGRR-IRVSGPSS 94
Score = 30.2 bits (69), Expect = 0.094
Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
YG + V I+Y++ + A + A A + + + G+++RV
Sbjct: 39 YGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 92
Score = 41.1 bits (97), Expect = 1e-05
Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 15/84 (17%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKG-----FTVKGFKFFPKDRKMALLQLDSIEEAI 152
S LH+ NI + T EL+ F E G VK + F + ++ E+A+
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAF---------VHMERAEDAV 58
Query: 153 TALIQMHNHQLSEQSHLRVSFSKS 176
A+ + N + + + V S S
Sbjct: 59 EAIRGLDNTEF-QGKRMHVQLSTS 81
Score = 33.7 bits (78), Expect = 0.005
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
YG V+ I KD A + M + A A+ +D GK+M V +S
Sbjct: 34 YGPVIECDI---VKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLST 80
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 40.8 bits (95), Expect = 2e-05
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 2/82 (2%)
Query: 100 SPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMH 159
S L L N+ A + L+ + G + F + +AL + + EEA A + ++
Sbjct: 7 SSWLLLKNLTAQIDGPTLRTLCMQHG-PLVSFHPYLNQG-IALCKYTTREEANKAQMALN 64
Query: 160 NHQLSEQSHLRVSFSKSNIQDI 181
N L+ + S S++ +Q I
Sbjct: 65 NCVLANTTIFAESPSENEVQSI 86
>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 93
Score = 40.7 bits (96), Expect = 2e-05
Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 16/82 (19%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTV-------KGFKFFPKDRKMALLQLDSIEEAITA 154
L++ N+ +VT D+L++ F ++ + G+ F + AI A
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAF---------VDYPDQNWAIRA 60
Query: 155 LIQMHNHQLSEQSHLRVSFSKS 176
+ + + V +S S
Sbjct: 61 IETLSGKVELHGKIMEVDYSVS 82
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 40.6 bits (96), Expect = 2e-05
Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 9/84 (10%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------ALLQLDSIEEA 151
S L++ ++ ++TED L+ F G + KD + E A
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFG-KIDNIV-LMKDSDTGRSKGYGFITFSDSECA 60
Query: 152 ITALIQMHNHQLSEQSHLRVSFSK 175
AL Q++ +L+ + +RV
Sbjct: 61 RRALEQLNGFELAGRP-MRVGHVT 83
Score = 27.5 bits (62), Expect = 0.95
Identities = 10/52 (19%), Positives = 24/52 (46%), Gaps = 7/52 (13%)
Query: 8 YGDVLRVKILYNKKDS------ALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+G + + ++ + D+ I ++S A A+ ++ + G+ MRV
Sbjct: 29 FGKIDNIVLMKDS-DTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRV 79
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 41.0 bits (96), Expect = 2e-05
Identities = 11/95 (11%), Positives = 29/95 (30%), Gaps = 12/95 (12%)
Query: 88 PGSKNFQNIYPPSPTLHLSNIPASV-TEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLD 146
GS + +H+ + +L + G + K A +++
Sbjct: 3 SGSSGQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFG-VISNHLILNK-INEAFIEMA 60
Query: 147 SIEEAITALIQMHNHQLSEQSHLR-----VSFSKS 176
+ E+A ++ + + + V S+
Sbjct: 61 TTEDAQA----AVDYYTTTPALVFGKPVRVHLSQK 91
>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP
domain, MIF4G domain, RNA maturation, RNA export,
nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP:
d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B
3fey_B 1h6k_X
Length = 156
Score = 41.7 bits (98), Expect = 2e-05
Identities = 16/91 (17%), Positives = 40/91 (43%), Gaps = 9/91 (9%)
Query: 91 KNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------ALLQ 144
+ + + S TL++ N+ TE+++ E F++ G +K D+ ++
Sbjct: 30 EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSG-DIKKII-MGLDKMKKTACGFCFVE 87
Query: 145 LDSIEEAITALIQMHNHQLSEQSHLRVSFSK 175
S +A A+ ++ +L ++ +R +
Sbjct: 88 YYSRADAENAMRYINGTRLDDRI-IRTDWDA 117
>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 1.54A {Homo sapiens}
Length = 95
Score = 40.3 bits (95), Expect = 2e-05
Identities = 20/94 (21%), Positives = 33/94 (35%), Gaps = 8/94 (8%)
Query: 88 PGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM-----AL 142
S F T+ + N+ A V E+ L E F + G + KDR+
Sbjct: 4 GSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAG-PLTKVT-ICKDREGKPKSFGF 61
Query: 143 LQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
+ E A+ ++ +L + VS S
Sbjct: 62 VCFKHPESVSYAIALLNGIRL-YGRPINVSGPSS 94
Score = 32.6 bits (75), Expect = 0.018
Identities = 8/50 (16%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 8 YGDVLRVKILYNK----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
G + +V I ++ K + A+ ++ +R++G+ + V
Sbjct: 40 AGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINV 89
>1x5p_A Negative elongation factor E; structure genomics, RRM domain,
PARP14, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 97
Score = 40.3 bits (95), Expect = 3e-05
Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 111 SVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLR 170
+T L+ AF+ G + R A + + +E A A+ +++ Q+ E L+
Sbjct: 24 DMTPTLLRGAFSPFG-NIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQV-ESVQLK 80
Query: 171 VSFSKS 176
V+ ++
Sbjct: 81 VNIARK 86
Score = 36.1 bits (84), Expect = 9e-04
Identities = 11/65 (16%), Positives = 30/65 (46%), Gaps = 4/65 (6%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEG 67
+G+++ + + + A + + A A+ ++ +V Q++V I++ Q +
Sbjct: 37 FGNIIDLSMDPPRN-CAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP---MLDS 92
Query: 68 QPDAG 72
P +G
Sbjct: 93 GPSSG 97
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H';
structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 102
Score = 40.1 bits (94), Expect = 3e-05
Identities = 11/80 (13%), Positives = 24/80 (30%), Gaps = 9/80 (11%)
Query: 89 GSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-----MALL 143
GS +H+ +P TE+++ F A +
Sbjct: 4 GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFF--SPLNPMRVH-IEIGPDGRVTGEADV 60
Query: 144 QLDSIEEAITALIQMHNHQL 163
+ + E+A+ A+ +
Sbjct: 61 EFATHEDAVAAM-AKDKANM 79
>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kg0_A
Length = 126
Score = 40.6 bits (95), Expect = 3e-05
Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 7/83 (8%)
Query: 86 KKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-----M 140
++ G + + L +P T++E+ + F+ G P D +
Sbjct: 28 QQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGIT-LPVDPEGKITGE 86
Query: 141 ALLQLDSIEEAITALIQMHNHQL 163
A +Q S E A AL H ++
Sbjct: 87 AFVQFASQELAEKAL-GKHKERI 108
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation
factors PAIP1 and PAIP2, translation-RNA complex; 2.00A
{Homo sapiens} PDB: 1cvj_A*
Length = 213
Score = 41.5 bits (98), Expect = 4e-05
Identities = 33/192 (17%), Positives = 65/192 (33%), Gaps = 59/192 (30%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMI 55
++ G +L +++ + A + + A A+ M+ + GK +R+M
Sbjct: 32 LYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW 91
Query: 56 SKHQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTED 115
S Q D L K NI+ + N+ S+
Sbjct: 92 S-----------QRDPSLRKSGVG---------------NIF-------IKNLDKSIDNK 118
Query: 116 ELKEAFTEKGFTV-----------KGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLS 164
L + F+ G + KG+ F + ++ E A A+ +M+ L+
Sbjct: 119 ALYDTFSAFGNILSCKVVCDENGSKGYGF---------VHFETQEAAERAIEKMNGMLLN 169
Query: 165 EQSHLRVSFSKS 176
++ + V KS
Sbjct: 170 DRK-VFVGRFKS 180
Score = 31.5 bits (72), Expect = 0.11
Identities = 17/93 (18%), Positives = 37/93 (39%), Gaps = 9/93 (9%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------ALLQLDSIEEA 151
P +L++ ++ VTE L E F+ G + + +D A + +A
Sbjct: 13 YPMASLYVGDLHPDVTEAMLYEKFSPAG-PILSIR-VCRDMITRRSLGYAYVNFQQPADA 70
Query: 152 ITALIQMHNHQLSEQSHLRVSFSKSNIQDIRDN 184
AL M+ + + +R+ +S+ + +
Sbjct: 71 ERALDTMNFDVIKGKP-VRIMWSQRDPSLRKSG 102
Score = 26.5 bits (59), Expect = 4.2
Identities = 12/80 (15%), Positives = 30/80 (37%), Gaps = 6/80 (7%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDS---ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
FS +G++L K++ ++ S + A A+ M+ + + +++ V K
Sbjct: 123 TFS---AFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK 179
Query: 58 HQAVQLPKEGQPDAGLTKDY 77
+ + + G
Sbjct: 180 SRKEREAELGARAKEFYPYD 199
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A
Length = 103
Score = 40.0 bits (94), Expect = 4e-05
Identities = 21/90 (23%), Positives = 44/90 (48%), Gaps = 12/90 (13%)
Query: 87 KPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLD 146
G + ++ + N+ +VTE+ L++AF++ G ++ K KD A + D
Sbjct: 5 SSGMAKVKVLF-------VRNLANTVTEEILEKAFSQFG-KLERVK-KLKD--YAFIHFD 53
Query: 147 SIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
+ A+ A+ +M+ L E ++ + F+K
Sbjct: 54 ERDGAVKAMEEMNGKDL-EGENIEIVFAKP 82
Score = 36.1 bits (84), Expect = 0.001
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
+G + RVK L KD A I E A AM M+ + G+ + ++ +K
Sbjct: 35 FGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAK 81
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein
biosynthesis, RNA recognition motif, RNA binding domain,
RRM, RBD, RNP; NMR {Homo sapiens}
Length = 100
Score = 39.9 bits (94), Expect = 4e-05
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 12/85 (14%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM-------ALLQLDSIEEA 151
P T L N+P VTE+ +KE F +G + + P++ + + ++
Sbjct: 18 PPYTAFLGNLPYDVTEESIKEFF--RGLNISAVR-LPREPSNPERLKGFGYAEFEDLDSL 74
Query: 152 ITALIQMHNHQLSEQSHLRVSFSKS 176
++AL ++ L + +RV +
Sbjct: 75 LSAL-SLNEESLGNRR-IRVDVADQ 97
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 91
Score = 39.6 bits (93), Expect = 5e-05
Identities = 11/70 (15%), Positives = 22/70 (31%), Gaps = 9/70 (12%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-----MALLQLDSIEEAIT 153
T+ L P +VTE + E + ++ + + EE
Sbjct: 9 TCHTVKLRGAPFNVTEKNVMEFL--APLKPVAIR-IVRNAHGNKTGYIFVDFSNEEEVKQ 65
Query: 154 ALIQMHNHQL 163
AL + + +
Sbjct: 66 AL-KCNREYM 74
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 39.6 bits (93), Expect = 5e-05
Identities = 15/84 (17%), Positives = 36/84 (42%), Gaps = 11/84 (13%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------ALLQLDSIEEA 151
P T ++ N+P + + ++ F K +++ + +D+ ++ D ++
Sbjct: 13 EPPYTAYVGNLPFNTVQGDIDAIF--KDLSIRSVR-LVRDKDTDKFKGFCYVEFDEVDSL 69
Query: 152 ITALIQMHNHQLSEQSHLRVSFSK 175
AL L ++S LRV ++
Sbjct: 70 KEAL-TYDGALLGDRS-LRVDIAE 91
>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 39.1 bits (92), Expect = 6e-05
Identities = 15/84 (17%), Positives = 34/84 (40%), Gaps = 15/84 (17%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKG-----FTVKGFKFFPKDRKMALLQLDSIEEAI 152
+ + + N+ A+ T EL+ F +G VK + F + ++ +A
Sbjct: 7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAF---------VHMEKEADAK 57
Query: 153 TALIQMHNHQLSEQSHLRVSFSKS 176
A+ Q++ ++ + + V S
Sbjct: 58 AAIAQLNGKEV-KGKRINVELSTK 80
Score = 33.0 bits (76), Expect = 0.011
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
G V+ + KD A + M + A A+ ++ V GK++ V +S
Sbjct: 33 RGRVIECDV---VKDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELST 79
>2la6_A RNA-binding protein FUS; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative, RNA recognition; NMR {Homo sapiens}
Length = 99
Score = 39.2 bits (92), Expect = 7e-05
Identities = 16/97 (16%), Positives = 36/97 (37%), Gaps = 13/97 (13%)
Query: 89 GSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKG------FTVKGFKFFPKDRK--- 139
G + + + + T+ + + +VT + + + F + G T + DR+
Sbjct: 2 GHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK 61
Query: 140 ---MALLQLDSIEEAITALIQMHNHQLSEQSHLRVSF 173
A + D A A+ + + ++VSF
Sbjct: 62 LKGEATVSFDDPPSAKAAIDWFDGKEF-SGNPIKVSF 97
Score = 28.0 bits (63), Expect = 0.71
Identities = 7/46 (15%), Positives = 16/46 (34%), Gaps = 5/46 (10%)
Query: 13 RVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+ + ++ K A + + A A+ D G ++V
Sbjct: 50 MINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKV 95
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 124
Score = 39.8 bits (93), Expect = 7e-05
Identities = 6/70 (8%), Positives = 17/70 (24%), Gaps = 7/70 (10%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-----MALLQLDSIEEAIT 153
++L +P + + F + ++ + +
Sbjct: 24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIY-IAYGPNGKATGEGFVEFRNEADYKA 82
Query: 154 ALIQMHNHQL 163
AL H +
Sbjct: 83 AL-CRHKQYM 91
>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA
splicing factor, RNA recognition motif, RNA binding
protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A
Length = 172
Score = 40.3 bits (95), Expect = 8e-05
Identities = 22/155 (14%), Positives = 45/155 (29%), Gaps = 45/155 (29%)
Query: 24 ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEGQPDAGLTKDYTASPLH 83
A ++ + AM D + G+ +++
Sbjct: 54 AFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPH-------------------------- 86
Query: 84 RFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM--- 140
++ + +P + +D++KE T G +K F KD
Sbjct: 87 --DYQPLPGAHKLF-------IGGLPNYLNDDQVKELLTSFG-PLKAFN-LVKDSATGLS 135
Query: 141 ---ALLQLDSIEEAITALIQMHNHQLSEQSHLRVS 172
A + I A+ ++ QL ++ L V
Sbjct: 136 KGYAFCEYVDINVTDQAIAGLNGMQLGDK-KLLVQ 169
Score = 38.0 bits (89), Expect = 5e-04
Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 13/88 (14%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFP----------KDRKMALLQLDS 147
+ L++ NIP +TE+ + + F + + G P +D+ A L+ S
Sbjct: 2 GSARRLYVGNIPFGITEEAMMDFFNAQM-RLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60
Query: 148 IEEAITALIQMHNHQLSEQSHLRVSFSK 175
++E A+ QS L++
Sbjct: 61 VDETTQAM-AFDGIIFQGQS-LKIRRPH 86
>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 39.1 bits (92), Expect = 8e-05
Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 9/84 (10%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEA 151
+ T+ ++N+ E +L+E F G ++ KD+ A + E+A
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFG-SISRIY-LAKDKTTGQSKGFAFISFHRREDA 70
Query: 152 ITALIQMHNHQLSEQSHLRVSFSK 175
A+ + L V ++K
Sbjct: 71 ARAIAGVSGFGYDHLI-LNVEWAK 93
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 39.4 bits (92), Expect = 8e-05
Identities = 15/86 (17%), Positives = 29/86 (33%), Gaps = 5/86 (5%)
Query: 83 HRFKKPGSKNFQNIYPPSP----TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDR 138
H G + P + + N+P + +LK+ E +D
Sbjct: 7 HHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDF 66
Query: 139 K-MALLQLDSIEEAITALIQMHNHQL 163
L+ S E + AL +++N +
Sbjct: 67 DGTGALEFPSEEILVEALERLNNIEF 92
>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing
factor, RNA protein complex, SMN, binding protein-RNA
complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A
Length = 129
Score = 39.7 bits (93), Expect = 9e-05
Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 9/84 (10%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------ALLQLDSIEEA 151
P+ L + + TE +L+E F++ G + D++ A + +++++A
Sbjct: 44 DPNCCLGVFGLSLYTTERDLREVFSKYG-PIADVS-IVYDQQSRRSRGFAFVYFENVDDA 101
Query: 152 ITALIQMHNHQLSEQSHLRVSFSK 175
A + + +L + +RV FS
Sbjct: 102 KEAKERANGMELDGRR-IRVDFSI 124
Score = 29.7 bits (67), Expect = 0.27
Identities = 12/51 (23%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNKK--DS---ALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
YG + V I+Y+++ S A + A A + + + G+++RV
Sbjct: 70 YGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA
recognition motif, RRM, RNA binding domain, RBD, RNP,
structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 38.8 bits (91), Expect = 1e-04
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 12/85 (14%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-------MALLQLDSIEEA 151
P T L N+P VTE+ +KE F +G + + P++ + + ++
Sbjct: 14 PPYTAFLGNLPYDVTEESIKEFF--RGLNISAVR-LPREPSNPERLKGFGYAEFEDLDSL 70
Query: 152 ITALIQMHNHQLSEQSHLRVSFSKS 176
++AL ++ L + +RV +
Sbjct: 71 LSAL-SLNEESLGNKR-IRVDVADQ 93
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 41.2 bits (96), Expect = 1e-04
Identities = 36/215 (16%), Positives = 67/215 (31%), Gaps = 58/215 (26%)
Query: 5 TGVYGDVLRVKI--LYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQ 62
T Y + LR + Y+ LI+ + + L +D +VF + + ++ + ++
Sbjct: 166 TDDYFEELR-DLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNIL----EWLE 220
Query: 63 LPKEGQPDAGLTKDYTAS-----PL-------H--RFKKPGSKNFQNIYP--PSPTLHLS 106
P PD KDY S PL H K + T H
Sbjct: 221 NP-SNTPD----KDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQ 275
Query: 107 NIPASV------TEDELKEAFTEKGFT------VKGFKFFPKDRKMALLQLDSIE----- 149
+ +V + + + K T V+ ++ +P + DS+E
Sbjct: 276 GLVTAVAIAETDSWESFFVS-VRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGV 334
Query: 150 ------------EAITALIQMHNHQLSEQSHLRVS 172
E + + N L + +S
Sbjct: 335 PSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEIS 369
Score = 37.7 bits (87), Expect = 0.002
Identities = 23/123 (18%), Positives = 38/123 (30%), Gaps = 53/123 (43%)
Query: 19 NKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEGQPDAGLTKDYT 78
K +SAL + A L +FG GQ G T DY
Sbjct: 139 KKSNSALFRAVGEGNAQLVA-------IFG------------------GQ---GNTDDY- 169
Query: 79 ASPLHRFKKPGSKNFQNIYPPSPTL----------HLSNIPASVTEDELKEAFTEKGFTV 128
F++ +++Y L LS + + + E + FT +G +
Sbjct: 170 ------FEE-----LRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAE--KVFT-QGLNI 215
Query: 129 KGF 131
+
Sbjct: 216 LEW 218
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 38.8 bits (91), Expect = 1e-04
Identities = 16/96 (16%), Positives = 34/96 (35%), Gaps = 9/96 (9%)
Query: 88 PGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKD-----RKMAL 142
GS ++ L + + +E+++ F G + + + A
Sbjct: 3 SGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFG-VIDECT-VLRGPDGSSKGCAF 60
Query: 143 LQLDSIEEAITALIQMHNHQLSEQSH--LRVSFSKS 176
++ S EA A+ +H Q + L V F+ +
Sbjct: 61 VKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADT 96
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 38.8 bits (91), Expect = 1e-04
Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 8/81 (9%)
Query: 89 GSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MAL 142
GS + L + + E L++ F++ G + KDR+
Sbjct: 1 GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYG-QISEVV-VVKDRETQRSRGFGF 58
Query: 143 LQLDSIEEAITALIQMHNHQL 163
+ ++I++A A++ M+ +
Sbjct: 59 VTFENIDDAKDAMMAMNGKSV 79
Score = 28.4 bits (64), Expect = 0.56
Identities = 13/71 (18%), Positives = 25/71 (35%), Gaps = 13/71 (18%)
Query: 8 YGDVLRVKILYNKKDS------ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAV 61
YG + V ++ ++ ++ + A AMM M+ V G+Q+RV +
Sbjct: 36 YGQISEVVVVKDR-ETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG---- 90
Query: 62 QLPKEGQPDAG 72
Sbjct: 91 --KSSDNRSGP 99
>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA
binding protein-RNA complex; 1.85A {Homo sapiens} PDB:
3nna_A 3nnc_A 2dhs_A 3nnh_A
Length = 175
Score = 39.9 bits (94), Expect = 1e-04
Identities = 26/187 (13%), Positives = 53/187 (28%), Gaps = 61/187 (32%)
Query: 8 YGDVLRVKILYNKKDS-------ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
YG V + +L ++ + + A A + ++V + K
Sbjct: 27 YGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMK--- 83
Query: 61 VQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEA 120
P + + K + + ++ + I TE++++
Sbjct: 84 ---PADSE------------------KNNAVEDRKLF-------IGMISKKCTENDIRVM 115
Query: 121 FTEKGFTV------------KGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSH 168
F+ G +G F + + A TA+ MH Q E
Sbjct: 116 FSSFGQIEECRILRGPDGLSRGCAF---------VTFTTRAMAQTAIKAMHQAQTMEGCS 166
Query: 169 --LRVSF 173
+ V F
Sbjct: 167 SPMVVKF 173
Score = 30.7 bits (70), Expect = 0.19
Identities = 15/84 (17%), Positives = 34/84 (40%), Gaps = 12/84 (14%)
Query: 107 NIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM--------ALLQLDSIEEAITALIQM 158
+P + +E +L+E F + G V +DR + + + A+ A +
Sbjct: 10 QVPRTWSEKDLRELFEQYG-AVYEIN-VLRDRSQNPPQSKGCCFVTFYTRKAALEAQNAL 67
Query: 159 HNHQLSEQSH--LRVSFSKSNIQD 180
HN ++ H +++ + S +
Sbjct: 68 HNMKVLPGMHHPIQMKPADSEKNN 91
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 38.9 bits (91), Expect = 1e-04
Identities = 15/90 (16%), Positives = 33/90 (36%), Gaps = 13/90 (14%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKG------FTVKGFKFFPKDRKM------ALLQL 145
+ T+ + + +VT + + + F + G T + DR+ A +
Sbjct: 5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 64
Query: 146 DSIEEAITALIQMHNHQLSEQSHLRVSFSK 175
D A A+ + + ++VSF+
Sbjct: 65 DDPPSAKAAIDWFDGKEF-SGNPIKVSFAT 93
Score = 28.9 bits (65), Expect = 0.38
Identities = 10/65 (15%), Positives = 21/65 (32%), Gaps = 5/65 (7%)
Query: 13 RVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEG 67
+ + ++ K A + + A A+ D G ++V + +A G
Sbjct: 44 MINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGG 103
Query: 68 QPDAG 72
G
Sbjct: 104 NGRGG 108
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 38.4 bits (90), Expect = 1e-04
Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 22/87 (25%)
Query: 89 GSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTV------------KGFKFFPK 136
GS LH+SNIP + +L++ F + G + KGF F
Sbjct: 4 GSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFG-KILDVEIIFNERGSKGFGF--- 59
Query: 137 DRKMALLQLDSIEEAITALIQMHNHQL 163
+ ++ +A A ++H +
Sbjct: 60 ------VTFENSADADRAREKLHGTVV 80
Score = 32.6 bits (75), Expect = 0.020
Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 8 YGDVLRVKILYNKKDS---ALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+G +L V+I++N++ S + S A A + V G+++ V
Sbjct: 39 FGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV 87
>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain,
RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 38.0 bits (89), Expect = 2e-04
Identities = 17/93 (18%), Positives = 38/93 (40%), Gaps = 7/93 (7%)
Query: 88 PGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM----ALL 143
GS TL++ N+ VTE + + F++ G K K + +
Sbjct: 3 SGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIG-PCKSCK-MITEHTSNDPYCFV 60
Query: 144 QLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
+ +A AL M+ ++ + ++V+++ +
Sbjct: 61 EFYEHRDAAAALAAMNGRKILGKE-VKVNWATT 92
Score = 36.8 bits (86), Expect = 6e-04
Identities = 9/53 (16%), Positives = 22/53 (41%), Gaps = 3/53 (5%)
Query: 8 YGDVLRVKILYNKKDS---ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
G K++ + ++ E A A+ M+ ++ GK+++V +
Sbjct: 39 IGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT 91
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 38.1 bits (89), Expect = 2e-04
Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 5/54 (9%)
Query: 8 YGDVLRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMIS 56
YG+V V+IL + + A + + A + ++ V G + +
Sbjct: 30 YGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD 83
Score = 37.8 bits (88), Expect = 3e-04
Identities = 11/85 (12%), Positives = 27/85 (31%), Gaps = 9/85 (10%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEA 151
P + + + +V E LK+ + G V+ + + +A + S A
Sbjct: 4 IPLKEVTFARLNDNVRETFLKDMCRKYG-EVEEVE-ILLHPRTRKHLGLARVLFTSTRGA 61
Query: 152 ITALIQMHNHQLSEQSHLRVSFSKS 176
+ +H + + +
Sbjct: 62 KETVKNLHLTSV-MGNIIHAQLDIK 85
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper),
RRM2 domain, solution structure, structural genomics,
PSI-2; NMR {Homo sapiens}
Length = 108
Score = 38.1 bits (89), Expect = 2e-04
Identities = 18/107 (16%), Positives = 41/107 (38%), Gaps = 16/107 (14%)
Query: 75 KDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFF 134
+ A+ + + GS +Y + ++ ++TED L+ F G ++ +
Sbjct: 8 HSHMAAAMANNLQKGSAGPMRLY-------VGSLHFNITEDMLRGIFEPFG-RIESIQ-L 58
Query: 135 PKDRK------MALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSK 175
D + + E A AL Q++ +L+ + ++V
Sbjct: 59 MMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRP-MKVGHVT 104
Score = 27.7 bits (62), Expect = 1.00
Identities = 9/51 (17%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+G + ++++ + K I ++S A A+ ++ + G+ M+V
Sbjct: 50 FGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 38.1 bits (89), Expect = 2e-04
Identities = 15/82 (18%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM---ALLQLDSIEEAITAL 155
+ L++ N+P +T +E+ + F + G ++ + + A + + I +A A+
Sbjct: 7 VNRILYIRNLPYKITAEEMYDIFGKYG-PIRQIR-VGNTPETRGTAYVVYEDIFDAKNAV 64
Query: 156 IQMHNHQLSEQSHLRVSFSKSN 177
+ +S + +L V + +N
Sbjct: 65 DHLSGFNVSNR-YLVVLYYNAN 85
Score = 31.6 bits (72), Expect = 0.058
Identities = 10/59 (16%), Positives = 26/59 (44%), Gaps = 2/59 (3%)
Query: 1 MFSLTGVYGDVLRVKILYNK--KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
M+ + G YG + ++++ + +A + + A A+ H+ V + + V+
Sbjct: 25 MYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN 83
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA binding
protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 38.7 bits (90), Expect = 2e-04
Identities = 18/112 (16%), Positives = 33/112 (29%), Gaps = 4/112 (3%)
Query: 54 MISKHQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVT 113
M S H P T S+ +H+ +P T
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQ-STTGHCVHMRGLPYKAT 59
Query: 114 EDELKEAFTEKGFTVKGFKFFPKDRKM--ALLQLDSIEEAITALIQMHNHQL 163
E+++ F+ + P R A ++ + EEA+ A+ +
Sbjct: 60 ENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANM 110
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 38.0 bits (89), Expect = 2e-04
Identities = 21/96 (21%), Positives = 33/96 (34%), Gaps = 15/96 (15%)
Query: 86 KKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKG-----FTVKGFKFFPKDRKM 140
+ + Q + L + P V E EL E F G + GF F
Sbjct: 17 RGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAF------- 69
Query: 141 ALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
++ + E A A+ ++H L V +SK
Sbjct: 70 --VEFEEAESAAKAIEEVHGKSF-ANQPLEVVYSKL 102
Score = 31.1 bits (71), Expect = 0.064
Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 3/50 (6%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
+G + VKI A ++ E+ A A+ + + + V+ SK
Sbjct: 55 FGPMKEVKI---LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSK 101
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 39.3 bits (91), Expect = 3e-04
Identities = 18/97 (18%), Positives = 35/97 (36%), Gaps = 9/97 (9%)
Query: 86 KKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFT-VKGFKFFPKDRK----- 139
K L++ N+ T+++L EA G + KFF ++R
Sbjct: 54 KGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFF-ENRANGQSK 112
Query: 140 -MALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSK 175
AL+ + S + + + +L Q+ V+
Sbjct: 113 GFALVGVGSEASSKKLMDLLPKRELHGQN-PVVTPVN 148
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 39.4 bits (91), Expect = 3e-04
Identities = 11/101 (10%), Positives = 42/101 (41%), Gaps = 6/101 (5%)
Query: 83 HRFKKPGSKNFQNIYPPSPTLHLSNIPAS--VTEDELKEAFTEKGFTVKGFKFFPKDRKM 140
H + + + + + +L ++N V+ ++L + G V P ++
Sbjct: 3 HTLLRH--EGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCG-LVDAL-LMPPNKPY 58
Query: 141 ALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKSNIQDI 181
+ + + EE+ A + ++ ++ + +++ + ++ +
Sbjct: 59 SFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKV 99
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural
genomics, joint center for struc genomics, JCSG, protein
structure initiative; HET: PGE; 1.95A {Homo sapiens}
PDB: 3b4d_A 3b4m_A
Length = 89
Score = 37.1 bits (87), Expect = 3e-04
Identities = 13/86 (15%), Positives = 33/86 (38%), Gaps = 10/86 (11%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------ALLQLDSIEEAI 152
+ ++++ N+ T +EL+ F G +V D+ A ++ E
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCG-SVNRVT-ILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 153 TALIQMHNHQLSEQSHLRVSFSKSNI 178
T+ + + + ++V ++N
Sbjct: 63 TS-LALDESLFRGRQ-IKVIPKRTNR 86
Score = 29.4 bits (67), Expect = 0.21
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
G V RV IL +K K A I+ ++ ++ +D+ G+Q++V+ +
Sbjct: 30 CGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLFRGRQIKVIPKR 83
>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 37.7 bits (88), Expect = 3e-04
Identities = 16/101 (15%), Positives = 28/101 (27%), Gaps = 13/101 (12%)
Query: 87 KPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------M 140
GS + T+ + N+ E+ L E + G +K +
Sbjct: 2 SSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFG-DLKYVR-VVLHPDTEHSKGC 59
Query: 141 ALLQLDSIEEAITALIQMHNHQLSEQS-----HLRVSFSKS 176
A Q + E A L L+V + +
Sbjct: 60 AFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 100
>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure
genomics, RRM domain, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 37.6 bits (88), Expect = 3e-04
Identities = 16/93 (17%), Positives = 32/93 (34%), Gaps = 30/93 (32%)
Query: 84 RFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTV-------------KG 130
+ K ++ N+Y +SN+P S+ E EL+ G V +G
Sbjct: 16 QMAKQQEQDPTNLY-------ISNLPLSMDEQELENMLKPFG-QVISTRILRDSSGTSRG 67
Query: 131 FKFFPKDRKMALLQLDSIEEAITALIQMHNHQL 163
F +++S E+ + + +
Sbjct: 68 VGF---------ARMESTEKCEAVIGHFNGKFI 91
>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 102
Score = 37.2 bits (87), Expect = 4e-04
Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 12/84 (14%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEA 151
PS TL + + TE+ LKE+F + DR+ + +S E+A
Sbjct: 13 QPSKTLFVKGLSEDTTEETLKESFDG----SVRAR-IVTDRETGSSKGFGFVDFNSEEDA 67
Query: 152 ITALIQMHNHQLSEQSHLRVSFSK 175
A M + ++ + + + + ++K
Sbjct: 68 KAAKEAMEDGEI-DGNKVTLDWAK 90
Score = 25.3 bits (56), Expect = 6.0
Identities = 7/57 (12%), Positives = 22/57 (38%), Gaps = 7/57 (12%)
Query: 3 SLTGVYGDVLRVKILYNKKDS------ALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+L + +R +I+ ++ ++ + A A M+ + G ++ +
Sbjct: 31 TLKESFDGSVRARIVTDR-ETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL 86
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} PDB: 2dgq_A
Length = 106
Score = 37.3 bits (87), Expect = 4e-04
Identities = 18/85 (21%), Positives = 28/85 (32%), Gaps = 24/85 (28%)
Query: 107 NIPASVTEDELKEAFTEKGFTV-------------KGFKFFPKDRKMALLQLDSIEEAIT 153
IP ++ E +LK F E G KG F L E A+
Sbjct: 20 QIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAF---------LTYCERESALK 70
Query: 154 ALIQMHNHQLSEQSH--LRVSFSKS 176
A +H + + ++V + S
Sbjct: 71 AQSALHEQKTLPGMNRPIQVKPADS 95
>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 36.8 bits (86), Expect = 5e-04
Identities = 18/94 (19%), Positives = 38/94 (40%), Gaps = 22/94 (23%)
Query: 88 PGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKG-----FTVKGFKFFPKDRKMAL 142
GS ++ + N+P TE E++ F + G +K + F
Sbjct: 3 SGSSGMVKLF-------IGNLPREATEQEIRSLFEQYGKVLECDIIKNYGF--------- 46
Query: 143 LQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
+ ++ A A+ +H+++L + + V SK+
Sbjct: 47 VHIEDKTAAEDAIRNLHHYKLHGVN-INVEASKN 79
>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger,
CYP33, MLL, RNA binding protein, ALT splicing, mRNA
processing, mRNA splicing; 1.85A {Homo sapiens} PDB:
2kyx_A 3lpy_A*
Length = 85
Score = 36.4 bits (85), Expect = 6e-04
Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 9/84 (10%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEA 151
L++ + V + L AF G + + P D + A ++ + E+A
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFG-DITDIQ-IPLDYETEKHRGFAFVEFELAEDA 62
Query: 152 ITALIQMHNHQLSEQSHLRVSFSK 175
A+ M+ +L ++ +RV+ +K
Sbjct: 63 AAAIDNMNESELFGRT-IRVNLAK 85
Score = 29.4 bits (67), Expect = 0.18
Identities = 11/51 (21%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+GD+ ++I + + A ++ + A A+ +M++ +FG+ +RV
Sbjct: 31 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 81
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding
protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi}
SCOP: d.58.7.1
Length = 139
Score = 37.4 bits (87), Expect = 6e-04
Identities = 24/127 (18%), Positives = 44/127 (34%), Gaps = 20/127 (15%)
Query: 62 QLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPT-LHLSNIPASVTEDELKEA 120
Q+P Q D + ++ N P L ++ IP +V E +L++
Sbjct: 3 QIPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQL 62
Query: 121 FTEKGFTVKGFKFFPKDR-----------KMALLQLDSIEEAITALIQMHNHQLSEQSHL 169
F G ++ K DR K S A A+ ++ + + L
Sbjct: 63 FERYG-PIESVKIV-CDRETRQSRGYGFVKF-----QSGSSAQQAIAGLNGFNILNKR-L 114
Query: 170 RVSFSKS 176
+V+ + S
Sbjct: 115 KVALAAS 121
Score = 26.6 bits (59), Expect = 3.6
Identities = 9/51 (17%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
YG + VKI+ ++ + ++ A A+ ++ + K+++V
Sbjct: 66 YGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV 116
>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 36.8 bits (86), Expect = 6e-04
Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 9/83 (10%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEAI 152
TL + N+ + D L+ F + G V P++ A ++ +A
Sbjct: 12 GMITLKVDNLTYRTSPDSLRRVFEKYG-RVGDVY-IPREPHTKAPRGFAFVRFHDRRDAQ 69
Query: 153 TALIQMHNHQLSEQSHLRVSFSK 175
A M +L + LRV ++
Sbjct: 70 DAEAAMDGAELDGRE-LRVQVAR 91
Score = 31.0 bits (71), Expect = 0.074
Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 10/71 (14%)
Query: 8 YGDVLRVKILYNKKDS------ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAV 61
YG V V I + A ++ + A A MD + G+++RV ++++
Sbjct: 37 YGRVGDVYIPREP-HTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGR- 94
Query: 62 QLPKEGQPDAG 72
P +G
Sbjct: 95 --RDLSGPSSG 103
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 37.6 bits (87), Expect = 6e-04
Identities = 14/119 (11%), Positives = 39/119 (32%), Gaps = 10/119 (8%)
Query: 65 KEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEK 124
+ +P + ++ + P + + + +++ + T+ +L +
Sbjct: 21 QSMEPPPPVRQEPSPKP-NNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSI 79
Query: 125 GFT-VKGFKFFPKDRK------MALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
G V KF ++R A + + S L + L+ + + V +
Sbjct: 80 GVYDVVELKFA-ENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEK-VDVRPATR 136
>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain,
poly(A) site recognition, RNA, nuclear, RNA BIND
protein; 2.70A {Homo sapiens} PDB: 3p6y_C
Length = 90
Score = 36.4 bits (85), Expect = 7e-04
Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 9/81 (11%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFT-VKGFKFFPKDRK------MALLQLDSIEEAITAL 155
L++ N+ T+++L EA G + KFF ++R AL+ + S + +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFF-ENRANGQSKGFALVGVGSEASSKKLM 62
Query: 156 IQMHNHQLSEQSHLRVSFSKS 176
+ +L Q+ V+ S
Sbjct: 63 DLLPKRELHGQN-PVVTPSNK 82
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 37.2 bits (86), Expect = 7e-04
Identities = 13/73 (17%), Positives = 23/73 (31%), Gaps = 8/73 (10%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFK--FFPKDRK-----MALLQLDSIEE 150
+ + +P + T +E+ F + G + F A + E
Sbjct: 21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEY 80
Query: 151 AITALIQMHNHQL 163
A AL + H L
Sbjct: 81 AQNAL-RKHKDLL 92
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 36.6 bits (85), Expect = 7e-04
Identities = 12/65 (18%), Positives = 25/65 (38%), Gaps = 6/65 (9%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEG 67
YG V + K A +Q + A A++ + + G+ + + ++ P
Sbjct: 52 YGRVAGCSV---HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPK---PDRS 105
Query: 68 QPDAG 72
P +G
Sbjct: 106 GPSSG 110
>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition
motif, RRM, RNA binding domain, RBD, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 36.9 bits (86), Expect = 7e-04
Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 7/71 (9%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK-----MALLQLDSIEEAI 152
T+ ++N+ V +LKE F+ G V +D+ + + + EA+
Sbjct: 13 RLGSTVFVANLDYKVGWKKLKEVFSMAG-VVVRADIL-EDKDGKSRGIGTVTFEQSIEAV 70
Query: 153 TALIQMHNHQL 163
A+ + L
Sbjct: 71 QAISMFNGQLL 81
Score = 32.3 bits (74), Expect = 0.031
Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 11/76 (14%)
Query: 8 YGDVLRVKILYNK----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK------ 57
G V+R IL +K + + +S +A A+ + +F + M V + +
Sbjct: 39 AGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKG 98
Query: 58 -HQAVQLPKEGQPDAG 72
+ P++ P +G
Sbjct: 99 DFFPPERPQQSGPSSG 114
>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 36.4 bits (85), Expect = 7e-04
Identities = 19/93 (20%), Positives = 39/93 (41%), Gaps = 9/93 (9%)
Query: 89 GSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MAL 142
GS + L++ + V + L AF G + + P D + A
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFG-DITDIQ-IPLDYETEKHRGFAF 58
Query: 143 LQLDSIEEAITALIQMHNHQLSEQSHLRVSFSK 175
++ + E+A A+ M+ +L ++ +RV+ +K
Sbjct: 59 VEFELAEDAAAAIDNMNESELFGRT-IRVNLAK 90
Score = 27.6 bits (62), Expect = 1.2
Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 11/70 (15%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQ 62
+GD+ ++I + + A ++ + A A+ +M++ +FG+ +RV ++K
Sbjct: 36 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK----- 90
Query: 63 LPKEGQPDAG 72
P +
Sbjct: 91 -PMRIKESGP 99
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 36.1 bits (83), Expect = 8e-04
Identities = 19/82 (23%), Positives = 42/82 (51%), Gaps = 8/82 (9%)
Query: 102 TLHLSNIPASVTEDELKE----AFTEKGFTVKGFKFFPKDRK--MALLQLDSIEEAITAL 155
+ +SNI ++ EL++ AF G VK + P A++Q++++++AI A+
Sbjct: 11 DVQVSNIDYRLSRKELQQLLQEAFARHG-KVKSVELSPHTDYQLKAVVQMENLQDAIGAV 69
Query: 156 IQMHNHQLSEQSHLRVSFSKSN 177
+H +++ + + VS +
Sbjct: 70 NSLHRYKIGSKK-ILVSLATGA 90
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 36.2 bits (84), Expect = 0.001
Identities = 13/71 (18%), Positives = 25/71 (35%), Gaps = 8/71 (11%)
Query: 107 NIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEAITALIQMHN 160
+ V + L F++ G V FP D ++ S+ +A + H
Sbjct: 19 SAKVPVLKKALTSLFSKAG-KVVNM-EFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76
Query: 161 HQLSEQSHLRV 171
+L + L +
Sbjct: 77 KRLDLKHRLFL 87
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 35.8 bits (83), Expect = 0.001
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 3/53 (5%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
YG ++++ I K IQ A+ + FGK++ + +S A
Sbjct: 47 YGHIMQINI---KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA 96
>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI, RNA binding
protein; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 36.1 bits (83), Expect = 0.001
Identities = 14/84 (16%), Positives = 34/84 (40%), Gaps = 8/84 (9%)
Query: 98 PPSPTLHLSNIPASV-TEDELKEAFTEKGFTVKG----FKFFPKDRKMALLQLDSIEEAI 152
S L V +E E + F E F F++F +++ + + A
Sbjct: 3 SGSSGLIACVANDDVFSESETRAKF-ESLFRTYDKDTTFQYFKSFKRV-RINFSNPLSAA 60
Query: 153 TALIQMHNHQLSEQSHLRVSFSKS 176
A +++H + + +++ F+++
Sbjct: 61 DARLRLHKTEFLGKE-MKLYFAQT 83
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 36.3 bits (84), Expect = 0.001
Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 9/84 (10%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEA 151
+L + N+ + D L+ F + G V P+DR A ++ +A
Sbjct: 45 EGMTSLKVDNLTYRTSPDTLRRVFEKYG-RVGDVY-IPRDRYTKESRGFAFVRFHDKRDA 102
Query: 152 ITALIQMHNHQLSEQSHLRVSFSK 175
A+ M L + LRV ++
Sbjct: 103 EDAMDAMDGAVLDGRE-LRVQMAR 125
Score = 29.3 bits (66), Expect = 0.42
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK--KDS---ALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
YG V V I ++ K+S A ++ + A AM MD + G+++RV
Sbjct: 71 YGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 35.8 bits (83), Expect = 0.001
Identities = 24/132 (18%), Positives = 40/132 (30%), Gaps = 35/132 (26%)
Query: 58 HQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDEL 117
A L L+ A+ + + P N L + ++P T+ +L
Sbjct: 8 GSASALSTSPLASVALSAAAAAAAGKQIEGPEGCN----------LFIYHLPQEFTDTDL 57
Query: 118 KEAFTEKGFTV--------------KGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQL 163
F G V K F F + D+ + A A+ M+ Q+
Sbjct: 58 ASTFLPFG-NVISAKVFIDKQTSLSKCFGF---------VSFDNPDSAQVAIKAMNGFQV 107
Query: 164 SEQSHLRVSFSK 175
L+V K
Sbjct: 108 -GTKRLKVQLKK 118
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 35.5 bits (82), Expect = 0.003
Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 8/72 (11%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEA 151
L++ + V + L AF G + + P D + A ++ + E+A
Sbjct: 61 TTKRVLYVGGLAEEVDDKVLHAAFIPFG-DITDIQ-IPLDYETEKHRGFAFVEFELAEDA 118
Query: 152 ITALIQMHNHQL 163
A+ M+ +L
Sbjct: 119 AAAIDNMNESEL 130
Score = 30.1 bits (68), Expect = 0.18
Identities = 11/51 (21%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+GD+ ++I + + A ++ + A A+ +M++ +FG+ +RV
Sbjct: 87 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 137
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49)
(SAP 49) (SF3B50)...; structure genomics,RRM
domain,splicing factor 3B; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 105
Score = 34.9 bits (81), Expect = 0.003
Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 9/83 (10%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEAI 152
T+++ + V+E L E F + G V PKDR ++ S E+A
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELFLQAG-PVVNTH-MPKDRVTGQHQGYGFVEFLSEEDAD 71
Query: 153 TALIQMHNHQLSEQSHLRVSFSK 175
A+ M +L + +RV+ +
Sbjct: 72 YAIKIMDMIKLYGKP-IRVNKAS 93
Score = 33.4 bits (77), Expect = 0.010
Identities = 11/66 (16%), Positives = 25/66 (37%), Gaps = 5/66 (7%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQ 62
G V+ + ++ + ++ A A+ MD ++++GK +RV +
Sbjct: 39 AGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKN 98
Query: 63 LPKEGQ 68
L
Sbjct: 99 LSGPSS 104
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 35.0 bits (81), Expect = 0.003
Identities = 19/103 (18%), Positives = 37/103 (35%), Gaps = 23/103 (22%)
Query: 85 FKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTV------------KGFK 132
GS LH+SNIP + +L++ F + G + KGF
Sbjct: 14 LVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFG-KILDVEIIFNERGSKGFG 72
Query: 133 FFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSK 175
F + ++ +A A ++H + + + V+ +
Sbjct: 73 F---------VTFENSADADRAREKLHGTVVEGRK-IEVNNAT 105
Score = 30.0 bits (68), Expect = 0.18
Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 8 YGDVLRVKILYNKKDS---ALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
+G +L V+I++N++ S + S A A + V G+++ V
Sbjct: 53 FGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV 101
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed
coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A
{Homo sapiens} PDB: 3sde_B
Length = 261
Score = 36.2 bits (84), Expect = 0.003
Identities = 25/187 (13%), Positives = 52/187 (27%), Gaps = 70/187 (37%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDS--ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKH 58
+F YG+ V I +D I++ A +A +D + + +R+ + H
Sbjct: 42 LFE---RYGEPSEVFIN---RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH 95
Query: 59 QAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELK 118
A + + N+ V+ + L+
Sbjct: 96 GA----------------------------------ALT-------VKNLSPVVSNELLE 114
Query: 119 EAFTEKGFTV------------KGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQ 166
+AF++ G G F ++ + A AL + +
Sbjct: 115 QAFSQFGPVEKAVVVVDDRGRATGKGF---------VEFAAKPPARKALERCGDGAFLLT 165
Query: 167 SHLRVSF 173
+ R
Sbjct: 166 TTPRPVI 172
Score = 35.4 bits (82), Expect = 0.005
Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 107 NIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQ 166
N+P +TE++ K F G +DR ++L+S A A ++ L +
Sbjct: 29 NLPTDITEEDFKRLFERYG-EPSEVF-INRDRGFGFIRLESRTLAEIAKAELDGTILKSR 86
Query: 167 SHLRVSFS 174
LR+ F+
Sbjct: 87 P-LRIRFA 93
>1x4e_A RNA binding motif, single-stranded interacting protein 2;
structural genomics, RRM domain, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 85
Score = 34.0 bits (79), Expect = 0.004
Identities = 14/94 (14%), Positives = 28/94 (29%), Gaps = 16/94 (17%)
Query: 89 GSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MAL 142
GS +Y + + T+ +L + G + K D+
Sbjct: 1 GSSGSSGLY-------IRGLQPGTTDQDLVKLCQPYG-KIVSTKAI-LDKTTNKCKGYGF 51
Query: 143 LQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
+ DS A A+ + + + + S S
Sbjct: 52 VDFDSPSAAQKAVTALKASGV-QAQMAKQSGPSS 84
Score = 25.2 bits (56), Expect = 6.4
Identities = 8/51 (15%), Positives = 17/51 (33%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
YG ++ K + +K K + A A+ + V + +
Sbjct: 29 YGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQ 79
>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 98
Score = 34.5 bits (80), Expect = 0.004
Identities = 23/87 (26%), Positives = 35/87 (40%), Gaps = 12/87 (13%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQL---------DSI 148
S L + N+ S TE+ LK F++ G +K K + A + L
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVG-AIKSCT-ISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 149 EEAITALIQMHNHQLSEQSHLRVSFSK 175
E+A AL Q+ H + L V S+
Sbjct: 61 EQAQKALKQLQGHTVDGHK-LEVRISE 86
>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1 PDB: 2rq4_A 2rqc_A
Length = 115
Score = 34.6 bits (80), Expect = 0.004
Identities = 21/118 (17%), Positives = 39/118 (33%), Gaps = 35/118 (29%)
Query: 72 GLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTV--- 128
GLT+ + + + P N L + ++P + +L + F G V
Sbjct: 7 GLTQQSIGAAGSQKEGPEGAN----------LFIYHLPQEFGDQDLLQMFMPFG-NVVSA 55
Query: 129 -----------KGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSK 175
K F F + D+ A A+ M+ Q+ + L+V +
Sbjct: 56 KVFIDKQTNLSKCFGF---------VSYDNPVSAQAAIQSMNGFQIGMKR-LKVQLKR 103
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 34.6 bits (80), Expect = 0.004
Identities = 16/94 (17%), Positives = 37/94 (39%), Gaps = 8/94 (8%)
Query: 89 GSKNFQNIYPPSP----TLHLSNIPASVTEDELKEAFTEKGFTVKGF--KFFPKDRKMAL 142
G I P+ +++ N+P + ++++ F + G ++ K A
Sbjct: 7 GMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYG-AIRDIDLKNRRGGPPFAF 65
Query: 143 LQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
++ + +A A+ + + LRV F +S
Sbjct: 66 VEFEDPRDAEDAVYGRDGYDY-DGYRLRVEFPRS 98
Score = 30.0 bits (68), Expect = 0.19
Identities = 9/52 (17%), Positives = 20/52 (38%), Gaps = 2/52 (3%)
Query: 8 YGDVLRVKILYNKKDS--ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
YG + + + + A ++ + A A+ D G ++RV +
Sbjct: 46 YGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR 97
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus}
Length = 118
Score = 34.5 bits (79), Expect = 0.004
Identities = 11/74 (14%), Positives = 27/74 (36%), Gaps = 11/74 (14%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFK---FFPKDRK-----MALLQLDSIE 149
+ L +P S + ++++ T+ F R+ A ++L+S +
Sbjct: 15 GEGYVVKLRGLPWSCSIEDVQNFL--SDCTIHDGVAGVHFIYTREGRQSGEAFVELESED 72
Query: 150 EAITALIQMHNHQL 163
+ AL + +
Sbjct: 73 DVKLAL-KKDRESM 85
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 34.1 bits (79), Expect = 0.004
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDR 138
+++ N+ S T +++KE F++ G V K DR
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFG-KVFNVK-LIYDR 37
>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 113
Score = 34.3 bits (79), Expect = 0.005
Identities = 13/84 (15%), Positives = 25/84 (29%), Gaps = 13/84 (15%)
Query: 106 SNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------------ALLQLDSIEEAIT 153
+ SVT D+L + F + G + + A + + A
Sbjct: 21 QGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKA 80
Query: 154 ALIQMHNHQLSEQSHLRVSFSKSN 177
A+ L+VS ++
Sbjct: 81 AVEWFDGKDFQGSK-LKVSLARKK 103
Score = 30.5 bits (69), Expect = 0.11
Identities = 12/65 (18%), Positives = 25/65 (38%), Gaps = 8/65 (12%)
Query: 13 RVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEG 67
+ I +K K A + + A A+ D G +++V +++ + P
Sbjct: 52 MIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP---PMNS 108
Query: 68 QPDAG 72
P +G
Sbjct: 109 GPSSG 113
>2kn4_A Immunoglobulin G-binding protein G, splicing FACT
arginine/serine-rich 2, S35, splicing factor SC35,; RRM
domain, cell WALL; NMR {Streptococcus SP}
Length = 158
Score = 34.8 bits (80), Expect = 0.006
Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 9/85 (10%)
Query: 97 YPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------ALLQLDSIEE 150
+L + N+ + D L+ F + G V P+DR A ++ +
Sbjct: 67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYG-RVGDVY-IPRDRYTKESRGFAFVRFHDKRD 124
Query: 151 AITALIQMHNHQLSEQSHLRVSFSK 175
A A+ M L + LRV ++
Sbjct: 125 AEDAMDAMDGAVLDGRE-LRVQMAR 148
Score = 28.3 bits (63), Expect = 1.0
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 8 YGDVLRVKILYNK--KDS---ALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
YG V V I ++ K+S A ++ + A AM MD + G+++RV
Sbjct: 94 YGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 144
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 33.7 bits (78), Expect = 0.007
Identities = 17/78 (21%), Positives = 27/78 (34%), Gaps = 22/78 (28%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTV------------KGFKFFPKDRKMALLQL 145
+ + + N+P T LK+ F E G V KG ++
Sbjct: 6 SGACQIFVRNLPFDFTWKMLKDKFNECG-HVLYADIKMENGKSKGCGV---------VKF 55
Query: 146 DSIEEAITALIQMHNHQL 163
+S E A A M+ +L
Sbjct: 56 ESPEVAERACRMMNGMKL 73
Score = 26.8 bits (60), Expect = 1.7
Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 3/49 (6%)
Query: 8 YGDVLRVKILYNK---KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRV 53
G VL I K +++ A A M+ +++ G+++ V
Sbjct: 32 CGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDV 80
>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A)
binding, structural genomics, protein structure
initiative, PSI-2; NMR {Xenopus laevis}
Length = 124
Score = 33.9 bits (78), Expect = 0.009
Identities = 11/83 (13%), Positives = 32/83 (38%), Gaps = 10/83 (12%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEAITAL 155
++++ N+ T +L+ F+ G ++ D+ A ++ A
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCG-SINRIT-ILCDKFSGHPKGYAYIEFAERNSVDAA- 94
Query: 156 IQMHNHQLSEQSHLRVSFSKSNI 178
+ M ++ ++V ++N+
Sbjct: 95 VAMDETVFRGRT-IKVLPKRTNM 116
Score = 32.0 bits (73), Expect = 0.043
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
G + R+ IL +K K A I+ AE + A+ MD+ G+ ++V+ +
Sbjct: 60 CGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKVLPKR 113
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 33.0 bits (76), Expect = 0.012
Identities = 13/52 (25%), Positives = 23/52 (44%)
Query: 6 GVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
YG + V I N A ++ + A A+ +D + G ++RV +S
Sbjct: 22 SYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELST 73
Score = 29.2 bits (66), Expect = 0.32
Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 18/82 (21%)
Query: 103 LHLSNIPASVTEDELKEAFTEKG--------FTVKGFKFFPKDRKMALLQLDSIEEAITA 154
+++ N+ + EL+ AF+ G GF F ++ + +A A
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAF---------VEFEDPRDAEDA 53
Query: 155 LIQMHNHQLSEQSHLRVSFSKS 176
+ + + S +RV S
Sbjct: 54 VRGLDGKVI-CGSRVRVELSTG 74
>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 33.1 bits (76), Expect = 0.014
Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 10/82 (12%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRK------MALLQLDSIEEAITAL 155
T+ + A + +L++ F+ G V+ + DR +A ++ I+ A
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVG-KVRDVR-IISDRNSRRSKGIAYVEFCEIQSVPLA- 83
Query: 156 IQMHNHQLSEQSHLRVSFSKSN 177
I + +L + V S++
Sbjct: 84 IGLTGQRLLGVP-IIVQASQAE 104
Score = 28.8 bits (65), Expect = 0.45
Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 6/55 (10%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
G V V+I+ ++ K A ++ E LA+ + R+ G + V S+
Sbjct: 49 VGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ 102
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding
factor, RNA binding domain, STRU genomics, joint center
for structural genomics, JCSG; NMR {Homo sapiens}
Length = 107
Score = 32.9 bits (75), Expect = 0.016
Identities = 12/68 (17%), Positives = 28/68 (41%), Gaps = 7/68 (10%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKF-FPKDRK-----MALLQLDSIEEAITAL 155
+ +P S T +++ F++ F +R AL++++S ++ AL
Sbjct: 13 LIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL 72
Query: 156 IQMHNHQL 163
+ H +
Sbjct: 73 -EKHRMYM 79
>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 32.6 bits (75), Expect = 0.016
Identities = 21/99 (21%), Positives = 42/99 (42%), Gaps = 23/99 (23%)
Query: 89 GSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTV------------KGFKFFPK 136
GS + L++ N+ + ++ L++AF+ G T+ KGF F
Sbjct: 4 GSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFG-TITSAKVMMEGGRSKGFGF--- 59
Query: 137 DRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSK 175
+ S EEA A+ +M+ ++ + L V+ ++
Sbjct: 60 ------VCFSSPEEATKAVTEMNGRIVATKP-LYVALAQ 91
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation,
RNA-binding, EIF4G-binding translation; 1.90A {Homo
sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 33.0 bits (76), Expect = 0.017
Identities = 13/119 (10%), Positives = 33/119 (27%), Gaps = 33/119 (27%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDS---ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
FS +G++L K++ ++ S + A A+ M+ + + +++ V
Sbjct: 25 TFS---AFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVG--- 78
Query: 58 HQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDE 116
+ +K +++ N T
Sbjct: 79 ------------------------RFKSRKEREAELGARAKEFTNVYIKNFGPGSTRAA 113
Score = 30.7 bits (70), Expect = 0.089
Identities = 17/91 (18%), Positives = 35/91 (38%), Gaps = 22/91 (24%)
Query: 98 PPSPT-LHLSNIPASVTEDELKEAFTEKGFTV-----------KGFKFFPKDRKMALLQL 145
P + + N+ S+ L + F+ G + KG+ F +
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGF---------VHF 52
Query: 146 DSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
++ E A A+ +M+ L+++ + V KS
Sbjct: 53 ETQEAAERAIEKMNGMLLNDRK-VFVGRFKS 82
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 32.2 bits (74), Expect = 0.022
Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 5/65 (7%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEG 67
YG ++++ I K IQ A+ + FGK++ + +S A P+
Sbjct: 35 YGHIMQINI---KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNAR--PQFD 89
Query: 68 QPDAG 72
D G
Sbjct: 90 HGDHG 94
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 32.5 bits (74), Expect = 0.026
Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 7/79 (8%)
Query: 89 GSKNFQNIYPPSP----TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQ 144
G PPS + +S +P S + +LK+ E G + +D +++
Sbjct: 1 GGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVC--YADVYRDG-TGVVE 57
Query: 145 LDSIEEAITALIQMHNHQL 163
E+ A+ ++ N +
Sbjct: 58 FVRKEDMTYAVRKLDNTKF 76
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 33.2 bits (75), Expect = 0.030
Identities = 17/157 (10%), Positives = 40/157 (25%), Gaps = 13/157 (8%)
Query: 20 KKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEGQPDAGLTKDYTA 79
+ S + Q + + G + + + K D
Sbjct: 56 QLHSGKTRGDNDGQLFFCLFFAKGMCCLGPKCEYLHHIPDEEDIGKLALRTE--VLDCFG 113
Query: 80 SPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVT---------EDELKEAFTEKGFTVKG 130
+ + + TL++ I ++ E ++ F+ G +
Sbjct: 114 REKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLG-DIDR 172
Query: 131 FKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQS 167
++ + ++ A A M N L S
Sbjct: 173 IRYVES-KNCGFVKFKYQANAEFAKEAMSNQTLLLPS 208
>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 108
Score = 32.1 bits (73), Expect = 0.030
Identities = 14/81 (17%), Positives = 31/81 (38%), Gaps = 8/81 (9%)
Query: 97 YPPSP----TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAI 152
PPS + +S +P S + +LK+ E G V + +++ E+
Sbjct: 8 GPPSRRSENRVVVSGLPPSGSWQDLKDHMREAG-DVCYADVYRDG--TGVVEFVRKEDMT 64
Query: 153 TALIQMHNHQLSEQSHLRVSF 173
A+ ++ N + ++
Sbjct: 65 YAVRKLDNTKFRSHE-GETAY 84
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 31.3 bits (72), Expect = 0.041
Identities = 13/85 (15%), Positives = 32/85 (37%), Gaps = 29/85 (34%)
Query: 107 NIPASVTEDELKEAFTEKGFTV--------------KGFKF--FPKDRKMALLQLDSIEE 150
++ +V ++ L+ AF + + +G+ F F ++
Sbjct: 8 DLNVNVDDETLRNAFKDFP-SYLSGHVMWDMQTGSSRGYGFVSFTSQ-----------DD 55
Query: 151 AITALIQMHNHQLSEQSHLRVSFSK 175
A A+ M L+ + LR++++
Sbjct: 56 AQNAMDSMQGQDLNGRP-LRINWAA 79
>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 101
Score = 31.1 bits (71), Expect = 0.054
Identities = 7/28 (25%), Positives = 12/28 (42%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKG 125
L + N+ + + ELK A +E
Sbjct: 15 TTPFNLFIGNLNPNKSVAELKVAISELF 42
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 99
Score = 31.1 bits (71), Expect = 0.054
Identities = 12/72 (16%), Positives = 28/72 (38%), Gaps = 7/72 (9%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------ALLQLDSIEEA 151
+ +L + ++ + E+ + AF G TV K ++R ++ + A
Sbjct: 7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVK-IIRNRLTGIPAGYCFVEFADLATA 65
Query: 152 ITALIQMHNHQL 163
L +++ L
Sbjct: 66 EKCLHKINGKPL 77
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 30.9 bits (70), Expect = 0.074
Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 12/75 (16%)
Query: 107 NIPASVTE------DELKEAFTEKGFTVKGFKFFPKD----RKMALLQLDSIEEAITALI 156
N+P + + + + F++ G F +P++ + L+ S A+ A+
Sbjct: 22 NVPQVGPDRLEKLKNVIHKIFSKFGKITNDF--YPEEDGKTKGYIFLEYASPAHAVDAVK 79
Query: 157 QMHNHQLSEQSHLRV 171
++L +Q RV
Sbjct: 80 NADGYKLDKQHTFRV 94
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 30.1 bits (68), Expect = 0.093
Identities = 12/63 (19%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 113 TEDELKEAFTEKGFTVKGFKFFPKD----RKMALLQLDSIEEAITALIQMHNHQLSEQSH 168
++ + + F++ G F+P++ + L+ S A+ A+ ++L +Q
Sbjct: 20 LKNVIHKIFSKFGKITN--DFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT 77
Query: 169 LRV 171
RV
Sbjct: 78 FRV 80
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 31.1 bits (70), Expect = 0.098
Identities = 11/74 (14%), Positives = 26/74 (35%), Gaps = 11/74 (14%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFK---FFPKDRK-----MALLQLDSIE 149
+ L +P S + ++++ T+ F R+ A ++L S +
Sbjct: 42 GEGFVVKLRGLPWSCSVEDVQNFL--SDCTIHDGAAGVHFIYTREGRQSGEAFVELGSED 99
Query: 150 EAITALIQMHNHQL 163
+ AL + +
Sbjct: 100 DVKMAL-KKDRESM 112
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and
splicing factor,...; protein-RNA complex RRM alpha-beta
sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR
{Streptococcus SP} PDB: 2i38_A
Length = 150
Score = 31.0 bits (70), Expect = 0.12
Identities = 12/50 (24%), Positives = 23/50 (46%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISK 57
YG + V + N A ++ + A A+ +D + G ++RV +S
Sbjct: 97 YGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSN 146
Score = 29.8 bits (67), Expect = 0.25
Identities = 14/78 (17%), Positives = 31/78 (39%), Gaps = 2/78 (2%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQ 157
P +++ N+ + + EL+ AF G ++ A ++ + +A A+ +
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYG-PLRSVWVARNPPGFAFVEFEDPRDAADAVRE 129
Query: 158 MHNHQLSEQSHLRVSFSK 175
+ L +RV S
Sbjct: 130 LDGRTL-CGCRVRVELSN 146
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 30.0 bits (68), Expect = 0.13
Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 11/77 (14%)
Query: 88 PGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM-ALLQLD 146
GS ++++ +S P V +L E F G V KD+ + A++++
Sbjct: 3 SGSSGLRSVF-------VSGFPRGVDSAQLSEYFLAFG-PVASV-VMDKDKGVFAIVEMG 53
Query: 147 SIEEAITALIQMHNHQL 163
A A++ H L
Sbjct: 54 D-VGAREAVLSQSQHSL 69
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 30.7 bits (70), Expect = 0.19
Identities = 13/91 (14%), Positives = 29/91 (31%), Gaps = 15/91 (16%)
Query: 79 ASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDR 138
A ++PG+ + + + I E L++ F + G DR
Sbjct: 89 AVSREDSQRPGA------HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI--EIMTDR 140
Query: 139 KM------ALLQLDSIEEAITALIQMHNHQL 163
A + D +++ ++ H +
Sbjct: 141 GSGKKRGFAFVTFDD-HDSVDKIVIQKYHTV 170
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 29.7 bits (66), Expect = 0.21
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 8 YGDVLRVKILYNKKDSALIQMAESHQAHLAM 38
YG+VL + + K +A+++ A A LA+
Sbjct: 41 YGEVLNLVLSSKKPGTAVVEFATVKAAELAV 71
>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding,
RNA processing, mRNA processing, nonsense-mediated mRNA
decay, cleavage; NMR {Saccharomyces cerevisiae} PDB:
2km8_C
Length = 167
Score = 30.2 bits (69), Expect = 0.24
Identities = 11/72 (15%), Positives = 23/72 (31%), Gaps = 9/72 (12%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKM------ALLQLDSIEEA 151
+ + + I V E +E F++ G + D+ + DS +A
Sbjct: 85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDA--QLMLDKDTGQSRGFGFVTYDS-ADA 141
Query: 152 ITALIQMHNHQL 163
+ + Q
Sbjct: 142 VDRVCQNKFIDF 153
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA
binding protein, structure, protein-RNA complex, RNA
stem-loop, structural protein/RNA complex; NMR {Homo
sapiens}
Length = 116
Score = 29.6 bits (67), Expect = 0.26
Identities = 13/78 (16%), Positives = 22/78 (28%), Gaps = 21/78 (26%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTV------------KGFKFFPKDRKMALLQL 145
L + + E LK F + G +GF F +
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAF---------ITF 55
Query: 146 DSIEEAITALIQMHNHQL 163
++ +A A M+ L
Sbjct: 56 ENPADAKNAAKDMNGKSL 73
Score = 28.8 bits (65), Expect = 0.53
Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 5/82 (6%)
Query: 8 YGDVLRVKILYNK----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQL 63
+G + V ++ ++ + A I A A M+ + GK ++V +K + Q
Sbjct: 31 HGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQS 90
Query: 64 P-KEGQPDAGLTKDYTASPLHR 84
+ P + + + S H
Sbjct: 91 GGRRRPPASSRNRSPSGSLEHH 112
>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA
binding domain, RBD, RNA splicing, apoptosis,
phosphoprotein, RNA-binding; 1.95A {Homo sapiens}
Length = 87
Score = 29.1 bits (66), Expect = 0.26
Identities = 15/84 (17%), Positives = 24/84 (28%), Gaps = 30/84 (35%)
Query: 98 PPSPTLHL--SNIPASVTEDELKEAFTEKGFTV--------------KGFKF--FPKDRK 139
P H+ ++ +T + AF G + KG+ F F
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFG-RISDARVVKDMATGKSKGYGFVSFFNK-- 58
Query: 140 MALLQLDSIEEAITALIQMHNHQL 163
+A A+ QM L
Sbjct: 59 ---------WDAENAIQQMGGQWL 73
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 29.2 bits (66), Expect = 0.31
Identities = 12/76 (15%), Positives = 21/76 (27%), Gaps = 26/76 (34%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTV-------------KGFKF--FPKDRKMALLQLD 146
+L + ++ V + L E F + + KG+ F F
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKF-----------T 59
Query: 147 SIEEAITALIQMHNHQ 162
E AL +
Sbjct: 60 DELEQKRALTECQGAV 75
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 28.9 bits (65), Expect = 0.33
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKG 125
++++ P T D++KE +KG
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKG 36
>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A
{Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A
Length = 102
Score = 29.1 bits (66), Expect = 0.34
Identities = 14/89 (15%), Positives = 27/89 (30%), Gaps = 29/89 (32%)
Query: 89 GSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTV------------KGFKF--F 134
G ++ + I + E E++ F G KG+ F F
Sbjct: 5 GKIMPNTVF-------VGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
Query: 135 PKDRKMALLQLDSIEEAITALIQMHNHQL 163
D +++ + + I H +L
Sbjct: 58 YND--------VDVQKIVESQINFHGKKL 78
>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain,
structural genomics, NPPSFA; NMR {Mus musculus} PDB:
2rne_A 2dh7_A
Length = 115
Score = 28.9 bits (65), Expect = 0.42
Identities = 14/73 (19%), Positives = 24/73 (32%), Gaps = 28/73 (38%)
Query: 107 NIPASVTEDELKEAFTEKGFTV--------------KGFKF--FPKDRKMALLQLDSIEE 150
++ +T +++K AF G + KG+ F F +
Sbjct: 22 DLSPEITTEDIKAAFAPFG-RISDARVVKDMATGKSKGYGFVSFFNK-----------WD 69
Query: 151 AITALIQMHNHQL 163
A A+ QM L
Sbjct: 70 AENAIQQMGGQWL 82
Score = 25.0 bits (55), Expect = 8.8
Identities = 12/77 (15%), Positives = 26/77 (33%), Gaps = 12/77 (15%)
Query: 8 YGDVLRVKILYNK-----KDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMIS------ 56
+G + +++ + K + A A+ M + G+Q+R +
Sbjct: 39 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPA 98
Query: 57 -KHQAVQLPKEGQPDAG 72
K K+ P +G
Sbjct: 99 PKSTYESNTKQSGPSSG 115
>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 96
Score = 28.3 bits (64), Expect = 0.60
Identities = 15/93 (16%), Positives = 32/93 (34%), Gaps = 24/93 (25%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTV--------------KGFKFFPKDRKMALL 143
S + + N+ + E L + F+ G + KG+ F +
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAF---------I 53
Query: 144 QLDSIEEAITALIQMHNHQLSEQSHLRVSFSKS 176
S + + A+ M+ L + + VS++
Sbjct: 54 NFASFDASDAAIEAMNGQYLCNRP-ITVSYAFK 85
>2odr_C Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 701
Score = 29.6 bits (66), Expect = 0.71
Identities = 18/134 (13%), Positives = 39/134 (29%), Gaps = 11/134 (8%)
Query: 52 RVMISKHQAVQLPKEGQPDAGL-TKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPA 110
M + + +++ + A + TKD + P K P H P
Sbjct: 18 SHMFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIK------PVFGKTH----PV 67
Query: 111 SVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLR 170
+ T + L++A+ GF +R + + + +
Sbjct: 68 NDTIENLRQAYLRMGFEEYINPVIVDERDIYKQFGPEAMAVLDRCFYLAGLPRPDVGLSD 127
Query: 171 VSFSKSNIQDIRDN 184
S+ I+ +
Sbjct: 128 EKISQIEKLGIKVS 141
>2i62_A Nicotinamide N-methyltransferase; structural genomics, structural
genomics consortium, SGC; HET: SAH; 1.80A {Mus musculus}
PDB: 2iip_A* 3rod_A*
Length = 265
Score = 28.9 bits (64), Expect = 0.93
Identities = 5/38 (13%), Positives = 18/38 (47%)
Query: 111 SVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSI 148
+ + +++A E G+T++ F+ ++ + +
Sbjct: 216 PLGWETVRDAVEEAGYTIEQFEVISQNYSSTTSNNEGL 253
>2odr_D Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 685
Score = 29.2 bits (65), Expect = 0.97
Identities = 18/132 (13%), Positives = 39/132 (29%), Gaps = 11/132 (8%)
Query: 54 MISKHQAVQLPKEGQPDAGL-TKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASV 112
M + + +++ + A + TKD + P K P H P +
Sbjct: 20 MFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIK------PVFGKTH----PVND 69
Query: 113 TEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVS 172
T + L++A+ GF +R + + + +
Sbjct: 70 TIENLRQAYLRMGFEEYINPVIVDERDIYKQFGPEAMAVLDRCFYLAGLPRPDVGLSDEK 129
Query: 173 FSKSNIQDIRDN 184
S+ I+ +
Sbjct: 130 ISQIEKLGIKVS 141
>1onf_A GR, grase, glutathione reductase; oxidoreductase; HET: FAD; 2.60A
{Plasmodium falciparum} SCOP: c.3.1.5 c.3.1.5 d.87.1.1
Length = 500
Score = 28.7 bits (65), Expect = 1.2
Identities = 11/53 (20%), Positives = 24/53 (45%), Gaps = 7/53 (13%)
Query: 86 KKPGSKNFQNIYPPSPTLHLSNIP-ASV--TEDELKEAFTEKGFTVKGFKFFP 135
KK N++ I PT+ S+ P ++ +E+ + + ++ + KF
Sbjct: 371 KKTRKTNYKLI----PTVIFSHPPIGTIGLSEEAAIQIYGKENVKIYESKFTN 419
>1dcs_A Deacetoxycephalosporin C synthase; ferrous oxygenase,
2-oxoglutarate, oxidoreduc antibiotics, merohedral
twinning; 1.30A {Streptomyces clavuligerus} SCOP:
b.82.2.1 PDB: 1rxf_A 1rxg_A* 1unb_A* 1uo9_A 1uob_A*
1uof_A* 1uog_A* 2jb8_A 1w28_A 1w2a_X 1w2n_A* 1w2o_A*
1hjg_A 1hjf_A 1e5h_A 1e5i_A*
Length = 311
Score = 28.1 bits (63), Expect = 1.9
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 101 PTLHLSNIPASVTEDELKEAFTEKGF 126
PT L+ + + +DE + +KG
Sbjct: 6 PTFSLAELQQGLHQDEFRRCLRDKGL 31
>2g72_A Phenylethanolamine N-methyltransferase; HET: SAM F21; 2.00A {Homo
sapiens} SCOP: c.66.1.15 PDB: 1yz3_A* 2an4_A* 2an5_A*
2g70_A* 2g71_A* 2an3_A* 2g8n_A* 2ony_A* 3hcb_A* 3hcc_A*
3hcd_A* 3hcf_A* 3kpj_A* 3kpu_A* 3kpv_A* 3kpw_A* 3kpy_A*
3kqm_A* 3kqo_A* 3kqp_A* ...
Length = 289
Score = 27.9 bits (61), Expect = 2.1
Identities = 7/30 (23%), Positives = 16/30 (53%)
Query: 111 SVTEDELKEAFTEKGFTVKGFKFFPKDRKM 140
V+E+E++EA G+ V+ + + +
Sbjct: 233 PVSEEEVREALVRSGYKVRDLRTYIMPAHL 262
>2odr_A Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 665
Score = 27.6 bits (61), Expect = 2.4
Identities = 18/134 (13%), Positives = 39/134 (29%), Gaps = 11/134 (8%)
Query: 52 RVMISKHQAVQLPKEGQPDAGL-TKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPA 110
M + + +++ + A + TKD + P K P H P
Sbjct: 18 SHMFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIK------PVFGKTH----PV 67
Query: 111 SVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLR 170
+ T + L++A+ GF +R + + + +
Sbjct: 68 NDTIENLRQAYLRMGFEEYINPVIVDERDIYKQFGPEAMAVLDRCFYLAGLPRPDVGLSD 127
Query: 171 VSFSKSNIQDIRDN 184
S+ I+ +
Sbjct: 128 EKISQIEKLGIKVS 141
>3lcc_A Putative methyl chloride transferase; halide methyltransferase;
HET: SAH; 1.80A {Arabidopsis thaliana}
Length = 235
Score = 27.3 bits (60), Expect = 2.8
Identities = 11/59 (18%), Positives = 21/59 (35%), Gaps = 3/59 (5%)
Query: 70 DAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTV 128
+ + + S ++ KP + +YP + H+ P V +E GF
Sbjct: 146 EPEMRPAWAKS-MYELLKPDGELITLMYPITD--HVGGPPYKVDVSTFEEVLVPIGFKA 201
>2xmm_A SSR2857 protein, ATX1; metal transport, copper homeostasis,
chaperone, P-type atpas; 1.65A {Synechocystis SP} PDB:
2xmv_A 1sb6_A 2xmj_A 2xmk_A 2xmt_A 2xmu_A
Length = 64
Score = 25.4 bits (56), Expect = 3.2
Identities = 6/22 (27%), Positives = 14/22 (63%)
Query: 108 IPASVTEDELKEAFTEKGFTVK 129
I +++ E++L+ A G+ V+
Sbjct: 43 ITSALGEEQLRTAIASAGYEVE 64
>2odr_B Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 648
Score = 27.3 bits (60), Expect = 4.0
Identities = 18/134 (13%), Positives = 39/134 (29%), Gaps = 11/134 (8%)
Query: 52 RVMISKHQAVQLPKEGQPDAGL-TKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPA 110
M + + +++ + A + TKD + P K P H P
Sbjct: 18 SHMFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIK------PVFGKTH----PV 67
Query: 111 SVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLR 170
+ T + L++A+ GF +R + + + +
Sbjct: 68 NDTIENLRQAYLRMGFEEYINPVIVDERDIYKQFGPEAMAVLDRCFYLAGLPRPDVGLSD 127
Query: 171 VSFSKSNIQDIRDN 184
S+ I+ +
Sbjct: 128 EKISQIEKLGIKVS 141
>2a14_A Indolethylamine N-methyltransferase; SGC,INMT, structural genomics,
structural genomics consortium; HET: SAH; 1.70A {Homo
sapiens} SCOP: c.66.1.15
Length = 263
Score = 26.6 bits (58), Expect = 4.9
Identities = 5/27 (18%), Positives = 15/27 (55%)
Query: 111 SVTEDELKEAFTEKGFTVKGFKFFPKD 137
++ + E+++A + GF ++ P+
Sbjct: 215 ALEKGEVEQAVLDAGFDIEQLLHSPQS 241
>1iug_A Putative aspartate aminotransferase; wild type,
pyridoxal-5'-phosphate form, riken structural
genomics/proteomics initiative, RSGI; HET: LLP; 2.20A
{Thermus thermophilus} SCOP: c.67.1.3
Length = 352
Score = 26.8 bits (60), Expect = 4.9
Identities = 18/71 (25%), Positives = 27/71 (38%), Gaps = 14/71 (19%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTV-------KGFKFF------PKDRKMALLQL 145
SP + +P V +KEAF ++G + KG K F DR AL
Sbjct: 280 FSPAVAAFYLPEGVPYARVKEAFAQRGAVIAGGQGPLKG-KVFRLSLMGAYDRYEALGVA 338
Query: 146 DSIEEAITALI 156
E + ++
Sbjct: 339 GMFREVLEEIL 349
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 25.7 bits (56), Expect = 5.1
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 107 NIPASVTEDELKEAFTEKG 125
+P + EDE+ +F G
Sbjct: 15 GLPPDIDEDEITASFRRFG 33
>2l3m_A Copper-ION-binding protein; structural genomics, center for
structural genomics of infec diseases, csgid, metal
binding protein; NMR {Bacillus anthracis}
Length = 71
Score = 24.9 bits (55), Expect = 5.4
Identities = 4/21 (19%), Positives = 11/21 (52%)
Query: 109 PASVTEDELKEAFTEKGFTVK 129
+ VT ++ ++G+ V+
Sbjct: 51 SSVVTLKDIVAVIEDQGYDVQ 71
>3bkx_A SAM-dependent methyltransferase; YP_807781.1,
cyclopropane-fatty-acyl-phospholipid synthase-L protein,
methyltransferase domain; 1.85A {Lactobacillus casei}
Length = 275
Score = 26.1 bits (57), Expect = 6.2
Identities = 6/30 (20%), Positives = 11/30 (36%)
Query: 106 SNIPASVTEDELKEAFTEKGFTVKGFKFFP 135
+NI +T D L + + +T
Sbjct: 191 ANIRTLITPDTLAQIAHDNTWTYTAGTIVE 220
>1m48_A Interleukin-2; four-helix bundle, small molecule complex, cytokine;
HET: FRG; 1.95A {Homo sapiens} SCOP: a.26.1.2 PDB:
1m47_A* 1m49_A* 1m4c_A 1pw6_A* 1z92_A 2b5i_A* 1py2_A*
3ink_C 2erj_D 1qvn_A* 1irl_A 1m4b_A* 1m4a_A* 1nbp_A*
3qb1_A 3qaz_A
Length = 133
Score = 25.8 bits (56), Expect = 7.2
Identities = 16/48 (33%), Positives = 23/48 (47%)
Query: 131 FKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKSNI 178
FKF+ + L L +EE + L ++ N S+ HLR SNI
Sbjct: 42 FKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNI 89
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.132 0.372
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,694,352
Number of extensions: 150586
Number of successful extensions: 946
Number of sequences better than 10.0: 1
Number of HSP's gapped: 887
Number of HSP's successfully gapped: 288
Length of query: 184
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 96
Effective length of database: 4,244,745
Effective search space: 407495520
Effective search space used: 407495520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (24.5 bits)