RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10320
(262 letters)
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 109 bits (274), Expect = 8e-31
Identities = 24/85 (28%), Positives = 47/85 (55%), Gaps = 2/85 (2%)
Query: 3 GTKVYIGGLPY-GVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKS 61
++++IG LP V + DL + YG I + +KN FGF++F++ + DA+ + +
Sbjct: 10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEM 69
Query: 62 LLGERVTVEIAKGIDRSQ-ERGRRG 85
G+++ +E++ R Q + G G
Sbjct: 70 NFGKKLILEVSSSNARPQFDHGDHG 94
Score = 44.9 bits (107), Expect = 1e-06
Identities = 15/91 (16%), Positives = 33/91 (36%), Gaps = 6/91 (6%)
Query: 110 TRSDHRLIVENLSSR-VSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALD 168
RL + NL + VS +DL G + + G ++F++ ++ A++
Sbjct: 7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIE 63
Query: 169 KLDNAELNGRRIRLIEDKPRGGGRGRSRSSS 199
G+++ L + R +
Sbjct: 64 CESQEMNFGKKLIL--EVSSSNARPQFDHGD 92
>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 = 103 bits (259), Expect = 1e-28
Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 4/85 (4%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLL 63
K++IG LP E+++ + YG++ + + +GFV ED A+DA+ L+ L
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLH 68
Query: 64 GERVTVEIAKGIDRSQERGRRGYGS 88
G + VE +K + + G S
Sbjct: 69 GVNINVEASKN----KSKASSGPSS 89
Score = 54.1 bits (131), Expect = 4e-10
Identities = 20/92 (21%), Positives = 39/92 (42%), Gaps = 5/92 (5%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKAL 167
+ +L + NL + Q+++ Q G+V D K + G V E + + A+
Sbjct: 3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNY---GFVHIEDKTAAEDAI 59
Query: 168 DKLDNAELNGRRIRLIEDKPRGGGRGRSRSSS 199
L + +L+G I + + + + S SS
Sbjct: 60 RNLHHYKLHGVNINV--EASKNKSKASSGPSS 89
>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 = 102 bits (256), Expect = 4e-28
Identities = 21/78 (26%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 1 MVGTKVYIGGLPY-GVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNG 59
+ ++++IG LP V + DL + YG I + +KN FGF++F++ + DA+ +
Sbjct: 20 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIEXESQ 79
Query: 60 KSLLGERVTVEIAKGIDR 77
+ G+++ +E++ R
Sbjct: 80 EMNFGKKLILEVSSSNAR 97
Score = 42.7 bits (101), Expect = 8e-06
Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 6/85 (7%)
Query: 109 PTRSDHRLIVENLSSR-VSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKAL 167
+ RL + NL + VS +DL G + + G ++F++ ++ A+
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAF---GFIQFDNPQSVRDAI 74
Query: 168 DKLDNAELNGRRIRLIEDKPRGGGR 192
+ G+++ L + R
Sbjct: 75 EXESQEMNFGKKLIL--EVSSSNAR 97
>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 = 101 bits (254), Expect = 8e-28
Identities = 18/85 (21%), Positives = 38/85 (44%)
Query: 1 MVGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGK 60
TK+++G + ++L + YG + + + + FV E DA +A+ L+
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNT 67
Query: 61 SLLGERVTVEIAKGIDRSQERGRRG 85
G+R+ V+++ R+ G
Sbjct: 68 EFQGKRMHVQLSTSRLRTASGPSSG 92
Score = 56.1 bits (136), Expect = 9e-11
Identities = 23/91 (25%), Positives = 38/91 (41%), Gaps = 3/91 (3%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKA 166
G ++ +L V N+S + Q+L+ + G V D K + V E + D +A
Sbjct: 4 GSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY---AFVHMERAEDAVEA 60
Query: 167 LDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
+ LDN E G+R+ + R S
Sbjct: 61 IRGLDNTEFQGKRMHVQLSTSRLRTASGPSS 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 = 100 bits (251), Expect = 2e-27
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSL 62
K+++G + ++L + GR+ + + + FV E DA A+ +LNGK +
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEV 68
Query: 63 LGERVTVEIAKGIDRSQERGRRG 85
G+R+ VE++ + G
Sbjct: 69 KGKRINVELSTKGQKKS-GPSSG 90
Score = 54.5 bits (132), Expect = 3e-10
Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 3/88 (3%)
Query: 109 PTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALD 168
+ + ++ V N+S+ + Q+L+ + G V D K + V E +D K A+
Sbjct: 5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDY---AFVHMEKEADAKAAIA 61
Query: 169 KLDNAELNGRRIRLIEDKPRGGGRGRSR 196
+L+ E+ G+RI + G S
Sbjct: 62 QLNGKEVKGKRINVELSTKGQKKSGPSS 89
>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 = 98.2 bits (245), Expect = 2e-26
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 2 VGTKVYIGGLPY-GVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGK 60
+ ++V+IG L V++ D+E YGR+ + G+ FV++ + R A AV NG+
Sbjct: 26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGR 85
Query: 61 SLLGERVTVEIAKGIDRSQERGRRG 85
L G+ + + +A + G
Sbjct: 86 VLAGQTLDINMAGEPKPDRSGPSSG 110
Score = 44.7 bits (106), Expect = 2e-06
Identities = 18/112 (16%), Positives = 37/112 (33%), Gaps = 4/112 (3%)
Query: 87 GSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLS-SRVSWQDLKDFMRQVGEVCYADA 145
GS + P + R+ + NL+ + V D++ + G V
Sbjct: 1 GSSGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV 60
Query: 146 HKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
HK + V++ + + A+ + L G+ + + R S
Sbjct: 61 HKGY---AFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPSS 109
>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 = 100 bits (251), Expect = 2e-26
Identities = 37/193 (19%), Positives = 76/193 (39%), Gaps = 38/193 (19%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-------GFGFVEFEDYRDADDAVYE 56
++IG L +L+ + D+ + + FG+V+FE D + A+ E
Sbjct: 14 FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-E 72
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRL 116
L G + G + + ++ + R + R+ L
Sbjct: 73 LTGLKVFGNEIKL------EKPKGRDSK------------------------KVRAARTL 102
Query: 117 IVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAELN 176
+ +NLS ++ +LK+ E+ + + +EF+S +D +K L++ AE++
Sbjct: 103 LAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEID 162
Query: 177 GRRIRLIEDKPRG 189
GR + L +G
Sbjct: 163 GRSVSLYYTGEKG 175
Score = 62.2 bits (152), Expect = 3e-12
Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 9/83 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN---GFGFVEFEDYRDADDAVYELNG 59
+ L + + E +L++ + IR V G ++EF+ DA+ + E G
Sbjct: 99 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 158
Query: 60 KSLLGERVTVEIAKGIDRSQERG 82
+ G V++ + E+G
Sbjct: 159 AEIDGRSVSL------YYTGEKG 175
Score = 53.0 bits (128), Expect = 6e-09
Identities = 25/112 (22%), Positives = 44/112 (39%), Gaps = 19/112 (16%)
Query: 87 GSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA--- 143
GS+ + L + NL+ S +LK + ++
Sbjct: 1 GSHMVEGSES--------------TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV 46
Query: 144 -DAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGR 194
+R G V+FES+ D++KAL +L ++ G I+L + K R + R
Sbjct: 47 DVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVR 97
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 97.0 bits (242), Expect = 6e-26
Identities = 39/96 (40%), Positives = 51/96 (53%), Gaps = 11/96 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN---GFGFVEFEDYRDADDAVYELNGKS 61
KVY+G L G + +LE+ YG +R V + GF FVEFED RDA+DAV L+GK
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 62 LLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRG 97
+ G RV VE++ G + PP RR
Sbjct: 62 ICGSRVRVELS--------TGMPRRSRFDRPPARRK 89
Score = 58.1 bits (141), Expect = 2e-11
Identities = 18/91 (19%), Positives = 32/91 (35%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
++ V NL + +L+ G + + VEFE D + A+ LD
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 175 LNGRRIRLIEDKPRGGGRGRSRSSSSRSRSK 205
+ G R+R+ R + R +
Sbjct: 62 ICGSRVRVELSTGMPRRSRFDRPPARRKLLE 92
>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 = 95.2 bits (237), Expect = 3e-25
Identities = 44/109 (40%), Positives = 54/109 (49%), Gaps = 7/109 (6%)
Query: 99 GHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFE 158
G P RS++R++V L SWQDLKD MR+ G+VCYAD ++ GVVEF
Sbjct: 1 GSSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR--DGTGVVEFV 58
Query: 159 SSSDMKKALDKLDNAELNGRRIRLI-----EDKPRGGGRGRSRSSSSRS 202
DM A+ KLDN + D PR GRSRSS S
Sbjct: 59 RKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGPSS 107
Score = 65.2 bits (159), Expect = 7e-14
Identities = 21/96 (21%), Positives = 36/96 (37%), Gaps = 3/96 (3%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKNGFGFVEFEDYRDADDAVYELNGKS 61
+V + GLP +DL+ ++ G + + ++G G VEF D AV +L+
Sbjct: 15 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTK 74
Query: 62 LLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRG 97
+ + YG R+ P G
Sbjct: 75 FRSHEGETAYIRV--KVDGPRSPSYGRSRSSGPSSG 108
>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 = 94.9 bits (236), Expect = 5e-25
Identities = 48/114 (42%), Positives = 61/114 (53%), Gaps = 2/114 (1%)
Query: 99 GHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFE 158
G R P RS++R++V L SWQDLKD MR+ G+VCYAD ++ GVVEF
Sbjct: 2 GAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFV 59
Query: 159 SSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRS 212
DM A+ KLDN + + + G SRSRS+SRSRSRS
Sbjct: 60 RKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRSRS 113
Score = 59.1 bits (143), Expect = 2e-11
Identities = 19/94 (20%), Positives = 33/94 (35%), Gaps = 1/94 (1%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKNGFGFVEFEDYRDADDAVYELNGKSLL 63
+V + GLP +DL+ ++ G + + ++G G VEF D AV +L+
Sbjct: 18 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFR 77
Query: 64 GERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRG 97
+ G R+ R
Sbjct: 78 SHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRS 111
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 94.5 bits (235), Expect = 7e-25
Identities = 27/104 (25%), Positives = 43/104 (41%), Gaps = 2/104 (1%)
Query: 87 GSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVG-EVCYADA 145
GS R +R+ ++NL SWQDLKD R+ E ++
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSV 61
Query: 146 H-KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPR 188
+ + G +EF S + +AL++L+N E G I + D
Sbjct: 62 NTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP 105
Score = 51.4 bits (123), Expect = 9e-09
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 9/85 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRI---RDVILKN--GFGFVEFEDYRDADDAVYELNG 59
++ + LP G +DL+ + V ++ G G +EF +A+ LN
Sbjct: 30 RITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNN 89
Query: 60 KSLLGERVTVEIAKGIDRSQERGRR 84
G +TVE D + RR
Sbjct: 90 IEFRGSVITVE----RDDNPPPIRR 110
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 93.9 bits (234), Expect = 1e-24
Identities = 23/74 (31%), Positives = 43/74 (58%)
Query: 1 MVGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGK 60
+ T++++ P V+E +L + +G +++V + NGF FVEFE+ A A+ E++GK
Sbjct: 29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGK 88
Query: 61 SLLGERVTVEIAKG 74
S + + V +K
Sbjct: 89 SFANQPLEVVYSKL 102
Score = 45.7 bits (109), Expect = 8e-07
Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 3/88 (3%)
Query: 101 DRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESS 160
S+ RL V V +L + G + K VEFE +
Sbjct: 19 SHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEV---KILNGFAFVEFEEA 75
Query: 161 SDMKKALDKLDNAELNGRRIRLIEDKPR 188
KA++++ + + ++ K
Sbjct: 76 ESAAKAIEEVHGKSFANQPLEVVYSKLP 103
>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 = 96.3 bits (240), Expect = 1e-24
Identities = 28/196 (14%), Positives = 66/196 (33%), Gaps = 31/196 (15%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-------------GFGFVEFEDYRDAD 51
++Y+G +P+G+ E + F R+ + F F+EF +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 52 DAVYELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTR 111
A+ +G G+ + + R + S G
Sbjct: 66 QAM-AFDGIIFQGQSLKI------RRPHDYQPLPGMSENPSVYVPG------VVSTVVPD 112
Query: 112 SDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKA 166
S H+L + L + ++ +K+ + G + + K + E+ + +A
Sbjct: 113 SAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 172
Query: 167 LDKLDNAELNGRRIRL 182
+ L+ +L +++ +
Sbjct: 173 IAGLNGMQLGDKKLLV 188
Score = 61.6 bits (150), Expect = 9e-12
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
K++IGGLP + + +++ + +G ++ L G+ F E+ D D A+
Sbjct: 114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173
Query: 55 YELNGKSLLGERVTVEIA 72
LNG L +++ V+ A
Sbjct: 174 AGLNGMQLGDKKLLVQRA 191
Score = 46.9 bits (112), Expect = 1e-06
Identities = 18/109 (16%), Positives = 35/109 (32%), Gaps = 11/109 (10%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVG----------EVCYADAHKRHRNEGVVEFESSSDMK 164
RL V N+ ++ + + DF A + +N +EF S +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 165 KALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSS 213
+A+ D G+ +++ G S + S + S
Sbjct: 66 QAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDS 113
>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 = 93.4 bits (232), Expect = 6e-24
Identities = 36/78 (46%), Positives = 47/78 (60%), Gaps = 3/78 (3%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN---GFGFVEFEDYRDADDAVYELNG 59
KVY+G L + +LE+ YG +R V + GF FVEFED RDA DAV EL+G
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDG 132
Query: 60 KSLLGERVTVEIAKGIDR 77
++L G RV VE++ G R
Sbjct: 133 RTLCGCRVRVELSNGEKR 150
Score = 63.4 bits (154), Expect = 9e-13
Identities = 29/136 (21%), Positives = 49/136 (36%), Gaps = 10/136 (7%)
Query: 56 ELNGKSLLGERVTVEI----AKGIDRSQERGRRGYGSYRAPPPRRGW------GHDRDDR 105
LNGK+L GE T + A+ + + G + + + H
Sbjct: 6 ILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHM 65
Query: 106 YGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKK 165
+ D ++ V NL + + +L+ G + + VEFE D
Sbjct: 66 HRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAAD 125
Query: 166 ALDKLDNAELNGRRIR 181
A+ +LD L G R+R
Sbjct: 126 AVRELDGRTLCGCRVR 141
>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 = 91.6 bits (228), Expect = 7e-24
Identities = 35/88 (39%), Positives = 47/88 (53%), Gaps = 5/88 (5%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-----GFGFVEFEDYRDADDAVYEL 57
++Y+G LP +R +D+E YG IRD+ LKN F FVEFED RDA+DAVY
Sbjct: 22 DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGR 81
Query: 58 NGKSLLGERVTVEIAKGIDRSQERGRRG 85
+G G R+ VE + + G
Sbjct: 82 DGYDYDGYRLRVEFPRSGRGTGSGPSSG 109
Score = 58.5 bits (142), Expect = 2e-11
Identities = 27/105 (25%), Positives = 42/105 (40%), Gaps = 3/105 (2%)
Query: 95 RRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGV 154
GP +D R+ V NL + +D++D + G + D R
Sbjct: 4 GSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPF 63
Query: 155 --VEFESSSDMKKALDKLDNAELNGRRIRLIEDKP-RGGGRGRSR 196
VEFE D + A+ D + +G R+R+ + RG G G S
Sbjct: 64 AFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPSS 108
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 92.0 bits (229), Expect = 7e-23
Identities = 39/192 (20%), Positives = 80/192 (41%), Gaps = 34/192 (17%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVY 55
++VY+G + Y + E + + +G I+ + + + GF FVE+E A A+
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHR 115
++N L G + V R G+ D+ R+ +R
Sbjct: 89 QMNSVMLGGRNIKV------GRPSNIGQA---------------QPIIDQLAEEARAFNR 127
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHK-RHRNEGVVEFESSSDMKKALDKL 170
+ V ++ +S D+K G++ A D +H+ G +E+E + + A+ +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 171 DNAELNGRRIRL 182
+ +L G+ +R+
Sbjct: 188 NLFDLGGQYLRV 199
Score = 58.9 bits (143), Expect = 1e-10
Identities = 19/79 (24%), Positives = 39/79 (49%), Gaps = 10/79 (12%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL---------KNGFGFVEFEDYRDADDA 53
++Y+ + + + D++ + +G+I+ L K G+GF+E+E + + DA
Sbjct: 125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHK-GYGFIEYEKAQSSQDA 183
Query: 54 VYELNGKSLLGERVTVEIA 72
V +N L G+ + V A
Sbjct: 184 VSSMNLFDLGGQYLRVGKA 202
Score = 50.4 bits (121), Expect = 9e-08
Identities = 15/120 (12%), Positives = 38/120 (31%), Gaps = 15/120 (12%)
Query: 101 DRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKRHRNEGVV 155
+ R+ V ++ + ++ G + + +H+ V
Sbjct: 16 GSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFV 75
Query: 156 EFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKS 215
E+E + AL+++++ L GR I++ GR + + +
Sbjct: 76 EYEVPEAAQLALEQMNSVMLGGRNIKV----------GRPSNIGQAQPIIDQLAEEARAF 125
>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 = 93.5 bits (233), Expect = 8e-23
Identities = 30/185 (16%), Positives = 58/185 (31%), Gaps = 44/185 (23%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-GFGFVEFEDYRDADDAVYELNGKS 61
K+ I GLP V +++ + Y + K G FV + A+ A+ +
Sbjct: 22 RRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSR 81
Query: 62 LLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENL 121
L ++V++ +D L V NL
Sbjct: 82 LRERELSVQLQ--------------------------------------PTDALLCVANL 103
Query: 122 SSRVSWQDLKDFMRQVGE-----VCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAELN 176
++ Q ++ +R G + Y++ + + G E+ +A L L
Sbjct: 104 PPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLG 163
Query: 177 GRRIR 181
R +
Sbjct: 164 PRTLY 168
Score = 85.0 bits (211), Expect = 1e-19
Identities = 33/193 (17%), Positives = 63/193 (32%), Gaps = 42/193 (21%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KN-GFGFVEFEDYRDADDAV 54
+ + LP + ++ E+ V+ +G + L ++ G+GF E+ A A
Sbjct: 95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDH 114
+L GK L + V D Q P
Sbjct: 155 SDLLGKPLGPRTLYVHWT---DAGQLT--------------------------PALLHSR 185
Query: 115 RLIVENLSSRVS-WQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDK 169
L V+ L + L + V + + + V+E+E++ ++A +
Sbjct: 186 CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQ 245
Query: 170 LDNAELNGRRIRL 182
D L G +R+
Sbjct: 246 ADGLSLGGSHLRV 258
Score = 48.4 bits (116), Expect = 7e-07
Identities = 12/81 (14%), Positives = 33/81 (40%), Gaps = 4/81 (4%)
Query: 102 RDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVG-EVCYADAHKRHRNEGVVEFESS 160
R + R+ ++++ L V+ Q++ D + + C+ D +++ V +
Sbjct: 11 RLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVD---KYKGTAFVTLLNG 67
Query: 161 SDMKKALDKLDNAELNGRRIR 181
+ A++ + L R +
Sbjct: 68 EQAEAAINAFHQSRLRERELS 88
>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 = 90.9 bits (225), Expect = 2e-22
Identities = 33/197 (16%), Positives = 70/197 (35%), Gaps = 20/197 (10%)
Query: 3 GTKVYIGGL-PYGVRERDLEKFVKGYGRIRDVIL---KNGFGFVEFEDYRDADDAVYELN 58
+ + GL + + YG + V K G VE D D A+ LN
Sbjct: 4 SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLN 63
Query: 59 GKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLI- 117
+ G+++ V ++K + + YG + + R++R+ P ++ I
Sbjct: 64 NNFMFGQKMNVCVSK---QPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQ 120
Query: 118 -------VENLSSRVSWQDLKDFMRQVGEVCYA-----DAHKRHRNEGVVEFESSSDMKK 165
N V+ ++ + ++G + G++E++S SD +
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180
Query: 166 ALDKLDNAELNGRRIRL 182
L L++ ++
Sbjct: 181 TLGFLNHYQMKNPNGPY 197
Score = 54.3 bits (130), Expect = 3e-09
Identities = 12/79 (15%), Positives = 23/79 (29%), Gaps = 8/79 (10%)
Query: 1 MVGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADD 52
++ P V E + + G R +K G +E++ DA +
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180
Query: 53 AVYELNGKSLLGERVTVEI 71
+ LN +
Sbjct: 181 TLGFLNHYQMKNPNGPYPY 199
Score = 46.2 bits (109), Expect = 2e-06
Identities = 26/126 (20%), Positives = 50/126 (39%), Gaps = 5/126 (3%)
Query: 107 GPPTRSDHRLIVENLS-SRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKK 165
G + L+V L S+++ + + G V K +VE + +
Sbjct: 1 GADSP---VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDR 57
Query: 166 ALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRS-KSRSRSRSSKSRSPRSRSKS 224
A+ L+N + G+++ + K G+S S S K S SR+++ +P +K+
Sbjct: 58 AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN 117
Query: 225 GSPRKS 230
S
Sbjct: 118 RIQHPS 123
>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 = 87.3 bits (217), Expect = 3e-22
Identities = 23/91 (25%), Positives = 42/91 (46%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLL 63
+++ L V E LEK +G++ V + F+ F++ A A+ E+NGK L
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLE 71
Query: 64 GERVTVEIAKGIDRSQERGRRGYGSYRAPPP 94
GE + + AK D+ ++ + + P
Sbjct: 72 GENIEIVFAKPPDQKRKERKAQRQAASGPSS 102
Score = 48.4 bits (116), Expect = 7e-08
Identities = 19/92 (20%), Positives = 42/92 (45%), Gaps = 3/92 (3%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
L V NL++ V+ + L+ Q G++ K+ ++ + F+ KA+++++ +
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERV---KKLKDYAFIHFDERDGAVKAMEEMNGKD 69
Query: 175 LNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKS 206
L G I ++ KP R ++ + S
Sbjct: 70 LEGENIEIVFAKPPDQKRKERKAQRQAASGPS 101
>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 = 87.6 bits (217), Expect = 2e-21
Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 20/196 (10%)
Query: 2 VGTKV-YIGGL-PYGVRERDLEKFVKGYGRIRDVIL---KNGFGFVEFEDYRDADDAVYE 56
+G V + L P V + L YG ++ V + K V+ D A A+
Sbjct: 1 MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSH 60
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSD--- 113
LNG L G+ + + ++K + + + +G+ R+ P +
Sbjct: 61 LNGHKLHGKPIRITLSK-----HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 115
Query: 114 -----HRLIVENLSSRVSWQDLKD-FMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKAL 167
L + N+ VS +DLK F G V ++ R +++ S + +AL
Sbjct: 116 IFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQAL 175
Query: 168 DKLDNAEL-NGRRIRL 182
L N +L +R+
Sbjct: 176 IDLHNHDLGENHHLRV 191
Score = 58.8 bits (142), Expect = 9e-11
Identities = 26/136 (19%), Positives = 49/136 (36%), Gaps = 16/136 (11%)
Query: 112 SDHRLIVENLS-SRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKL 170
+ L+V NL+ RV+ Q L G+V + +V+ + + A+ L
Sbjct: 2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHL 61
Query: 171 DNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKS 230
+ +L+G+ IR+ + S+ ++ R + S R
Sbjct: 62 NGHKLHGKPIRI---------------TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFK 106
Query: 231 KSKAKSVSRSPSPSKT 246
K +K+ PS T
Sbjct: 107 KPGSKNFQNIFPPSAT 122
>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 = 88.5 bits (220), Expect = 5e-21
Identities = 29/211 (13%), Positives = 64/211 (30%), Gaps = 52/211 (24%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN------GFGFVEFEDYRDADDAVYE 56
T V + LP + + K+ K G I V + + F +EF Y A A+ +
Sbjct: 41 LTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITK 100
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRL 116
+ + + V + L
Sbjct: 101 THKV-VGQNEIIVSHLT---------------------------------------ECTL 120
Query: 117 IVENLSSRVSWQDLKDFMRQVGEVCYA-----DAHKRHRNEGVVEFESSSDMKKALDKLD 171
+ N + ++++D ++ + V + R ++ S D + ++KL+
Sbjct: 121 WMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLN 180
Query: 172 NAELNGRRIRL-IEDKPRGGGRGRSRSSSSR 201
++ G + + + R S + R
Sbjct: 181 GLKIEGYTLVTKVSNPLEKSKRTDSATLEGR 211
Score = 76.6 bits (189), Expect = 1e-16
Identities = 27/194 (13%), Positives = 69/194 (35%), Gaps = 41/194 (21%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIR-DVILKN-------GFGFVEFEDYRDADDAVY 55
+++ P +R++ ++ + + L + F +++ DA V
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHR 115
+LNG + G + +++ +++S+ R T
Sbjct: 178 KLNGLKIEGYTLVTKVSNPLEKSK-------------------------RTDSATLEGRE 212
Query: 116 LIVENLSSRVS-WQDLKDFMRQVGEV------CYADAHKRHRNEGVVEFESSSDMKKALD 168
+++ NLS+ + L++ G + H + + FE+ ++AL
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL- 271
Query: 169 KLDNAELNGRRIRL 182
+++ + L R I +
Sbjct: 272 QMNRSLLGNREISV 285
Score = 57.7 bits (140), Expect = 6e-10
Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 11/81 (13%)
Query: 3 GTKVYIGGLPYGVR-ERDLEKFVKGYGRIRDVIL---------KNGFGFVEFEDYRDADD 52
G ++ I L + E L + +G+G I + + N F+ FE+ A+
Sbjct: 210 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 269
Query: 53 AVYELNGKSLLGERVTVEIAK 73
A+ ++N L ++V +A
Sbjct: 270 AL-QMNRSLLGNREISVSLAD 289
Score = 51.5 bits (124), Expect = 6e-08
Identities = 14/94 (14%), Positives = 31/94 (32%), Gaps = 6/94 (6%)
Query: 92 PPPRRGWGHDRDDRYGPPTRSDHR-LIVENLSSRVSWQDLKDFMRQVGEV--C-YADAHK 147
P G + + ++V+NL + + + + G + AD+ K
Sbjct: 20 SPAAAGLTS-KKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK 78
Query: 148 RHRNEGVVEFESSSDMKKALDKLDNAELNGRRIR 181
++ +EF A+ K + + I
Sbjct: 79 KNFRFARIEFARYDGALAAITKT-HKVVGQNEII 111
>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 = 84.3 bits (209), Expect = 6e-21
Identities = 35/108 (32%), Positives = 49/108 (45%), Gaps = 7/108 (6%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-------GFGFVEFEDYRDADDAVY 55
K++IGGL E+ L+ +G I +V+L GF F+ FE+ DA +A
Sbjct: 7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAK 66
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRD 103
++NGKSL G+ + VE AK RR S R P H
Sbjct: 67 DMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEHHHH 114
Score = 56.6 bits (137), Expect = 1e-10
Identities = 23/102 (22%), Positives = 44/102 (43%), Gaps = 4/102 (3%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKL 170
+L + L+ + + LK + G + D + R + FE+ +D K A +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 171 DNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRS 212
+ L+G+ I++ + K G R + SR++S S S
Sbjct: 69 NGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLE 110
>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 = 83.8 bits (208), Expect = 4e-20
Identities = 26/195 (13%), Positives = 63/195 (32%), Gaps = 51/195 (26%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-------------GFGFVEFEDYRDAD 51
++Y+G +P+G+ E + F R+ + F F+EF +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 52 DAVYELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTR 111
A+ +G G+ + + R + P
Sbjct: 66 QAM-AFDGIIFQGQSLKI------RRPHDY--------------------------QPLP 92
Query: 112 SDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKA 166
H+L + L + ++ +K+ + G + + K + E+ + +A
Sbjct: 93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152
Query: 167 LDKLDNAELNGRRIR 181
+ L+ +L +++
Sbjct: 153 IAGLNGMQLGDKKLL 167
Score = 63.4 bits (155), Expect = 1e-12
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
K++IGGLP + + +++ + +G ++ L G+ F E+ D D A+
Sbjct: 94 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
Query: 55 YELNGKSLLGERVTVEIA 72
LNG L +++ V+ A
Sbjct: 154 AGLNGMQLGDKKLLVQRA 171
Score = 48.4 bits (116), Expect = 2e-07
Identities = 15/80 (18%), Positives = 30/80 (37%), Gaps = 11/80 (13%)
Query: 112 SDHRLIVENLSSRVSWQDLKDFMRQVGEV----------CYADAHKRHRNEGVVEFESSS 161
S RL V N+ ++ + + DF + A + +N +EF S
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 162 DMKKALDKLDNAELNGRRIR 181
+ +A+ D G+ ++
Sbjct: 63 ETTQAM-AFDGIIFQGQSLK 81
>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 = 82.4 bits (203), Expect = 4e-19
Identities = 43/192 (22%), Positives = 74/192 (38%), Gaps = 15/192 (7%)
Query: 3 GTKVYIGGL-PYGVRERDLEKFVKGYGRIRDVIL---KNGFGFVEFEDYRDADDAVYELN 58
+ + + L P V + L YG ++ V + K V+ D A A+ LN
Sbjct: 34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 93
Query: 59 GKSLLGERVTVEIAKG----IDRSQERGRRGYGSYRAPPPRR--GWGHDRDDRYGPPTRS 112
G L G+ + + ++K + R + + Y P R G PP+
Sbjct: 94 GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS-- 151
Query: 113 DHRLIVENLSSRVSWQDLKD-FMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLD 171
L + N+ VS +DLK F G V ++ R +++ S + +AL L
Sbjct: 152 -ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLH 210
Query: 172 NAEL-NGRRIRL 182
N +L +R+
Sbjct: 211 NHDLGENHHLRV 222
Score = 58.5 bits (141), Expect = 2e-10
Identities = 32/168 (19%), Positives = 58/168 (34%), Gaps = 21/168 (12%)
Query: 82 GRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLS-SRVSWQDLKDFMRQVGEV 140
+ PR G R G + L+V NL+ RV+ Q L G+V
Sbjct: 4 SHHHHHHSSGLVPR-GSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDV 62
Query: 141 CYADAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSS 200
+ +V+ + + A+ L+ +L+G+ IR+ +
Sbjct: 63 QRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRI-----------------T 105
Query: 201 RSRSKSRSRSRSSKSRSPRSRSKSGSP--RKSKSKAKSVSRSPSPSKT 246
S+ ++ R + ++ SP R K +K+ PS T
Sbjct: 106 LSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT 153
>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 = 78.1 bits (193), Expect = 6e-19
Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 3/85 (3%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRD--VILKNGFGFVEFEDYRDADDAVYELNGKS 61
K+YIG L V DL + V+LK+G+ FV++ D A A+ L+GK
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKV 68
Query: 62 -LLGERVTVEIAKGIDRSQERGRRG 85
L G+ + V+ + G
Sbjct: 69 ELHGKIMEVDYSVSKKLRSSGPSSG 93
Score = 50.7 bits (122), Expect = 1e-08
Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 5/88 (5%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLD-N 172
++L + NLS V+ DL+ V++ + +A++ L
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSGYAFVDYPDQNWAIRAIETLSGK 67
Query: 173 AELNGRRIRLIEDKPRGGGRGRSRSSSS 200
EL+G+ + + + + RS SS
Sbjct: 68 VELHGKIMEVDYSVSK---KLRSSGPSS 92
>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 = 76.2 bits (188), Expect = 5e-18
Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 3/84 (3%)
Query: 4 TKVYIGGLPYGVRERDLEK-FVK-GYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKS 61
+Y+ L E +EK F G + V + FV F + DA +A+ LNGK
Sbjct: 16 KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKV 75
Query: 62 LLGERVTVEIAKGIDRSQERGRRG 85
L G + V +AK +D+ G
Sbjct: 76 LDGSPIEVTLAKPVDK-DSSGPSS 98
Score = 50.0 bits (120), Expect = 2e-08
Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 1/82 (1%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
L V NL S + ++ + K+ R+ V F + D +A+ L+ L
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNGKVL 76
Query: 176 NGRRIRLIEDKPRGGGRGRSRS 197
+G I + KP S
Sbjct: 77 DGSPIEVTLAKPVDKDSSGPSS 98
>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 = 75.8 bits (187), Expect = 5e-18
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 2/85 (2%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--GFGFVEFEDYRDADDAVYELNGK 60
+++++G LP + E ++ K + YG+ +V + GFGF+ E A+ A EL+
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNM 74
Query: 61 SLLGERVTVEIAKGIDRSQERGRRG 85
L G+++ V A G
Sbjct: 75 PLRGKQLRVRFACHSASLTSGPSSG 99
Score = 48.8 bits (117), Expect = 6e-08
Identities = 19/92 (20%), Positives = 39/92 (42%), Gaps = 2/92 (2%)
Query: 107 GPPTRSDH-RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKK 165
G T + RL V NL ++ ++++ + G+ H + + G + E+ + +
Sbjct: 8 GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEI 66
Query: 166 ALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
A +LDN L G+++R+ S
Sbjct: 67 AKVELDNMPLRGKQLRVRFACHSASLTSGPSS 98
>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 = 78.6 bits (194), Expect = 2e-17
Identities = 44/192 (22%), Positives = 70/192 (36%), Gaps = 45/192 (23%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--GFGFVEFEDYRDADDAVYELNGKS 61
++++G LP + E D ++ + YG +V + GFGF+ E A+ A EL+G
Sbjct: 23 CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTI 82
Query: 62 LLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENL 121
L + + A L V+NL
Sbjct: 83 LKSRPLRIRFA--------------------------------------THGAALTVKNL 104
Query: 122 SSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKLDNAE-LN 176
S VS + L+ Q G V A D R +G VEF + +KAL++ + L
Sbjct: 105 SPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLL 164
Query: 177 GRRIRLIEDKPR 188
R + +P
Sbjct: 165 TTTPRPVIVEPM 176
Score = 59.7 bits (145), Expect = 9e-11
Identities = 24/110 (21%), Positives = 35/110 (31%), Gaps = 17/110 (15%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVY 55
G + + L V LE+ +G + ++ G GFVEF A A+
Sbjct: 96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALE 155
Query: 56 ELNGKSLLGER----VTVEIAKGIDRSQERGRR------GYGSYRAPPPR 95
+ L V VE + D + Y R PPR
Sbjct: 156 RCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPR 205
Score = 49.3 bits (118), Expect = 3e-07
Identities = 20/91 (21%), Positives = 32/91 (35%), Gaps = 6/91 (6%)
Query: 92 PPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAH-KRHR 150
RL V NL + ++ +D K + GE ++ R R
Sbjct: 4 FTIDIKS---FLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEP--SEVFINRDR 58
Query: 151 NEGVVEFESSSDMKKALDKLDNAELNGRRIR 181
G + ES + + A +LD L R +R
Sbjct: 59 GFGFIRLESRTLAEIAKAELDGTILKSRPLR 89
>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 = 76.5 bits (189), Expect = 2e-17
Identities = 28/198 (14%), Positives = 62/198 (31%), Gaps = 47/198 (23%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN---------GFGFVEFEDYRDADDA 53
K+++G +P E+DL + + YG + ++ +L++ G FV F + A +A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 54 VYELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSD 113
L+ +L K D +
Sbjct: 64 QNALHNMKVLPGMHHPIQMKPADSEKNNAVED---------------------------- 95
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDK 169
+L + +S + + D++ G++ R V F + + + A+
Sbjct: 96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK- 154
Query: 170 LDNAELNGRRIRLIEDKP 187
++ + P
Sbjct: 155 ----AMHQAQTMEGCSSP 168
Score = 59.2 bits (144), Expect = 4e-11
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 7/68 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN------GFGFVEFEDYRDADDAVY 55
K++IG + E D+ +G+I + IL+ G FV F A A+
Sbjct: 95 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 154
Query: 56 ELNGKSLL 63
++ +
Sbjct: 155 AMHQAQTM 162
Score = 42.6 bits (101), Expect = 3e-05
Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 8/92 (8%)
Query: 112 SDHR-LIVENLSSRVSWQDLKDFMRQVGEVC-------YADAHKRHRNEGVVEFESSSDM 163
SD + V + S +DL++ Q G V + + + V F +
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 164 KKALDKLDNAELNGRRIRLIEDKPRGGGRGRS 195
+A + L N ++ I+ KP + +
Sbjct: 61 LEAQNALHNMKVLPGMHHPIQMKPADSEKNNA 92
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 74.4 bits (183), Expect = 3e-17
Identities = 21/100 (21%), Positives = 36/100 (36%), Gaps = 8/100 (8%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAV 54
+V L VRE L+ + YG + +V IL + G V F R A + V
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPP 94
L+ S++G + ++ + + P
Sbjct: 66 KNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTPQT 105
Score = 59.3 bits (144), Expect = 1e-11
Identities = 20/107 (18%), Positives = 34/107 (31%), Gaps = 8/107 (7%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKRHRNEGVVEFESSS 161
G + L+ V LKD R+ GEV ++H V F S+
Sbjct: 2 GQIPLK--EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTR 59
Query: 162 DMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRS 208
K+ + L + G I + +G R + ++
Sbjct: 60 GAKETVKNLHLTSVMGNIIH-AQLDIKGQQRMKYYELIVNGSYTPQT 105
>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 = 73.4 bits (181), Expect = 4e-17
Identities = 26/91 (28%), Positives = 38/91 (41%), Gaps = 8/91 (8%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAV 54
+ + L Y L + + YGR+ DV + GF FV F D RDA DA
Sbjct: 13 MITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAE 72
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
++G L G + V++A+ R G
Sbjct: 73 AAMDGAELDGRELRVQVARYGRRDLSGPSSG 103
Score = 52.2 bits (126), Expect = 3e-09
Identities = 24/98 (24%), Positives = 35/98 (35%), Gaps = 5/98 (5%)
Query: 105 RYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFES 159
GP L V+NL+ R S L+ + G V + R V F
Sbjct: 5 SSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64
Query: 160 SSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
D + A +D AEL+GR +R+ + S
Sbjct: 65 RRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPSS 102
>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 = 71.4 bits (176), Expect = 2e-16
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 9/82 (10%)
Query: 1 MVGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN---------GFGFVEFEDYRDAD 51
M TKV+IG L V + + + YG+I+ + + G+ +VEFE+ +A+
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61
Query: 52 DAVYELNGKSLLGERVTVEIAK 73
A+ ++G + G+ +T
Sbjct: 62 KALKHMDGGQIDGQEITATAVL 83
Score = 53.7 bits (130), Expect = 7e-10
Identities = 14/85 (16%), Positives = 33/85 (38%), Gaps = 6/85 (7%)
Query: 110 TRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK------RHRNEGVVEFESSSDM 163
+ ++ + L+ V+ + + G++ D + VEFE+ +
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60
Query: 164 KKALDKLDNAELNGRRIRLIEDKPR 188
+KAL +D +++G+ I
Sbjct: 61 EKALKHMDGGQIDGQEITATAVLAP 85
>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 = 71.1 bits (175), Expect = 3e-16
Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 8/78 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAV 54
+ VY+ LP+ + DL + YG++ V + G F+ F D A +
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75
Query: 55 YELNGKSLLGERVTVEIA 72
+N K L G + IA
Sbjct: 76 RAINNKQLFGRVIKASIA 93
Score = 49.1 bits (118), Expect = 3e-08
Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 5/80 (6%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSS 161
G S + V NL ++ DL + G+V K + + + F
Sbjct: 10 GGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD 69
Query: 162 DMKKALDKLDNAELNGRRIR 181
+ ++N +L GR I+
Sbjct: 70 SAQNCTRAINNKQLFGRVIK 89
>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 = 70.5 bits (173), Expect = 9e-16
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 5/88 (5%)
Query: 2 VGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-----GFGFVEFEDYRDADDAVYE 56
V +YI LPY + ++ YG IR + + N G +V +ED DA +AV
Sbjct: 7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDH 66
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRR 84
L+G ++ + V Q+ +
Sbjct: 67 LSGFNVSNRYLVVLYYNANRAFQKMDTK 94
Score = 50.8 bits (122), Expect = 1e-08
Identities = 15/86 (17%), Positives = 33/86 (38%), Gaps = 2/86 (2%)
Query: 109 PTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK--RHRNEGVVEFESSSDMKKA 166
P + L + NL +++ +++ D + G + R V +E D K A
Sbjct: 4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 63
Query: 167 LDKLDNAELNGRRIRLIEDKPRGGGR 192
+D L ++ R + ++ +
Sbjct: 64 VDHLSGFNVSNRYLVVLYYNANRAFQ 89
>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 = 70.0 bits (172), Expect = 9e-16
Identities = 25/89 (28%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN------GFGFVEFEDYRDADDAVYE 56
++++ +P+ R+ DL + +G+I DV + GFGFV FE+ DAD A +
Sbjct: 15 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREK 74
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRG 85
L+G + G ++ V A + G
Sbjct: 75 LHGTVVEGRKIEVNNATARVMTNSGPSSG 103
Score = 51.5 bits (124), Expect = 6e-09
Identities = 23/93 (24%), Positives = 37/93 (39%), Gaps = 3/93 (3%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK---RHRNEGVVEFESSSDMK 164
+ RL V N+ R DL+ Q G++ + + G V FE+S+D
Sbjct: 10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADAD 69
Query: 165 KALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
+A +KL + GR+I + R S
Sbjct: 70 RAREKLHGTVVEGRKIEVNNATARVMTNSGPSS 102
>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 = 70.0 bits (172), Expect = 1e-15
Identities = 24/93 (25%), Positives = 38/93 (40%), Gaps = 8/93 (8%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVY 55
V++G +PY E L+ G + L G+GF E++D A A+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRGYGS 88
LNG+ G + V+ A +E G G+
Sbjct: 69 NLNGREFSGRALRVDNAASEKNKEELKSLGTGA 101
Score = 43.8 bits (104), Expect = 4e-06
Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 9/85 (10%)
Query: 111 RSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEFESSSDM 163
RS + V N+ + + LKD +VG V + + G E++
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPV--VSFRLVYDRETGKPKGYGFCEYQDQETA 63
Query: 164 KKALDKLDNAELNGRRIRLIEDKPR 188
A+ L+ E +GR +R+
Sbjct: 64 LSAMRNLNGREFSGRALRVDNAASE 88
>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 = 69.6 bits (171), Expect = 1e-15
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 4/75 (5%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNG--FGFVEFEDYRDADDAVYELNGKS 61
T++++GGL L + +G IR + G F ++++E A A ++ G
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFP 77
Query: 62 LLGE--RVTVEIAKG 74
L G R+ V+ AK
Sbjct: 78 LGGPDRRLRVDFAKS 92
Score = 46.1 bits (110), Expect = 4e-07
Identities = 19/75 (25%), Positives = 28/75 (37%), Gaps = 4/75 (5%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKAL 167
PT RL V L S L + G + D H + + +++ES + A
Sbjct: 15 NPTT---RLWVGGLGPNTSLAALAREFDRFGSIRTID-HVKGDSFAYIQYESLDAAQAAC 70
Query: 168 DKLDNAELNGRRIRL 182
K+ L G RL
Sbjct: 71 AKMRGFPLGGPDRRL 85
>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 = 69.7 bits (171), Expect = 2e-15
Identities = 24/109 (22%), Positives = 40/109 (36%), Gaps = 7/109 (6%)
Query: 87 GSYRAPPPRRGWGHDR---DDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA 143
G + W HD G + +L+V NL VS D+++ + G + A
Sbjct: 6 GGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA 65
Query: 144 DAHK----RHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPR 188
R V FE +D KA+ + L+GR + + +
Sbjct: 66 AVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 114
Score = 59.3 bits (144), Expect = 2e-11
Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 8/87 (9%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK-------NGFGFVEFEDYRDADDAVY 55
G K+ + L +GV + D+++ +G ++ + G V FE DA A+
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 56 ELNGKSLLGERVTVEIAKG-IDRSQER 81
+ G L G + +++ ID
Sbjct: 95 QYKGVPLDGRPMDIQLVASQIDLEHHH 121
>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 = 68.8 bits (169), Expect = 2e-15
Identities = 26/90 (28%), Positives = 39/90 (43%), Gaps = 8/90 (8%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVY 55
+Y+GGL V ++ L +G I D+ + GF FVEFE DA A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
+N L G + V +AK + + G
Sbjct: 73 NMNESELFGRTIRVNLAKPMRIKESGPSSG 102
Score = 55.7 bits (135), Expect = 2e-10
Identities = 25/95 (26%), Positives = 38/95 (40%), Gaps = 9/95 (9%)
Query: 110 TRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEFESSSD 162
+ L V L+ V + L G++ D ++HR VEFE + D
Sbjct: 9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDI--TDIQIPLDYETEKHRGFAFVEFELAED 66
Query: 163 MKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
A+D ++ +EL GR IR+ KP S
Sbjct: 67 AAAAIDNMNESELFGRTIRVNLAKPMRIKESGPSS 101
>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 = 70.7 bits (174), Expect = 3e-15
Identities = 37/193 (19%), Positives = 64/193 (33%), Gaps = 45/193 (23%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAV 54
T + + LP + +R+L + G I I+++ G+ FV+F D+ A+
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDH 114
LNG ++ +R+ V SY P D
Sbjct: 63 KVLNGITVRNKRLKV------------------SYARPGGES--------------IKDT 90
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYA-----DAHKRHRNEGVVEFESSSDMKKALDK 169
L V NL ++ L + G + R R V + + ++A+
Sbjct: 91 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 150
Query: 170 LDNAELNGRRIRL 182
L+N G L
Sbjct: 151 LNNVIPEGGSQPL 163
Score = 51.4 bits (124), Expect = 2e-08
Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 5/83 (6%)
Query: 112 SDHRLIVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKRHRNEGVVEFESSSDMKKA 166
S+ LIV L ++ ++L R +G + V+F S D ++A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 167 LDKLDNAELNGRRIRLIEDKPRG 189
+ L+ + +R+++ +P G
Sbjct: 62 IKVLNGITVRNKRLKVSYARPGG 84
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 68.7 bits (168), Expect = 3e-15
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 3/75 (4%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN---GFGFVEFEDYRDADDAVYELNG 59
VY+G LP R DL++ ++ G + + F+ + D A AV L G
Sbjct: 19 AADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQG 78
Query: 60 KSLLGERVTVEIAKG 74
L + + V +A+
Sbjct: 79 LRLGTDTLRVALARQ 93
Score = 53.3 bits (128), Expect = 1e-09
Identities = 17/98 (17%), Positives = 33/98 (33%), Gaps = 4/98 (4%)
Query: 91 APPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHR 150
G G + + V NL DLK +R++G V + R
Sbjct: 1 GSSGSSGPGSPPGE----GAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPR 56
Query: 151 NEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPR 188
+ + S+ ++A+ L L +R+ + +
Sbjct: 57 RRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 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 = 68.2 bits (167), Expect = 3e-15
Identities = 12/71 (16%), Positives = 28/71 (39%), Gaps = 1/71 (1%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYG-RIRDVILKNGFGFVEFEDYRDADDAVYELNGKSL 62
+ + + LP +++ +K Y + V FV + A +A+ + S
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSF 65
Query: 63 LGERVTVEIAK 73
G+ + V++
Sbjct: 66 RGKDLIVQLQP 76
Score = 50.1 bits (120), Expect = 1e-08
Identities = 15/85 (17%), Positives = 34/85 (40%), Gaps = 5/85 (5%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVG-EVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
++V+NL + Q++ D ++ + CY D R++ V + + A+
Sbjct: 7 GILVKNLPQDSNCQEVHDLLKDYDLKYCYVD---RNKRTAFVTLLNGEQAQNAIQMFHQY 63
Query: 174 ELNGRRIRLIEDKPRGGGRGRSRSS 198
G+ + ++ +P SS
Sbjct: 64 SFRGKDLI-VQLQPTDALLCSGPSS 87
>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 = 68.4 bits (168), Expect = 4e-15
Identities = 30/89 (33%), Positives = 49/89 (55%), Gaps = 8/89 (8%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVYE 56
K+++GGL + E+ LE+ YG+I +V++ GFGFV FE+ DA DA+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRG 85
+NGKS+ G ++ V+ A ++ G
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSDNRSGPSSG 102
Score = 51.1 bits (123), Expect = 8e-09
Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 9/92 (9%)
Query: 113 DHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEFESSSDMKK 165
+ +L V LS + Q L+ + G++ ++ +R R G V FE+ D K
Sbjct: 12 EGKLFVGGLSFDTNEQSLEQVFSKYGQI--SEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 166 ALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
A+ ++ ++GR+IR+ + R S
Sbjct: 70 AMMAMNGKSVDGRQIRVDQAGKSSDNRSGPSS 101
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 68.1 bits (167), Expect = 4e-15
Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 2/72 (2%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-GFGFVEFEDYRDADDAVYELNGKS 61
T YIG +P+ E DL + +G I D G F++++ + A + L
Sbjct: 28 TTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFP 87
Query: 62 LLGERVTVEIAK 73
G + K
Sbjct: 88 FQGRNLRTGWGK 99
Score = 53.5 bits (129), Expect = 1e-09
Identities = 18/104 (17%), Positives = 34/104 (32%), Gaps = 3/104 (2%)
Query: 85 GYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYAD 144
G + PP D R PP + + N+ + DL + G +
Sbjct: 1 GSQTIGLPPQVNPQAVDHIIRSAPPRVT--TAYIGNIPHFATEADLIPLFQNFGFILDFK 58
Query: 145 AHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPR 188
+ + +++++ + L N GR +R K R
Sbjct: 59 HYP-EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER 101
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 68.1 bits (167), Expect = 5e-15
Identities = 22/90 (24%), Positives = 42/90 (46%), Gaps = 13/90 (14%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVY 55
K++I GLP+ + +LE+ K +G ++D+ L G +VE+E+ A AV
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVM 76
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
+++G ++ + V I+ G
Sbjct: 77 KMDGMTIKENIIKVAISN------SGPSSG 100
Score = 54.6 bits (132), Expect = 4e-10
Identities = 14/85 (16%), Positives = 34/85 (40%), Gaps = 4/85 (4%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDM 163
+ H+L + L + ++L++ + G V + + + VE+E+ S
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQA 71
Query: 164 KKALDKLDNAELNGRRIRLIEDKPR 188
+A+ K+D + I++
Sbjct: 72 SQAVMKMDGMTIKENIIKVAISNSG 96
>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 = 67.6 bits (166), Expect = 5e-15
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVY 55
+Y+GGL V ++ L +G I D+ + GF FVEFE DA A+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 56 ELNGKSLLGERVTVEIAK 73
+N L G + V +AK
Sbjct: 68 NMNESELFGRTIRVNLAK 85
Score = 58.3 bits (142), Expect = 1e-11
Identities = 22/80 (27%), Positives = 33/80 (41%), Gaps = 5/80 (6%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSS 161
G + L V L+ V + L G++ +HR VEFE +
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 162 DMKKALDKLDNAELNGRRIR 181
D A+D ++ +EL GR IR
Sbjct: 61 DAAAAIDNMNESELFGRTIR 80
>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 = 68.6 bits (168), Expect = 7e-15
Identities = 27/103 (26%), Positives = 49/103 (47%), Gaps = 8/103 (7%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
G +++ G+ E D+ YG I+++ L G+ VE+E Y++A A+
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRG 97
LNG+ L+G+ ++V+ + + R G R+P RR
Sbjct: 82 EGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPDRRRR 124
Score = 57.0 bits (138), Expect = 1e-10
Identities = 29/119 (24%), Positives = 52/119 (43%), Gaps = 11/119 (9%)
Query: 101 DRDDRYGPPTRSDH--RLIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRN 151
++D P RS L V + + +D+ D + GE+ + H +
Sbjct: 8 EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEI--KNIHLNLDRRTGYLKG 65
Query: 152 EGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRS 210
+VE+E+ + + A++ L+ +L G+ I + RG +G+ R RSRS R R
Sbjct: 66 YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPDRRRR 124
>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 = 68.7 bits (169), Expect = 1e-14
Identities = 37/189 (19%), Positives = 71/189 (37%), Gaps = 42/189 (22%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN------GFGFVEFEDYRDADDAVYELN 58
+Y+G L + E L+++ + G I ++ I+ + + FVE+ DA+ A+ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 59 GKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIV 118
GK + V + + + + + + L V
Sbjct: 63 GKQIENNIVKI------NWAFQSQQS------------------------SSDDTFNLFV 92
Query: 119 ENLSSRVSWQDLKDFMRQVGEVCYA-----DAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
+L+ V + L++ + R G V F S D + A+D +
Sbjct: 93 GDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQ 152
Query: 174 ELNGRRIRL 182
+LNGR +R+
Sbjct: 153 DLNGRPLRI 161
Score = 53.3 bits (129), Expect = 5e-09
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 8/79 (10%)
Query: 2 VGTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDA 53
+++G L V + L K + ++ + G+GFV F DA +A
Sbjct: 86 DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 145
Query: 54 VYELNGKSLLGERVTVEIA 72
+ + G+ L G + + A
Sbjct: 146 MDSMQGQDLNGRPLRINWA 164
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 66.8 bits (164), Expect = 1e-14
Identities = 25/89 (28%), Positives = 42/89 (47%), Gaps = 3/89 (3%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK---RHRNEGVVEFESSSDMK 164
+ ++ V NL +W+ LKD + G V YAD + + GVV+FES +
Sbjct: 3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAE 62
Query: 165 KALDKLDNAELNGRRIRLIEDKPRGGGRG 193
+A ++ +L+GR I + D+ G
Sbjct: 63 RACRMMNGMKLSGREIDVRIDRNASGPSS 91
Score = 61.1 bits (149), Expect = 1e-12
Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 10/89 (11%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIR--DVILKN----GFGFVEFEDYRDADDAVYE 56
++++ LP+ + L+ G + D+ ++N G G V+FE A+ A
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRM 67
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRG 85
+NG L G + V IDR+ G
Sbjct: 68 MNGMKLSGREIDV----RIDRNASGPSSG 92
>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 = 66.5 bits (163), Expect = 2e-14
Identities = 26/79 (32%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAV 54
+ + GL ERDL + YG I DV + GF FV FE+ DA +A
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 55 YELNGKSLLGERVTVEIAK 73
NG L G R+ V
Sbjct: 75 ERANGMELDGRRIRVSGPS 93
Score = 50.3 bits (121), Expect = 1e-08
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 5/79 (6%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAH-KRHRNEGVVEFESSSD 162
+ L V LS + +DL++ + G + D +R R V FE+ D
Sbjct: 10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69
Query: 163 MKKALDKLDNAELNGRRIR 181
K+A ++ + EL+GRRIR
Sbjct: 70 AKEAKERANGMELDGRRIR 88
>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 = 66.2 bits (162), Expect = 2e-14
Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 8/80 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
T + + +P+ V ++ F GY I + G V FE +A AV
Sbjct: 15 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 74
Query: 55 YELNGKSLLGERVTVEIAKG 74
+LN + + +V + + G
Sbjct: 75 IDLNDRPIGSRKVKLVLGSG 94
Score = 54.2 bits (131), Expect = 6e-10
Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 5/85 (5%)
Query: 112 SDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA-----DAHKRHRNEGVVEFESSSDMKKA 166
+ V+N+ VS ++ DF + + + E +V FES + A
Sbjct: 14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 167 LDKLDNAELNGRRIRLIEDKPRGGG 191
+ L++ + R+++L+ G
Sbjct: 74 VIDLNDRPIGSRKVKLVLGSGPSSG 98
>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 = 66.1 bits (162), Expect = 3e-14
Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 4/87 (4%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN----GFGFVEFEDYRDADDAVYELN 58
+ + L Y E L++ + I+ +N G+ F+EF + DA +A+ N
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 59 GKSLLGERVTVEIAKGIDRSQERGRRG 85
+ + G + +E+ G
Sbjct: 75 KREIEGRAIRLELQGPRGSPNSGPSSG 101
Score = 56.9 bits (138), Expect = 7e-11
Identities = 22/91 (24%), Positives = 39/91 (42%), Gaps = 1/91 (1%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADA-HKRHRNEGVVEFESSSDMKKA 166
+ L++ NLS + + L++ + + + + + +EF S D K+A
Sbjct: 10 TWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEA 69
Query: 167 LDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
L+ + E+ GR IRL PRG S
Sbjct: 70 LNSCNKREIEGRAIRLELQGPRGSPNSGPSS 100
>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 = 65.7 bits (161), Expect = 3e-14
Identities = 20/90 (22%), Positives = 32/90 (35%), Gaps = 8/90 (8%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVY 55
VY+G +PY E + G + ++ + G+ F+EF D + AV
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
LNG L + + D S
Sbjct: 63 NLNGYQLGSRFLKCGYSSNSDISGVSLEHH 92
Score = 49.5 bits (119), Expect = 2e-08
Identities = 11/86 (12%), Positives = 24/86 (27%), Gaps = 5/86 (5%)
Query: 118 VENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKALDKLDN 172
+ ++ + + + D VG V R + +EF A+ L+
Sbjct: 7 LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG 66
Query: 173 AELNGRRIRLIEDKPRGGGRGRSRSS 198
+L R ++
Sbjct: 67 YQLGSRFLKCGYSSNSDISGVSLEHH 92
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 66.2 bits (162), Expect = 3e-14
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN------GFGFVEFEDYRDADDAVYE 56
++++ +P+ R+ DL + +G+I DV + GFGFV FE+ DAD A +
Sbjct: 29 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREK 88
Query: 57 LNGKSLLGERVTVEIAK 73
L+G + G ++ V A
Sbjct: 89 LHGTVVEGRKIEVNNAT 105
Score = 51.9 bits (125), Expect = 5e-09
Identities = 26/115 (22%), Positives = 45/115 (39%), Gaps = 13/115 (11%)
Query: 77 RSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQ 136
S + RG + +++ P RL V N+ R DL+ Q
Sbjct: 3 SSHHHHHH-----SSGLVPRGSHMNTENKSQP-----KRLHVSNIPFRFRDPDLRQMFGQ 52
Query: 137 VGEVCYADA---HKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPR 188
G++ + + + G V FE+S+D +A +KL + GR+I + R
Sbjct: 53 FGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
>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 = 65.7 bits (161), Expect = 3e-14
Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 5/83 (6%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRI---RDVILKNGFGFVEFEDYRDADDAVYELNG 59
+ L + + E +L++ + I G ++EF+ DA+ + E G
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 75
Query: 60 KSLLGERVTVEIAKGIDRSQERG 82
+ G V++ ++ RG
Sbjct: 76 AEIDGRSVSLYYTG--EKGGTRG 96
Score = 61.5 bits (150), Expect = 1e-12
Identities = 23/86 (26%), Positives = 43/86 (50%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKAL 167
R+ L+ +NLS ++ +LK+ E+ + + +EF+S +D +K L
Sbjct: 11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNL 70
Query: 168 DKLDNAELNGRRIRLIEDKPRGGGRG 193
++ AE++GR + L +GG RG
Sbjct: 71 EEKQGAEIDGRSVSLYYTGEKGGTRG 96
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 66.7 bits (163), Expect = 5e-14
Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVY 55
+Y+GGL V ++ L +G I D+ + GF FVEFE DA A+
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 56 ELNGKSLLGERVTVEIA 72
+N L G + V +A
Sbjct: 124 NMNESELFGRTIRVNLA 140
Score = 62.1 bits (151), Expect = 2e-12
Identities = 23/92 (25%), Positives = 34/92 (36%), Gaps = 5/92 (5%)
Query: 95 RRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RH 149
G G + L V L+ V + L G++ +H
Sbjct: 45 HVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKH 104
Query: 150 RNEGVVEFESSSDMKKALDKLDNAELNGRRIR 181
R VEFE + D A+D ++ +EL GR IR
Sbjct: 105 RGFAFVEFELAEDAAAAIDNMNESELFGRTIR 136
>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 = 65.9 bits (161), Expect = 5e-14
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 4/73 (5%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-GFGFVEFEDYRDADDAVYELNGK 60
G +Y+ G + L +G I D+ + FV +E AD AV ELNG
Sbjct: 39 GNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGT 96
Query: 61 SLLGERVTVEIAK 73
+ ++ V IA+
Sbjct: 97 QVESVQLKVNIAR 109
Score = 43.6 bits (103), Expect = 6e-06
Identities = 17/112 (15%), Positives = 38/112 (33%), Gaps = 8/112 (7%)
Query: 87 GSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAH 146
GS+ P R +R P + L V ++ L+ G +
Sbjct: 18 GSHMGPFRRSD---SFPERRAPRKGN--TLYVYGED--MTPTLLRGAFSPFGNIIDLSMD 70
Query: 147 KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSS 198
RN V +E +A+ +L+ ++ ++++ + + + S
Sbjct: 71 P-PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDAATGKS 121
>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 = 64.9 bits (159), Expect = 6e-14
Identities = 25/94 (26%), Positives = 41/94 (43%), Gaps = 14/94 (14%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVY 55
+ +Y+G L + + E L + +G+I +++L G+GF+ F D A A+
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSY 89
+LNG L G + V ER G G
Sbjct: 66 QLNGFELAGRPMRV------GHVTERLDGGSGPS 93
Score = 55.3 bits (134), Expect = 2e-10
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 5/88 (5%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKALDK 169
L V +L ++ L+ G++ K R + G + F S ++AL++
Sbjct: 7 GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 170 LDNAELNGRRIRLIEDKPRGGGRGRSRS 197
L+ EL GR +R+ R G S
Sbjct: 67 LNGFELAGRPMRVGHVTERLDGGSGPSS 94
>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 = 66.4 bits (163), Expect = 8e-14
Identities = 35/189 (18%), Positives = 66/189 (34%), Gaps = 47/189 (24%)
Query: 4 TKVYIGGLPYGVRERDL-EKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAV 54
T + + LP + + + F G I ++++ G+GFV + D +DA+ A+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGS-IGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDH 114
LNG L + + V SY P D
Sbjct: 62 NTLNGLRLQTKTIKV------------------SYARPSSAS--------------IRDA 89
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGE-----VCYADAHKRHRNEGVVEFESSSDMKKALDK 169
L V L ++ ++L+ Q G + R G + F+ + ++A+
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149
Query: 170 LDNAELNGR 178
L+ + +G
Sbjct: 150 LNGQKPSGA 158
Score = 59.1 bits (144), Expect = 4e-11
Identities = 26/80 (32%), Positives = 43/80 (53%), Gaps = 10/80 (12%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAV 54
+Y+ GLP + +++LE+ YGRI IL + G GF+ F+ +A++A+
Sbjct: 88 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
Query: 55 YELNGKSLLG--ERVTVEIA 72
LNG+ G E +TV+ A
Sbjct: 148 KGLNGQKPSGATEPITVKFA 167
Score = 50.3 bits (121), Expect = 5e-08
Identities = 16/83 (19%), Positives = 33/83 (39%), Gaps = 5/83 (6%)
Query: 112 SDHRLIVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKRHRNEGVVEFESSSDMKKA 166
S LIV L ++ ++ + +GE+ + G V + D +KA
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 167 LDKLDNAELNGRRIRLIEDKPRG 189
++ L+ L + I++ +P
Sbjct: 61 INTLNGLRLQTKTIKVSYARPSS 83
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 65.0 bits (159), Expect = 9e-14
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 8/79 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
G +++ G+ E D+ YG I+++ L G+ VE+E Y++A A+
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82
Query: 55 YELNGKSLLGERVTVEIAK 73
LNG+ L+G+ ++V+
Sbjct: 83 EGLNGQDLMGQPISVDWCF 101
Score = 51.1 bits (123), Expect = 8e-09
Identities = 20/96 (20%), Positives = 41/96 (42%), Gaps = 7/96 (7%)
Query: 101 DRDDRYGPPTRSD--HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEG 153
++D P RS L V + + +D+ D + GE+ + +
Sbjct: 9 EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 68
Query: 154 VVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRG 189
+VE+E+ + + A++ L+ +L G+ I + RG
Sbjct: 69 LVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG 104
>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 = 65.0 bits (159), Expect = 9e-14
Identities = 24/113 (21%), Positives = 38/113 (33%), Gaps = 4/113 (3%)
Query: 99 GHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK----RHRNEGV 154
G R + V NL +V W+ LK+ G V AD + + R G
Sbjct: 1 GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGT 60
Query: 155 VEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSR 207
V FE S + +A+ + L R + + D+ + S
Sbjct: 61 VTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSS 113
Score = 63.9 bits (156), Expect = 2e-13
Identities = 21/99 (21%), Positives = 39/99 (39%), Gaps = 7/99 (7%)
Query: 2 VGTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN------GFGFVEFEDYRDADDAV 54
+G+ V++ L Y V + L++ G + IL++ G G V FE +A A+
Sbjct: 14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAI 73
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPP 93
NG+ L + V++ + + P
Sbjct: 74 SMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPS 112
>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 = 64.6 bits (158), Expect = 1e-13
Identities = 22/91 (24%), Positives = 34/91 (37%), Gaps = 11/91 (12%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
+ + L RE DL++ + +G I + L GF F+ F DA A+
Sbjct: 15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
++G + VE AK S G
Sbjct: 75 AGVSGFGYDHLILNVEWAK---PSTNSGPSS 102
Score = 52.2 bits (126), Expect = 3e-09
Identities = 19/100 (19%), Positives = 33/100 (33%), Gaps = 7/100 (7%)
Query: 103 DDRYGPPTRSD--HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVV 155
GP R+D + V NLS DL++ R G + K + + +
Sbjct: 3 SGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFI 62
Query: 156 EFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRS 195
F D +A+ + + + + KP S
Sbjct: 63 SFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPSS 102
>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 = 66.0 bits (161), Expect = 1e-13
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAV 54
T + + L Y L + + YGR+ DV + GF FV F D RDA+DA+
Sbjct: 70 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129
Query: 55 YELNGKSLLGERVTVEIAK 73
++G L G + V++A+
Sbjct: 130 DAMDGAVLDGRELRVQMAR 148
Score = 49.8 bits (119), Expect = 8e-08
Identities = 25/120 (20%), Positives = 39/120 (32%), Gaps = 13/120 (10%)
Query: 76 DRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMR 135
+ + H T L V+NL+ R S L+
Sbjct: 37 NGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTS----LKVDNLTYRTSPDTLRRVFE 92
Query: 136 QVGEVCYADAH-------KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPR 188
+ G V D + K R V F D + A+D +D A L+GR +R+ +
Sbjct: 93 KYGRV--GDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG 150
>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 = 64.6 bits (158), Expect = 1e-13
Identities = 24/88 (27%), Positives = 36/88 (40%), Gaps = 7/88 (7%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI------RDVILKNGFGFVEFEDYRDADDAVYEL 57
++I L + + L +G I D G+GFV FE A+ A+ ++
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 65
Query: 58 NGKSLLGERVTVEIAKG-IDRSQERGRR 84
NG L +V V K +R E G R
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAELGAR 93
Score = 41.1 bits (97), Expect = 4e-05
Identities = 17/91 (18%), Positives = 37/91 (40%), Gaps = 5/91 (5%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKLD 171
+ ++NL + + L D G + D + + G V FE+ ++A++K++
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMN 66
Query: 172 NAELNGRRIRLIEDKPRGGGRGRSRSSSSRS 202
LN R++ + K R + +
Sbjct: 67 GMLLNDRKVFVGRFKSRKEREAELGARAKEF 97
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 64.0 bits (156), Expect = 1e-13
Identities = 16/82 (19%), Positives = 28/82 (34%), Gaps = 5/82 (6%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-----GFGFVEFEDYRDADDAVYEL 57
K+ I +P ++ L+ + YG + N V + A A+ +L
Sbjct: 15 IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKL 74
Query: 58 NGKSLLGERVTVEIAKGIDRSQ 79
NG L + V +Q
Sbjct: 75 NGFQLENFTLKVAYIPDEMAAQ 96
Score = 61.3 bits (149), Expect = 1e-12
Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 4/92 (4%)
Query: 99 GHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGV--VE 156
G P + +L + N+ + W+ L + Q G V + V V
Sbjct: 1 GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVT 60
Query: 157 FESSSDMKKALDKLDNAELNGRRIR--LIEDK 186
+ S ++ALDKL+ +L ++ I D+
Sbjct: 61 YSSKDQARQALDKLNGFQLENFTLKVAYIPDE 92
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 64.7 bits (158), Expect = 1e-13
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAV 54
G ++I LP + DL +G + + + FGFV F++ A A+
Sbjct: 40 GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAI 99
Query: 55 YELNGKSLLGERVTVEIAK 73
+NG + +R+ V++ K
Sbjct: 100 KAMNGFQVGTKRLKVQLKK 118
Score = 33.9 bits (78), Expect = 0.013
Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 5/71 (7%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHK-RHRNEGVVEFESSSDMKKALDKL 170
L + +L + DL G V A D + G V F++ + A+ +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 171 DNAELNGRRIR 181
+ ++ +R++
Sbjct: 103 NGFQVGTKRLK 113
>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 = 63.9 bits (156), Expect = 1e-13
Identities = 17/85 (20%), Positives = 27/85 (31%), Gaps = 16/85 (18%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN----------------GFGFVEFEDY 47
+++ GL V + + K G I+ G V F+D
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73
Query: 48 RDADDAVYELNGKSLLGERVTVEIA 72
A A+ +GK G + V A
Sbjct: 74 PSAKAAIDWFDGKEFSGNPIKVSFA 98
Score = 49.2 bits (118), Expect = 4e-08
Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 14/92 (15%)
Query: 104 DRYGPPTRSDHRLI-VENLSSRVSWQDLKDFMRQVGEVCYADAHK-------------RH 149
+ + SD+ I V+ L V+ + + D+ +Q+G + +
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62
Query: 150 RNEGVVEFESSSDMKKALDKLDNAELNGRRIR 181
+ E V F+ K A+D D E +G I+
Sbjct: 63 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIK 94
>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 = 63.8 bits (156), Expect = 2e-13
Identities = 21/90 (23%), Positives = 35/90 (38%), Gaps = 8/90 (8%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVY 55
++++ L Y E DLEK YG + ++ GF FV F A A
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
E++G+ G + V + + + G
Sbjct: 69 EVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98
Score = 50.7 bits (122), Expect = 1e-08
Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 9/91 (9%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEFESSSDMKKAL 167
RL V NLS S +DL+ G + ++ H K+ + V F KA
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPL--SELHYPIDSLTKKPKGFAFVTFMFPEHAVKAY 67
Query: 168 DKLDNAELNGRRIRLIEDKPRGGGRGRSRSS 198
++D GR + ++ + SS
Sbjct: 68 AEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98
>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 = 63.0 bits (154), Expect = 3e-13
Identities = 23/87 (26%), Positives = 35/87 (40%), Gaps = 5/87 (5%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-----GFGFVEFEDYRDADDAVYELN 58
+++ GL E L++ G R R V + GFGFV+F DA A +
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 59 GKSLLGERVTVEIAKGIDRSQERGRRG 85
+ G +VT++ AK G
Sbjct: 76 DGEIDGNKVTLDWAKPKGEGGSGPSSG 102
Score = 50.7 bits (122), Expect = 1e-08
Identities = 25/95 (26%), Positives = 40/95 (42%), Gaps = 4/95 (4%)
Query: 107 GPPTRSD--HRLIVENLSSRVSWQDLKDFMRQVGEVC--YADAHKRHRNEGVVEFESSSD 162
GP RS L V+ LS + + LK+ + G V+F S D
Sbjct: 7 GPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEED 66
Query: 163 MKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
K A + +++ E++G ++ L KP+G G S
Sbjct: 67 AKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101
>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 = 63.0 bits (154), Expect = 3e-13
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-------GFGFVEFEDYRDADDAVYEL 57
++IG L +L+ + D+ + + FG+V+FE D + A+ EL
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-EL 77
Query: 58 NGKSLLGERVTVEIAKGIDRSQ 79
G + G + +E KG D ++
Sbjct: 78 TGLKVFGNEIKLEKPKGRDGTR 99
Score = 53.4 bits (129), Expect = 1e-09
Identities = 27/95 (28%), Positives = 45/95 (47%), Gaps = 5/95 (5%)
Query: 103 DDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFE 158
D G + + L + NL+ S +LK + ++ +R G V+FE
Sbjct: 7 DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFE 66
Query: 159 SSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRG 193
S+ D++KAL+ L ++ G I+L + K R G RG
Sbjct: 67 SAEDLEKALE-LTGLKVFGNEIKLEKPKGRDGTRG 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 = 63.4 bits (155), Expect = 4e-13
Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 7/78 (8%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN------GFGFVEFEDYRDADDAVY 55
T +YI LP + E++LE +K +G++ IL++ G GF E + +
Sbjct: 25 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIG 84
Query: 56 ELNGKSLLGERVTVEIAK 73
NGK + +
Sbjct: 85 HFNGKFIKTPPGVSAPTE 102
Score = 38.8 bits (91), Expect = 3e-04
Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 4/77 (5%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKLD 171
L + NL + Q+L++ ++ G+V D+ R G ES+ + + +
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN 87
Query: 172 NAELNGRRIRLIEDKPR 188
+ +P
Sbjct: 88 GKFIKTPPGVSAPTEPL 104
>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 = 63.1 bits (154), Expect = 4e-13
Identities = 17/79 (21%), Positives = 38/79 (48%), Gaps = 8/79 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
G +++ + +E ++++ YG I+++ L G+ VE+E ++ A A
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 85
Query: 55 YELNGKSLLGERVTVEIAK 73
LNG ++G+ + V+
Sbjct: 86 EALNGAEIMGQTIQVDWCF 104
Score = 48.8 bits (117), Expect = 7e-08
Identities = 17/95 (17%), Positives = 38/95 (40%), Gaps = 6/95 (6%)
Query: 101 DRDDRYGPPTRSD-HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGV 154
D + GP + L V ++ ++++ GE+ + + +
Sbjct: 13 DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 72
Query: 155 VEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRG 189
VE+E+ A + L+ AE+ G+ I++ +G
Sbjct: 73 VEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG 107
>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 = 62.7 bits (153), Expect = 4e-13
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 4/73 (5%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-GFGFVEFEDYRDADDAVYELNGK 60
G +Y+ G + L +G I D+ + FV +E AD AV ELNG
Sbjct: 15 GNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGT 72
Query: 61 SLLGERVTVEIAK 73
+ ++ V IA+
Sbjct: 73 QVESVQLKVNIAR 85
Score = 37.3 bits (87), Expect = 6e-04
Identities = 8/61 (13%), Positives = 23/61 (37%), Gaps = 1/61 (1%)
Query: 128 QDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKP 187
L+ G + RN V +E +A+ +L+ ++ ++++ +
Sbjct: 28 TLLRGAFSPFGNIIDLSMDP-PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK 86
Query: 188 R 188
+
Sbjct: 87 Q 87
>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 = 65.4 bits (160), Expect = 5e-13
Identities = 40/191 (20%), Positives = 72/191 (37%), Gaps = 45/191 (23%)
Query: 4 TKVYIGGLPYGVRERDL-EKFVKGYGR------IRDVILKN--GFGFVEFEDYRDADDAV 54
+Y+G L V E L EKF G RD+I + G+ +V F+ DA+ A+
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSP-AGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDH 114
+N + G+ V + + R P R+
Sbjct: 75 DTMNFDVIKGKPVRIMWS----------------QRDPSLRKS--------------GVG 104
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKL 170
+ ++NL + + L D G + D + + G V FE+ ++A++K+
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKM 163
Query: 171 DNAELNGRRIR 181
+ LN R++
Sbjct: 164 NGMLLNDRKVF 174
Score = 55.7 bits (135), Expect = 1e-09
Identities = 24/100 (24%), Positives = 39/100 (39%), Gaps = 7/100 (7%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-----GFGFVEFEDYRDADDAVYE 56
++I L + + L +G I ++ + G+GFV FE A+ A+ +
Sbjct: 103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 162
Query: 57 LNGKSLLGERVTVEIA-KGIDRSQERGRRGYGSYRAPPPR 95
+NG L +V V +R E G R Y P
Sbjct: 163 MNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPD 202
Score = 48.8 bits (117), Expect = 3e-07
Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 5/81 (6%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKRHRNEGVVEFESSS 161
P+ L V +L V+ L + G + C +R V F+ +
Sbjct: 9 SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 68
Query: 162 DMKKALDKLDNAELNGRRIRL 182
D ++ALD ++ + G+ +R+
Sbjct: 69 DAERALDTMNFDVIKGKPVRI 89
>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 = 63.1 bits (154), Expect = 5e-13
Identities = 19/91 (20%), Positives = 41/91 (45%), Gaps = 8/91 (8%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAV 54
G ++I LP ++DL + +G + + + FGFV +++ A A+
Sbjct: 25 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 84
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
+NG + +R+ V++ + + S+ G
Sbjct: 85 QSMNGFQIGMKRLKVQLKRSKNDSKSGPSSG 115
Score = 34.2 bits (79), Expect = 0.009
Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 5/87 (5%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA-----DAHKRHRNEGVVEFESSSDMKKALDKL 170
L + +L QDL G V A + G V +++ + A+ +
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 171 DNAELNGRRIRLIEDKPRGGGRGRSRS 197
+ ++ +R+++ + + + S
Sbjct: 88 NGFQIGMKRLKVQLKRSKNDSKSGPSS 114
>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 = 62.7 bits (153), Expect = 5e-13
Identities = 26/91 (28%), Positives = 41/91 (45%), Gaps = 10/91 (10%)
Query: 4 TKVYIGGLPYGVRERDL-EKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
VY+GGL V E L E F++ G + + + G+GFVEF DAD A+
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQ-AGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
++ L G+ + V A +++ G
Sbjct: 75 KIMDMIKLYGKPIRVNKASAHNKNLSGPSSG 105
Score = 55.3 bits (134), Expect = 2e-10
Identities = 25/100 (25%), Positives = 39/100 (39%), Gaps = 11/100 (11%)
Query: 107 GPPTRSDH--RLIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEF 157
GP + + + V L +VS L + Q G V + H +H+ G VEF
Sbjct: 7 GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPV--VNTHMPKDRVTGQHQGYGFVEF 64
Query: 158 ESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
S D A+ +D +L G+ IR+ + S
Sbjct: 65 LSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSS 104
>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 = 62.7 bits (153), Expect = 5e-13
Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 11/94 (11%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-----------GFGFVEFEDYRDAD 51
+ ++I L + E L+ G I+ + GFGFVE++ A
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 52 DAVYELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
A+ +L G ++ G ++ V I++ + G
Sbjct: 65 KALKQLQGHTVDGHKLEVRISERATKPASGPSSG 98
Score = 45.7 bits (109), Expect = 7e-07
Identities = 16/91 (17%), Positives = 33/91 (36%), Gaps = 8/91 (8%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYAD--------AHKRHRNEGVVEFESSSDMKKA 166
L ++NL+ + + LK +VG + G VE++ +KA
Sbjct: 7 GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66
Query: 167 LDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
L +L ++G ++ + + S
Sbjct: 67 LKQLQGHTVDGHKLEVRISERATKPASGPSS 97
>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 = 62.7 bits (153), Expect = 5e-13
Identities = 28/103 (27%), Positives = 45/103 (43%), Gaps = 8/103 (7%)
Query: 87 GSYRAPPPRRGWGHDR-DDRYGPPTRSD--HRLIVENLSSRVSWQDLKDFMRQVGEVCYA 143
GS P + W HD D +G + +L+V NL VS D+++ + G + A
Sbjct: 1 GSRPKQLPDK-WQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKA 59
Query: 144 DAHK----RHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
H R V FE +D KA+ + + L+GR + +
Sbjct: 60 AVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 102
Score = 59.6 bits (145), Expect = 7e-12
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 7/77 (9%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK-------NGFGFVEFEDYRDADDAVY 55
G K+ + L +GV + D+++ +G ++ + G V FE DA A+
Sbjct: 29 GGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMK 88
Query: 56 ELNGKSLLGERVTVEIA 72
+ NG L G + +++
Sbjct: 89 QYNGVPLDGRPMNIQLV 105
>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 = 62.7 bits (153), Expect = 6e-13
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV--ILKNGFGFVEFEDYRDADDAVYELNGKS 61
VY GG+ G+ ++ + + +G+I ++ + G+ FV F + A A+ +NG +
Sbjct: 26 CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTT 85
Query: 62 LLGERVTVEIAK 73
+ G V K
Sbjct: 86 IEGHVVKCYWGK 97
Score = 49.3 bits (118), Expect = 4e-08
Identities = 12/111 (10%), Positives = 32/111 (28%), Gaps = 3/111 (2%)
Query: 87 GSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAH 146
GS + + + P + ++S ++ Q ++ G++
Sbjct: 1 GSSGSSGNTKQLRFEDVVNQSSPKNC--TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF 58
Query: 147 KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
+ V F + A+ ++ + G ++ K S
Sbjct: 59 -PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPSS 108
>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 = 62.7 bits (153), Expect = 6e-13
Identities = 23/93 (24%), Positives = 40/93 (43%), Gaps = 10/93 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL---------KNGFGFVEFEDYRDADDA 53
+K+ + +P+ +R++ + +G ++ V L GFGFV+F +DA A
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74
Query: 54 VYEL-NGKSLLGERVTVEIAKGIDRSQERGRRG 85
L + L G R+ +E A Q G
Sbjct: 75 FNALCHSTHLYGRRLVLEWADSEVTVQSGPSSG 107
Score = 50.4 bits (121), Expect = 2e-08
Identities = 21/97 (21%), Positives = 41/97 (42%), Gaps = 7/97 (7%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA------DAHKRHRNEGVVEFESSS 161
P ++ +++V N+ + + +++++ GE+ HR G V+F +
Sbjct: 10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 69
Query: 162 DMKKALDKLDN-AELNGRRIRLIEDKPRGGGRGRSRS 197
D KKA + L + L GRR+ L + S
Sbjct: 70 DAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106
>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 = 62.3 bits (152), Expect = 7e-13
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVY 55
++Y+G L + + E L + +GRI + L G+GF+ F D A A+
Sbjct: 27 MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
Query: 56 ELNGKSLLGERVTVEIAK 73
+LNG L G + V
Sbjct: 87 QLNGFELAGRPMKVGHVT 104
Score = 55.8 bits (135), Expect = 2e-10
Identities = 20/90 (22%), Positives = 35/90 (38%), Gaps = 5/90 (5%)
Query: 104 DRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFE 158
+ + RL V +L ++ L+ G + R + G + F
Sbjct: 17 NNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76
Query: 159 SSSDMKKALDKLDNAELNGRRIRLIEDKPR 188
S KKAL++L+ EL GR +++ R
Sbjct: 77 DSECAKKALEQLNGFELAGRPMKVGHVTER 106
>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 = 61.9 bits (151), Expect = 7e-13
Identities = 23/77 (29%), Positives = 31/77 (40%), Gaps = 7/77 (9%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN------GFGFVEFEDYRDADDAVY 55
V++G L VRE L + G + V I K+ FGFV F+ A+
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIA 75
Query: 56 ELNGKSLLGERVTVEIA 72
LNG L G + V
Sbjct: 76 LLNGIRLYGRPINVSGP 92
Score = 54.2 bits (131), Expect = 5e-10
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 4/75 (5%)
Query: 111 RSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKA 166
+D + V NL +RV + L + Q G + D + ++ G V F+ + A
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYA 73
Query: 167 LDKLDNAELNGRRIR 181
+ L+ L GR I
Sbjct: 74 IALLNGIRLYGRPIN 88
>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 = 62.8 bits (153), Expect = 9e-13
Identities = 26/95 (27%), Positives = 41/95 (43%), Gaps = 10/95 (10%)
Query: 1 MVGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADD 52
V + + +P V E L + + YG I V + G+GFV+F+ A
Sbjct: 40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99
Query: 53 AVYELNGKSLLGERVTVEIAKGIDRSQERGRRGYG 87
A+ LNG ++L +R+ V +A Q G G
Sbjct: 100 AIAGLNGFNILNKRLKVALAA--SGHQRPGIAGAV 132
Score = 45.1 bits (107), Expect = 2e-06
Identities = 16/103 (15%), Positives = 38/103 (36%), Gaps = 5/103 (4%)
Query: 105 RYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFES 159
+ P L+V + + V L+ + G + + R G V+F+S
Sbjct: 34 QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93
Query: 160 SSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRS 202
S ++A+ L+ + +R+++ G + + +
Sbjct: 94 GSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGN 136
>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 = 61.6 bits (150), Expect = 9e-13
Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 8/78 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
T + + +P+ V ++ F GY I + G V FE +A AV
Sbjct: 15 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 74
Query: 55 YELNGKSLLGERVTVEIA 72
+LN + + +V +
Sbjct: 75 IDLNDRPIGSRKVKLSGP 92
Score = 53.1 bits (128), Expect = 1e-09
Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 5/76 (6%)
Query: 112 SDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA-----DAHKRHRNEGVVEFESSSDMKKA 166
+ V+N+ VS ++ DF + + + E +V FES + A
Sbjct: 14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 167 LDKLDNAELNGRRIRL 182
+ L++ + R+++L
Sbjct: 74 VIDLNDRPIGSRKVKL 89
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 61.6 bits (150), Expect = 1e-12
Identities = 23/86 (26%), Positives = 36/86 (41%), Gaps = 6/86 (6%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL---KNGFGFVEFEDYRDADDAVYELNGKS 61
V++ G P GV L ++ +G + V++ K F VE D A +AV + S
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDV-GAREAVLSQSQHS 68
Query: 62 LLGERVTVEIA--KGIDRSQERGRRG 85
L G R+ V K + +G
Sbjct: 69 LGGHRLRVRPREQKEFQSPASKSPKG 94
Score = 44.2 bits (105), Expect = 2e-06
Identities = 15/80 (18%), Positives = 24/80 (30%), Gaps = 1/80 (1%)
Query: 118 VENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAELNG 177
V V L ++ G V K +VE + L L G
Sbjct: 13 VSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVL-SQSQHSLGG 71
Query: 178 RRIRLIEDKPRGGGRGRSRS 197
R+R+ + + S+S
Sbjct: 72 HRLRVRPREQKEFQSPASKS 91
>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 = 62.3 bits (152), Expect = 1e-12
Identities = 27/95 (28%), Positives = 39/95 (41%), Gaps = 15/95 (15%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVYE 56
V+ L +R RDLE F G++RDV + + G +VEF + + A+
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-G 85
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRA 91
L G+ LLG + V SQ R G
Sbjct: 86 LTGQRLLGVPIIV------QASQAEKNRLSGPSSG 114
Score = 45.4 bits (108), Expect = 1e-06
Identities = 19/85 (22%), Positives = 31/85 (36%), Gaps = 6/85 (7%)
Query: 118 VENLSSRVSWQDLKDFMRQVGEVCYA-----DAHKRHRNEGVVEFESSSDMKKALDKLDN 172
L++R+ +DL+DF VG+V +R + VEF + A+ L
Sbjct: 30 CMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTG 88
Query: 173 AELNGRRIRLIEDKPRGGGRGRSRS 197
L G I + + S
Sbjct: 89 QRLLGVPIIVQASQAEKNRLSGPSS 113
>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 = 61.5 bits (150), Expect = 1e-12
Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 9/77 (11%)
Query: 6 VYIGGLPYGVRERDLEKFVKG----YGRIRDVILKN-----GFGFVEFEDYRDADDAVYE 56
+YI L +++ +L+K + +G+I D+++ G FV F++ A +A+
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 57 LNGKSLLGERVTVEIAK 73
+ G + + ++ AK
Sbjct: 71 MQGFPFYDKPMRIQYAK 87
Score = 45.3 bits (108), Expect = 8e-07
Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 6/80 (7%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMRQV----GEV--CYADAHKRHRNEGVVEFESSS 161
P TR +H + + NL+ ++ +LK + + G++ + R + V F+ S
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 62
Query: 162 DMKKALDKLDNAELNGRRIR 181
AL + + +R
Sbjct: 63 SATNALRSMQGFPFYDKPMR 82
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 62.0 bits (151), Expect = 1e-12
Identities = 22/113 (19%), Positives = 34/113 (30%), Gaps = 20/113 (17%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN----------------GFGFVEFEDY 47
+++ GL V + + K G I+ G V F+D
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 48 RDADDAVYELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGH 100
A A+ +GK G + V A + RG G+ R H
Sbjct: 68 PSAKAAIDWFDGKEFSGNPIKVSFA----TRRADFNRGGGNGRGGLEHHHHHH 116
Score = 50.1 bits (120), Expect = 2e-08
Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 18/99 (18%)
Query: 118 VENLSSRVSWQDLKDFMRQVGEVC------------YADAHK-RHRNEGVVEFESSSDMK 164
V+ L V+ + + D+ +Q+G + Y D + + E V F+ K
Sbjct: 12 VQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAK 71
Query: 165 KALDKLDNAELNGRRIRLIE-----DKPRGGGRGRSRSS 198
A+D D E +G I++ D RGGG GR
Sbjct: 72 AAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLE 110
>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 = 61.0 bits (149), Expect = 1e-12
Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 8/76 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAV 54
+ +YI GL G ++DL K + YG+I G+GFV+F+ A AV
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Query: 55 YELNGKSLLGERVTVE 70
L + +
Sbjct: 65 TALKASGVQAQMAKQS 80
Score = 44.4 bits (106), Expect = 1e-06
Identities = 18/89 (20%), Positives = 34/89 (38%), Gaps = 9/89 (10%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSS 161
G L + L + QDL + G++ A + + G V+F+S S
Sbjct: 1 GSS--GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPS 58
Query: 162 DMKKALDKLDNAELNGRRIRLIEDKPRGG 190
+KA+ L + + + + + P G
Sbjct: 59 AAQKAVTALKASGVQAQMAK--QSGPSSG 85
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 62.1 bits (151), Expect = 2e-12
Identities = 27/94 (28%), Positives = 42/94 (44%), Gaps = 13/94 (13%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAV 54
T + + L Y L + + YGR+ DV + GF FV F D RDA+DA+
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRGYGS 88
++G L G + V++A+ R + S
Sbjct: 107 DAMDGAVLDGRELRVQMAR-----YGRPPDSHHS 135
Score = 47.8 bits (114), Expect = 2e-07
Identities = 28/121 (23%), Positives = 41/121 (33%), Gaps = 8/121 (6%)
Query: 76 DRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSD---HRLIVENLSSRVSWQDLKD 132
G GS+ A YG P L V+NL+ R S L+
Sbjct: 7 HHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRR 66
Query: 133 FMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKP 187
+ G V + R V F D + A+D +D A L+GR +R+ +
Sbjct: 67 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARY 126
Query: 188 R 188
Sbjct: 127 G 127
>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 = 61.0 bits (148), Expect = 3e-12
Identities = 22/92 (23%), Positives = 40/92 (43%), Gaps = 12/92 (13%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGR-IRDVILKN---------GFGFVEFEDYRDADDA 53
+++IGG+P + ++ + + + DVI+ GF FVE+E +R A A
Sbjct: 9 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68
Query: 54 VYELNGKS--LLGERVTVEIAKGIDRSQERGR 83
+L L G ++ V+ A+ E
Sbjct: 69 RRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVM 100
Score = 41.3 bits (97), Expect = 3e-05
Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 9/82 (10%)
Query: 109 PTRSDHRLIVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKRHRNEGV--VEFESSS 161
+ + RL + + +++ + + +V E YA A + +N G VE+ES
Sbjct: 4 GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63
Query: 162 DMKKALDKLDNA--ELNGRRIR 181
A KL +L G +I
Sbjct: 64 AAAMARRKLMPGRIQLWGHQIA 85
>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 = 60.2 bits (147), Expect = 3e-12
Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVY 55
+++G L V + L K + + G+GFV F DA +A+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 56 ELNGKSLLGERVTVEIAK 73
+ G+ L G + + A
Sbjct: 62 SMQGQDLNGRPLRINWAA 79
Score = 46.3 bits (111), Expect = 2e-07
Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 9/81 (11%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEFESSSDMKKAL 167
L V +L+ V + L++ + H R G V F S D + A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSY--LSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 168 DKLDNAELNGRRIRLIEDKPR 188
D + +LNGR +R+
Sbjct: 61 DSMQGQDLNGRPLRINWAAKL 81
>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 = 60.8 bits (148), Expect = 3e-12
Identities = 21/93 (22%), Positives = 41/93 (44%), Gaps = 13/93 (13%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN------GFGFVEFEDYRDADDAVY 55
K+++G L E D+ + + +G I + +L+ G FV+F + +A A++
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74
Query: 56 ELNGKSLL---GERVTVEIAKGIDRSQERGRRG 85
L+G + + V+ A D +E G
Sbjct: 75 ALHGSQTMPGASSSLVVKFA---DTDKESGPSS 104
Score = 29.2 bits (66), Expect = 0.45
Identities = 13/79 (16%), Positives = 28/79 (35%), Gaps = 9/79 (11%)
Query: 113 DHRLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALD 168
D +L V L+ + S +D+ + G + + V+F S ++ + A+
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74
Query: 169 KLDNAELNGRRIRLIEDKP 187
L+G +
Sbjct: 75 -----ALHGSQTMPGASSS 88
>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 = 60.3 bits (147), Expect = 3e-12
Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 9/88 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
+Y+G L Y +++ +G++ +V L GFGFVE ++ +A+ +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRR 84
L+ +G + V A +
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSLEHHHHH 89
Score = 46.4 bits (111), Expect = 3e-07
Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 10/89 (11%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEFESSSDMKKAL 167
+ V NL + + +K+ Q G+V + K+ + G VE + +A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKV--FNVKLIYDRETKKPKGFGFVEM-QEESVSEAI 59
Query: 168 DKLDNAELNGRRIRLIEDKPRGGGRGRSR 196
KLDN + GR IR+ E P+
Sbjct: 60 AKLDNTDFMGRTIRVTEANPKKSLEHHHH 88
>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 = 60.4 bits (147), Expect = 4e-12
Identities = 21/94 (22%), Positives = 41/94 (43%), Gaps = 11/94 (11%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAV 54
K++IG +P + E+DL+ + +G+I ++ +LK+ G F+ + + A A
Sbjct: 13 AIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQ 72
Query: 55 YELNGKSLL---GERVTVEIAKGIDRSQERGRRG 85
L+ + L + V+ A R G
Sbjct: 73 SALHEQKTLPGMNRPIQVKPADSESRGGSGPSSG 106
Score = 31.9 bits (73), Expect = 0.056
Identities = 17/103 (16%), Positives = 32/103 (31%), Gaps = 14/103 (13%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEFES 159
G +L + + + +DLK + G++ + H+ + +
Sbjct: 7 GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKI--YELTVLKDRFTGMHKGCAFLTYCE 64
Query: 160 SSDMKKALDKLDNAEL---NGRRIRLIEDKPRGGGRGRSRSSS 199
KA L + R I++ RG S SS
Sbjct: 65 RESALKAQSALHEQKTLPGMNRPIQVKPADSE--SRGGSGPSS 105
>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 = 63.7 bits (154), Expect = 4e-12
Identities = 19/100 (19%), Positives = 45/100 (45%), Gaps = 12/100 (12%)
Query: 6 VYIGGLPYGVRERDLEKFV----KGYGRIRDVILKN-----GFGFVEFEDYRDADDAVYE 56
+YI L +++ +L+K + +G+I D+++ G FV F++ A +A+
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRR 96
+ G + + ++ AK + + G++ +R
Sbjct: 72 MQGFPFYDKPMRIQYAK---TDSDIIAKMKGTFVERDRKR 108
Score = 51.8 bits (123), Expect = 5e-08
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 4/71 (5%)
Query: 7 YIGGLPYGVRERDLEKFVKGYGRIRDVIL---KNGFGFVEFEDYRDADDAVYELNGKSLL 63
++ LP E L + ++V L ++ FVEF++ A A L G +
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKIT 270
Query: 64 GER-VTVEIAK 73
+ + AK
Sbjct: 271 QNNAMKISFAK 281
Score = 46.8 bits (110), Expect = 2e-06
Identities = 24/142 (16%), Positives = 47/142 (33%), Gaps = 6/142 (4%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMR----QVGEV--CYADAHKRHRNEGVVEFESSS 161
P TR +H + + NL+ ++ +LK + Q G++ + R + V F+ S
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVS 63
Query: 162 DMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSR 221
AL + + +R+ K + + + K R S+ +
Sbjct: 64 SATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKK 123
Query: 222 SKSGSPRKSKSKAKSVSRSPSP 243
+ G A P
Sbjct: 124 AVQGGGATPVVGAVQGPVPGMP 145
Score = 35.6 bits (81), Expect = 0.010
Identities = 12/84 (14%), Positives = 24/84 (28%), Gaps = 1/84 (1%)
Query: 100 HDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFES 159
+ +H L + NL + L Q + VEF++
Sbjct: 194 QMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDN 253
Query: 160 SSDMKKALDKLDNAEL-NGRRIRL 182
A D L ++ +++
Sbjct: 254 EVQAGAARDALQGFKITQNNAMKI 277
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 62.2 bits (151), Expect = 4e-12
Identities = 27/115 (23%), Positives = 42/115 (36%), Gaps = 7/115 (6%)
Query: 81 RGRRGYGSYRAPPPRRGWGHDRDDRY---GPPTRSDHRLIVENLSSRVSWQDLKDFMRQV 137
R R P W HD D G + +L+V NL VS D+++ +
Sbjct: 53 GRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEF 112
Query: 138 GEVCYADAHK----RHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPR 188
G + A R V FE +D KA+ + L+GR + + +
Sbjct: 113 GTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 167
Score = 52.9 bits (127), Expect = 8e-09
Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 7/78 (8%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK-------NGFGFVEFEDYRDADDAVY 55
G K+ + L +GV + D+++ +G ++ + G V FE DA A+
Sbjct: 88 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 147
Query: 56 ELNGKSLLGERVTVEIAK 73
+ G L G + +++
Sbjct: 148 QYKGVPLDGRPMDIQLVA 165
>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 = 59.8 bits (146), Expect = 4e-12
Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 9/79 (11%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAV 54
+Y+G + YG +LE G G + V IL + GF ++EF D ++
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Query: 55 YELNGKSLLGERVTVEIAK 73
L+ G ++ V +
Sbjct: 66 -ALDESLFRGRQIKVIPKR 83
Score = 42.9 bits (102), Expect = 5e-06
Identities = 19/86 (22%), Positives = 35/86 (40%), Gaps = 7/86 (8%)
Query: 112 SDHRLI-VENLSSRVSWQDLKDFMRQVGEVCYA----DAH-KRHRNEGVVEFESSSDMKK 165
+D R I V N+ + ++L+ G V D + +EF ++
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63
Query: 166 ALDKLDNAELNGRRIRLIEDKPRGGG 191
+L LD + GR+I++I + G
Sbjct: 64 SL-ALDESLFRGRQIKVIPKRTNRPG 88
>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 = 60.0 bits (146), Expect = 5e-12
Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 9/89 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVYE 56
++G LPY V E +++F +G + + GFG+ EFED A+
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRG 85
LN +SL +R+ V++A G
Sbjct: 76 LNEESLGNKRIRVDVADQAQDKDSGPSSG 104
Score = 45.3 bits (108), Expect = 9e-07
Identities = 21/104 (20%), Positives = 34/104 (32%), Gaps = 6/104 (5%)
Query: 99 GHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGE-----VCYADAHKRHRNEG 153
G P + + NL V+ + +K+F R + +R + G
Sbjct: 1 GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60
Query: 154 VVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
EFE + AL L+ L +RIR+ S
Sbjct: 61 YAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKDSGPSS 103
>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 = 60.9 bits (148), Expect = 5e-12
Identities = 26/79 (32%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAV 54
+ + GL ERDL + YG I DV + GF FV FE+ DA +A
Sbjct: 46 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
Query: 55 YELNGKSLLGERVTVEIAK 73
NG L G R+ V+ +
Sbjct: 106 ERANGMELDGRRIRVDFSI 124
Score = 54.0 bits (130), Expect = 1e-09
Identities = 29/119 (24%), Positives = 45/119 (37%), Gaps = 7/119 (5%)
Query: 77 RSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSD--HRLIVENLSSRVSWQDLKDFM 134
G GS+ A G D L V LS + +DL++
Sbjct: 8 HHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVF 67
Query: 135 RQVGEVCYA----DAH-KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPR 188
+ G + D +R R V FE+ D K+A ++ + EL+GRRIR+ +
Sbjct: 68 SKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126
>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 = 59.5 bits (145), Expect = 6e-12
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 6/90 (6%)
Query: 2 VGTKVYIGGLPYGVRERDLEKFVKGYGRIRD--VILKN----GFGFVEFEDYRDADDAVY 55
+Y+ L G+ + L K +G I V+++ GFGFV F +A AV
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVT 73
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
E+NG+ + + + V +A+ + Q G
Sbjct: 74 EMNGRIVATKPLYVALAQRKEERQSGPSSG 103
Score = 35.7 bits (83), Expect = 0.003
Identities = 15/86 (17%), Positives = 33/86 (38%), Gaps = 3/86 (3%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK---RHRNEGVVEFESSSDMKKALDKLD 171
L V+NL + + L+ G + A R + G V F S + KA+ +++
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 172 NAELNGRRIRLIEDKPRGGGRGRSRS 197
+ + + + + + + S
Sbjct: 77 GRIVATKPLYVALAQRKEERQSGPSS 102
>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 = 61.9 bits (151), Expect = 7e-12
Identities = 36/211 (17%), Positives = 68/211 (32%), Gaps = 43/211 (20%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVYE 56
K++IGGL + + L + +G + D ++ GFGFV + + DA
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV-DAAMN 73
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTR-SDHR 115
+ G V + RA R+D P + +
Sbjct: 74 ARPHKVDGRVVEPK-------------------RAVS--------REDSQRPGAHLTVKK 106
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYAD-----AHKRHRNEGVVEFESSSDMKKALDKL 170
+ V + L+D+ Q G++ + + R V F+ + K + +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ- 165
Query: 171 DNAELNGRRIRLIEDKPRGGGRGRSRSSSSR 201
+NG + + + S S R
Sbjct: 166 KYHTVNGHNCEVRKALSKQEMASASSSQRGR 196
>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 = 60.0 bits (146), Expect = 7e-12
Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 8/79 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAV 54
+Y+ L V ERDL + + ++ G F+ F + A A+
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
Query: 55 YELNGKSLLGERVTVEIAK 73
+ +NG L G+ + +E K
Sbjct: 85 HLVNGYKLYGKILVIEFGK 103
Score = 48.1 bits (115), Expect = 1e-07
Identities = 23/99 (23%), Positives = 40/99 (40%), Gaps = 11/99 (11%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHK-RHRNEGVVEFESSS 161
G P L ++NLS RV+ +DL + E R R + + F +
Sbjct: 22 GEPN---KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKE 78
Query: 162 DMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSS 200
+AL ++ +L G+ + + K + + RS SS
Sbjct: 79 IAWQALHLVNGYKLYGKILVIEFGKNK---KQRSSGPSS 114
>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 = 59.2 bits (144), Expect = 9e-12
Identities = 21/99 (21%), Positives = 40/99 (40%), Gaps = 16/99 (16%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVYE 56
V++GG+ + E ++ F YG +++V + G+GFV F + D V
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV-- 67
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPR 95
+ + G+++ + A R Q + P P
Sbjct: 68 ESQINFHGKKLKLGPAI---RKQNLSTY----HVQPRPL 99
Score = 38.4 bits (90), Expect = 3e-04
Identities = 16/102 (15%), Positives = 38/102 (37%), Gaps = 14/102 (13%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKL 170
+ V + R+ +++ F + G V D + G V F + D++K ++
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES- 69
Query: 171 DNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRS 212
+G++++L G + + S + R +
Sbjct: 70 -QINFHGKKLKL--------GPAIRKQNLSTYHVQPRPLIFN 102
>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 = 59.3 bits (144), Expect = 1e-11
Identities = 22/99 (22%), Positives = 33/99 (33%), Gaps = 16/99 (16%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN----------------GFGFVEFED 46
+ +Y+ GL V DL F K G ++ G V +ED
Sbjct: 15 NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74
Query: 47 YRDADDAVYELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
A AV +GK G ++ V +A+ G
Sbjct: 75 PPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSSG 113
Score = 52.4 bits (126), Expect = 3e-09
Identities = 23/110 (20%), Positives = 41/110 (37%), Gaps = 14/110 (12%)
Query: 102 RDDRYGPPTRSDHRLI-VENLSSRVSWQDLKDFMRQVGEVC------------YADAHK- 147
P SD+ I V+ L+ V+ DL DF +Q G V Y D
Sbjct: 3 SGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG 62
Query: 148 RHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
+ + + V +E K A++ D + G ++++ + + S
Sbjct: 63 KPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSS 112
>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 = 62.0 bits (150), Expect = 1e-11
Identities = 21/124 (16%), Positives = 39/124 (31%), Gaps = 12/124 (9%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK----------NGFGFVEFEDYRDADDA 53
+YIG L + + DL + V G + +K GF V +
Sbjct: 69 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 128
Query: 54 VYELNGKSLLGERVTVEIA--KGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTR 111
+ L + L G+ V + + + + + R+ S + + R P
Sbjct: 129 MDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQG 188
Query: 112 SDHR 115
R
Sbjct: 189 GRGR 192
Score = 60.1 bits (145), Expect = 4e-11
Identities = 22/166 (13%), Positives = 48/166 (28%), Gaps = 8/166 (4%)
Query: 71 IAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSD-HRLIVENLSSRVSWQD 129
I+ + R Y P G L + NL+ + +D
Sbjct: 25 ISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDED 84
Query: 130 LKDFMRQVGEVCYADAH-------KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
L + + +G + + + +V S + KK +D L EL+G+ +
Sbjct: 85 LTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVV 144
Query: 183 IEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPR 228
+ + +S + + ++ + R
Sbjct: 145 TPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGR 190
>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 = 58.4 bits (142), Expect = 1e-11
Identities = 16/90 (17%), Positives = 29/90 (32%), Gaps = 13/90 (14%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYG--RIRDVILKN--------GFGFVEFEDYRDADDAV 54
+YIG L + + DL + V G I ++ GF V + +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRR 84
L + L G+ V + + +
Sbjct: 63 DLLPKRELHGQNPVVTPSN---KLEHHHHH 89
Score = 51.4 bits (124), Expect = 4e-09
Identities = 15/88 (17%), Positives = 31/88 (35%), Gaps = 7/88 (7%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEFESSSDMKKA 166
L + NL+ + +DL + + +G + + + +V S + KK
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61
Query: 167 LDKLDNAELNGRRIRLIEDKPRGGGRGR 194
+D L EL+G+ +
Sbjct: 62 MDLLPKRELHGQNPVVTPSNKLEHHHHH 89
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 59.5 bits (144), Expect = 2e-11
Identities = 14/91 (15%), Positives = 28/91 (30%), Gaps = 11/91 (12%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKG----YGRIRDVILKN-----GFGFVEFEDYRDADDAV 54
V I + V + L+ + G I D+++ G ++ F A V
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFV 89
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
G G + + ++ + G
Sbjct: 90 EAFQGYPFQGNPLVITFSET--PQSQVAEDG 118
Score = 49.5 bits (118), Expect = 5e-08
Identities = 11/99 (11%), Positives = 31/99 (31%), Gaps = 6/99 (6%)
Query: 90 RAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMR----QVGEV--CYA 143
A R+ P T +++ N++ V + L+ + G++
Sbjct: 6 AAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVV 65
Query: 144 DAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
D + + + F + + ++ G + +
Sbjct: 66 DLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI 104
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 59.5 bits (144), Expect = 2e-11
Identities = 20/103 (19%), Positives = 34/103 (33%), Gaps = 14/103 (13%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV---ILKN-------GFGFVEFEDYRDADD 52
VY+G + ++ L + ++ G V +N G+ V
Sbjct: 55 RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHK 114
Query: 53 AVYELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPR 95
+ L GK L GE+V V A Q + + + R
Sbjct: 115 LLELLPGKVLNGEKVDVRPA----TRQNLSQFEAQARKRECVR 153
Score = 53.8 bits (129), Expect = 3e-09
Identities = 17/125 (13%), Positives = 36/125 (28%), Gaps = 7/125 (5%)
Query: 90 RAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAH--- 146
P Y + V + S + Q L +R +G +
Sbjct: 32 EPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAE 91
Query: 147 ----KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRS 202
+ + V S + + K L+ L LNG ++ + + + +++
Sbjct: 92 NRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKREC 151
Query: 203 RSKSR 207
R
Sbjct: 152 VRVPR 156
>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 = 59.0 bits (143), Expect = 3e-11
Identities = 24/109 (22%), Positives = 43/109 (39%), Gaps = 8/109 (7%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
+Y+G L + E + + G I+ +I+ GF FVE+ DA++A+
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRD 103
+NG L + + G ++ GR G R+ + R
Sbjct: 99 RYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAGRG 147
Score = 52.1 bits (125), Expect = 1e-08
Identities = 24/126 (19%), Positives = 40/126 (31%), Gaps = 7/126 (5%)
Query: 92 PPPRRGWGHDRDDRYGPPTRSDH--RLIVENLSSRVSWQDLKDFMRQVGEV-----CYAD 144
+ H R D L V NLS + + + + + G++
Sbjct: 16 ELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK 75
Query: 145 AHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRS 204
K VE+ S +D + A+ ++ L+ R IR D GR R S
Sbjct: 76 MKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVR 135
Query: 205 KSRSRS 210
+
Sbjct: 136 DEYRQD 141
>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 = 59.1 bits (144), Expect = 4e-11
Identities = 36/194 (18%), Positives = 72/194 (37%), Gaps = 54/194 (27%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAV-- 54
K++IGGL + E +L ++ YG + D+ + GFGF+ FE D+ V
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 55 -YELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSD 113
+ L+GK ++ + I R ++ T
Sbjct: 65 QHILDGK-------VIDPKRAIPRDEQ---------------------------DKTG-- 88
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYAD-----AHKRHRNEGVVEFESSSDMKKALD 168
++ V + V ++ ++F Q G + A + R G V ++S+ + +
Sbjct: 89 -KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC- 146
Query: 169 KLDNAELNGRRIRL 182
+ + R+I +
Sbjct: 147 QNKFIDFKDRKIEI 160
Score = 51.8 bits (125), Expect = 1e-08
Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 9/76 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K+++GG+ VR ++ E+F +G I D L GFGFV ++ D +
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-Q 147
Query: 57 LNGKSLLGERVTVEIA 72
++ ++ A
Sbjct: 148 NKFIDFKDRKIEIKRA 163
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 99
Score = 57.2 bits (139), Expect = 5e-11
Identities = 25/89 (28%), Positives = 48/89 (53%), Gaps = 9/89 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVYE 56
K+++GG+P+ E +L ++ K +G + +V++ GFGF+ FED + D AV
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-N 70
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRG 85
++ ++G++V V+ A+ D G
Sbjct: 71 MHFHDIMGKKVEVKRAEPRDSKSSGPSSG 99
Score = 36.0 bits (84), Expect = 0.002
Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAH-KRHRNEGVVEFESSSDMKKALDK 169
++ V + +L+++ ++ G V DA +R R G + FE + +A+
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-N 70
Query: 170 LDNAELNGRRIRLIEDKPRGGGRGRSRS 197
+ ++ G+++ + +PR S
Sbjct: 71 MHFHDIMGKKVEVKRAEPRDSKSSGPSS 98
>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 = 56.5 bits (137), Expect = 5e-11
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-GFGFVEFEDYRDADDAVYE-LNGK 60
T +Y+GGL + E DL +G IR + +++ F++F + A+ A + N
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKL 72
Query: 61 SLLGERVTVEIAK 73
+ G R+ V+ +
Sbjct: 73 IVNGRRLNVKWGR 85
Score = 36.9 bits (86), Expect = 7e-04
Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 2/77 (2%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKA 166
++ L V L ++ DL++ Q GE+ + + ++F + + A
Sbjct: 6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTIT-VVQRQQCAFIQFATRQAAEVA 64
Query: 167 LDKLDN-AELNGRRIRL 182
+K N +NGRR+ +
Sbjct: 65 AEKSFNKLIVNGRRLNV 81
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 56.9 bits (138), Expect = 6e-11
Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 10/89 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
Y+G LP+ + D++ K IR V L GF +VEF++ +A+
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-T 74
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRG 85
+G L + V+IA+G + + G
Sbjct: 75 YDGALLGDRSLRVDIAEGRKQDKSGPSSG 103
Score = 41.5 bits (98), Expect = 2e-05
Identities = 20/103 (19%), Positives = 34/103 (33%), Gaps = 5/103 (4%)
Query: 99 GHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVG----EVCYADAHKRHRNEGV 154
G PT + V NL D+ + + + + +
Sbjct: 1 GSSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCY 60
Query: 155 VEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
VEF+ +K+AL D A L R +R+ + R + S
Sbjct: 61 VEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQDKSGPSS 102
>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 = 57.0 bits (138), Expect = 9e-11
Identities = 21/102 (20%), Positives = 44/102 (43%), Gaps = 14/102 (13%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVY 55
V++G L + D++ +GRI D + G+GFV F + DA++A+
Sbjct: 16 FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRG 97
++ G+ L G ++ + + + +Y + + G
Sbjct: 76 QMGGQWLGGRQIRT------NWATRKPPAPKSTYESNTKQSG 111
Score = 47.3 bits (113), Expect = 2e-07
Identities = 21/102 (20%), Positives = 42/102 (41%), Gaps = 5/102 (4%)
Query: 110 TRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMK 164
T + + V +LS ++ +D+K G + A K + + G V F + D +
Sbjct: 12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 71
Query: 165 KALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKS 206
A+ ++ L GR+IR + + S+++ S
Sbjct: 72 NAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPS 113
>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 = 56.7 bits (137), Expect = 9e-11
Identities = 15/72 (20%), Positives = 27/72 (37%), Gaps = 2/72 (2%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--GFGFVEFEDYRDADDAVYELNGKS 61
T + LP G ++++ +G + V+L VEF + +A A L
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSK 70
Query: 62 LLGERVTVEIAK 73
+ +E A
Sbjct: 71 FHHVPLYLEWAP 82
Score = 46.0 bits (109), Expect = 7e-07
Identities = 12/72 (16%), Positives = 29/72 (40%), Gaps = 1/72 (1%)
Query: 111 RSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKL 170
RS ++ +NL + ++++ + G + +VEF + +KA L
Sbjct: 8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHL 66
Query: 171 DNAELNGRRIRL 182
++ + + L
Sbjct: 67 AYSKFHHVPLYL 78
>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 = 56.5 bits (137), Expect = 1e-10
Identities = 25/91 (27%), Positives = 42/91 (46%), Gaps = 10/91 (10%)
Query: 4 TKVYIGGLPYGVRERDL-EKFVKGYGR------IRDVILKNGFGFVEFEDYRDADDAVYE 56
+Y+G L V E + + F + G I + + + FVEF ++RDA A+
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQ-IGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAA 74
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRGYG 87
+NG+ +LG+ V V A S ++ G
Sbjct: 75 MNGRKILGKEVKVNWAT--TPSSQKSGPSSG 103
Score = 43.8 bits (104), Expect = 3e-06
Identities = 16/93 (17%), Positives = 30/93 (32%), Gaps = 5/93 (5%)
Query: 109 PTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMK 164
L V NLS V+ + Q+G + + VEF D
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAA 69
Query: 165 KALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
AL ++ ++ G+ +++ + S
Sbjct: 70 AALAAMNGRKILGKEVKVNWATTPSSQKSGPSS 102
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM
domain, riken structural genomics/proteomics initiative
RSGI, RNA binding protein; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 88
Score = 56.1 bits (136), Expect = 1e-10
Identities = 19/90 (21%), Positives = 32/90 (35%), Gaps = 13/90 (14%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN---GFGFVEFEDYRDADDAV---YEL 57
+ V++G + E +L +F YG + DV + F FV F D + A +
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLII 65
Query: 58 NGKSLLGERVTVEIAKGIDRSQERGRRGYG 87
G +V I+ + G
Sbjct: 66 KGI-------SVHISNAEPKHNSNSGPSSG 88
Score = 36.4 bits (85), Expect = 0.001
Identities = 13/88 (14%), Positives = 30/88 (34%), Gaps = 2/88 (2%)
Query: 110 TRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDK 169
+ + V + ++ +L++F Q G+V K R V F + +
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE 61
Query: 170 LDNAELNGRRIRLIEDKPRGGGRGRSRS 197
+ + G + + +P+ S
Sbjct: 62 --DLIIKGISVHISNAEPKHNSNSGPSS 87
>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 = 57.1 bits (138), Expect = 2e-10
Identities = 19/96 (19%), Positives = 44/96 (45%), Gaps = 10/96 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
G +++ + +E ++++ YG I+++ L G+ VE+E ++ A A
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYR 90
LNG ++G+ + V+ + +R ++ R
Sbjct: 132 EALNGAEIMGQTIQVDWCF--VKGPKRVKKSEKRRR 165
Score = 53.7 bits (129), Expect = 3e-09
Identities = 27/170 (15%), Positives = 60/170 (35%), Gaps = 18/170 (10%)
Query: 43 EFEDYRDADDAVYELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDR 102
+ D +A++ + +G ++ V + + + RG + R +
Sbjct: 3 DVLDIDNAEEFEVDEDG-----DQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNE 57
Query: 103 DDRYGPPTRSD----HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRN 151
DD P L V ++ ++++ GE+ + H +
Sbjct: 58 DDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEI--KNIHLNLDRRTGFSKG 115
Query: 152 EGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSR 201
+VE+E+ A + L+ AE+ G+ I++ +G R + R
Sbjct: 116 YALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKRRR 165
>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 = 55.6 bits (134), Expect = 2e-10
Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--GFGFVEFEDYRDADDAV--YELNGKS 61
V++ GL V E DL + ++ +G I V++ VEFE+ A + V
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVY 77
Query: 62 LLGERVTVEIAK 73
+ G++ +
Sbjct: 78 IAGQQAFFNYST 89
Score = 40.9 bits (96), Expect = 4e-05
Identities = 16/86 (18%), Positives = 30/86 (34%), Gaps = 6/86 (6%)
Query: 99 GHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFE 158
G + H V L V DL + + + G +CY + + +VEFE
Sbjct: 4 GSSGSHHKVSVSPVVH---VRGLCESVVEADLVEALEKFGTICYVMMM-PFKRQALVEFE 59
Query: 159 SSSDMKKALD--KLDNAELNGRRIRL 182
+ K+ + + G++
Sbjct: 60 NIDSAKECVTFAADVPVYIAGQQAFF 85
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 55.5 bits (134), Expect = 2e-10
Identities = 16/89 (17%), Positives = 33/89 (37%), Gaps = 13/89 (14%)
Query: 2 VGTKVYIGGLPYGVRER--DLEKFVKG----YGRIRDVILKN------GFGFVEFEDYRD 49
+ + + + +P +R L+ + +G+I + G+ F+E+
Sbjct: 14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAH 73
Query: 50 ADDAVYELNGKSLLG-ERVTVEIAKGIDR 77
A DAV +G L V + D+
Sbjct: 74 AVDAVKNADGYKLDKQHTFRVNLFTDFDK 102
Score = 33.2 bits (76), Expect = 0.019
Identities = 10/62 (16%), Positives = 25/62 (40%), Gaps = 6/62 (9%)
Query: 130 LKDFMRQVGEVC---YADAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGR---RIRLI 183
+ + G++ Y + + + +E+ S + A+ D +L+ + R+ L
Sbjct: 38 IHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLF 97
Query: 184 ED 185
D
Sbjct: 98 TD 99
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 55.0 bits (133), Expect = 2e-10
Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 14/86 (16%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGR--IRDVIL-KN-------GFGFVEFEDYRDADD 52
+ + + + + Y + ++ L K+ GF FV+ DA
Sbjct: 9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQ 68
Query: 53 AVYELNGK----SLLGERVTVEIAKG 74
+ L + G+ + V+ AK
Sbjct: 69 LLQILQSLHPPLKIDGKTIGVDFAKS 94
Score = 38.5 bits (90), Expect = 2e-04
Identities = 10/78 (12%), Positives = 29/78 (37%), Gaps = 11/78 (14%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEFESSSDMKKALD 168
+I+ N++ + + + + +++R V+ S+ D + L
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
Query: 169 KLDNAE----LNGRRIRL 182
L + ++G+ I +
Sbjct: 72 ILQSLHPPLKIDGKTIGV 89
>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 = 55.4 bits (134), Expect = 2e-10
Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 14/97 (14%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAV 54
G V+I L + E L + ++ +G ++ V + G F +F A +
Sbjct: 15 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
Query: 55 ------YELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
E G L G ++ V++A D + G
Sbjct: 75 AAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSSG 111
Score = 45.0 bits (107), Expect = 1e-06
Identities = 15/94 (15%), Positives = 34/94 (36%), Gaps = 11/94 (11%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYAD-----AHKRHRNEGVVEFESSSDMKKALDK 169
+ + NLS + L + ++Q G++ Y + + +F + +K L
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 170 LDNA------ELNGRRIRLIEDKPRGGGRGRSRS 197
+L+GR++++ R S
Sbjct: 77 ASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSS 110
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43
inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA;
1.65A {Mus musculus}
Length = 89
Score = 54.2 bits (131), Expect = 5e-10
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 6/66 (9%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN---GFGFVEFEDYRDADDAV---YE 56
G+KV++G + +L++F YG + DV + F FV F D + A
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCGEDLI 70
Query: 57 LNGKSL 62
+ G S+
Sbjct: 71 IKGISV 76
Score = 34.5 bits (80), Expect = 0.005
Identities = 13/78 (16%), Positives = 29/78 (37%), Gaps = 2/78 (2%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
++ V + ++ ++L+ F Q GEV K R V F + + +
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCGE--DLI 70
Query: 175 LNGRRIRLIEDKPRGGGR 192
+ G + + +P+
Sbjct: 71 IKGISVHISNAEPKHNKL 88
>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 = 54.6 bits (132), Expect = 5e-10
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 9/77 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYG--RIRDVILKN------GFGFVEFEDYRDADDAVYE 56
++G LPY V E +++F +G +R + GFG+ EFED A+
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 79
Query: 57 LNGKSLLGERVTVEIAK 73
LN +SL R+ V++A
Sbjct: 80 LNEESLGNRRIRVDVAD 96
Score = 45.3 bits (108), Expect = 8e-07
Identities = 24/98 (24%), Positives = 36/98 (36%), Gaps = 6/98 (6%)
Query: 96 RGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGE-----VCYADAHKRHR 150
RG H R P + + NL V+ + +K+F R + +R +
Sbjct: 2 RGSHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLK 61
Query: 151 NEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPR 188
G EFE + AL L+ L RRIR+
Sbjct: 62 GFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQA 98
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 54.4 bits (131), Expect = 6e-10
Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--KNGFGFVEFEDYRDADDAV--YELNGKS 61
V+I GL GV E DL + ++ +G I V++ K VEFED A +AV N
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIY 83
Query: 62 LLGERVTVEIAK 73
+ G V +
Sbjct: 84 IAGHPAFVNYST 95
Score = 42.4 bits (100), Expect = 9e-06
Identities = 14/94 (14%), Positives = 31/94 (32%), Gaps = 6/94 (6%)
Query: 91 APPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHR 150
+ D P + + + L V DL + +++ G + Y +
Sbjct: 2 GHHHHHHMENYDDPHKTPASPV---VHIRGLIDGVVEADLVEALQEFGPISYV-VVMPKK 57
Query: 151 NEGVVEFESSSDMKKALDKL--DNAELNGRRIRL 182
+ +VEFE A++ + + G +
Sbjct: 58 RQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV 91
>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 = 54.7 bits (132), Expect = 6e-10
Identities = 17/98 (17%), Positives = 35/98 (35%), Gaps = 9/98 (9%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
+I +P+ + + D+ +F++G + + G V+F++ DA +
Sbjct: 15 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE 74
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAP 92
L+ K L G V + D + P
Sbjct: 75 -RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGP 111
Score = 48.6 bits (116), Expect = 1e-07
Identities = 19/106 (17%), Positives = 42/106 (39%), Gaps = 10/106 (9%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA-----DAHKRHRNEGVVEFESSS 161
G + + N+ ++ D+ F+ + A D + + + +V+F++
Sbjct: 9 GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNED 68
Query: 162 DMKKALDKLDNAELNGRRIRL----IEDKPRGGGRGRSRSSSSRSR 203
D +K+ +L +LNGR + +ED ++ S S
Sbjct: 69 DARKSE-RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSS 113
>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 = 53.7 bits (130), Expect = 7e-10
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
V++G L + + +GRI D + G+GFV F + DA++A+ +
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 57 LNGKSLLGERVTVEIAK 73
+ G+ L G ++ A
Sbjct: 68 MGGQWLGGRQIRTNWAT 84
Score = 48.3 bits (116), Expect = 6e-08
Identities = 18/85 (21%), Positives = 33/85 (38%), Gaps = 5/85 (5%)
Query: 109 PTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAH-KRHRNEGVVEFESSSDM 163
P S + V +LS ++ + G + A D + + G V F + D
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61
Query: 164 KKALDKLDNAELNGRRIRLIEDKPR 188
+ A+ ++ L GR+IR +
Sbjct: 62 ENAIQQMGGQWLGGRQIRTNWATRK 86
>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 = 54.8 bits (132), Expect = 8e-10
Identities = 25/124 (20%), Positives = 40/124 (32%), Gaps = 7/124 (5%)
Query: 77 RSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQ 136
RG RG D + + + H + + L + + D+ +F
Sbjct: 13 GLVPRGSHMASMTGGQQMGRG---SGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSP 69
Query: 137 VGEVC---YADAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRG 193
+ V R E VEF + + A+ K D A + R I L + G G
Sbjct: 70 LNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSK-DRANMQHRYIELFLNSTTGASNG 128
Query: 194 RSRS 197
S
Sbjct: 129 AYSS 132
Score = 46.8 bits (111), Expect = 5e-07
Identities = 20/95 (21%), Positives = 35/95 (36%), Gaps = 11/95 (11%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN------GFGFVEFEDYRDADDAVYE 56
G V++ GLPY E D+ F +R I G VEF + +A A+
Sbjct: 46 GHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-S 104
Query: 57 LNGKSLLGERVTVEIAKGIDRSQE----RGRRGYG 87
+ ++ + + + S + +G G
Sbjct: 105 KDRANMQHRYIELFLNSTTGASNGAYSSQVMQGMG 139
>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 = 54.3 bits (131), Expect = 8e-10
Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 9/77 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYE 56
VY+G + YG +DLE G I + IL + G+ ++EF + D AV
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-A 96
Query: 57 LNGKSLLGERVTVEIAK 73
++ G + V +
Sbjct: 97 MDETVFRGRTIKVLPKR 113
Score = 40.9 bits (96), Expect = 6e-05
Identities = 18/111 (16%), Positives = 37/111 (33%), Gaps = 9/111 (8%)
Query: 91 APPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAH 146
A +++ RS + V N+ + QDL+ G + D
Sbjct: 17 AYTEGPPQPLSAEEKKEIDKRS---VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKF 73
Query: 147 -KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSR 196
+ +EF + + A+ +D GR I+++ + G +
Sbjct: 74 SGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMPGISSTD 123
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 52.8 bits (127), Expect = 1e-09
Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 12/71 (16%)
Query: 4 TKVYIGGLPYGVRER--DLEKFVKG----YGRIRDVILKN------GFGFVEFEDYRDAD 51
+ + + +P +R L+ + +G+I + G+ F+E+ A
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 61
Query: 52 DAVYELNGKSL 62
DAV +G L
Sbjct: 62 DAVKNADGYKL 72
Score = 30.4 bits (69), Expect = 0.10
Identities = 11/77 (14%), Positives = 30/77 (38%), Gaps = 9/77 (11%)
Query: 113 DHRLIVENL--SSRVSWQDLKDFMRQ-------VGEVCYADAHKRHRNEGVVEFESSSDM 163
D ++V+N+ + LK+ + + + Y + + + +E+ S +
Sbjct: 1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHA 60
Query: 164 KKALDKLDNAELNGRRI 180
A+ D +L+ +
Sbjct: 61 VDAVKNADGYKLDKQHT 77
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 52.5 bits (127), Expect = 1e-09
Identities = 14/76 (18%), Positives = 33/76 (43%), Gaps = 9/76 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVYE 56
K+++GGL E + ++ G+G + + L GF F+ F++ + E
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-E 59
Query: 57 LNGKSLLGERVTVEIA 72
++ + +++A
Sbjct: 60 KKYHNVGLSKCEIKVA 75
Score = 31.7 bits (73), Expect = 0.031
Identities = 12/72 (16%), Positives = 27/72 (37%), Gaps = 6/72 (8%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAH-KRHRNEGVVEFESSSDMKKALDK 169
++ V LS + ++++ GEV D + R + F+ +KK ++K
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 170 LDNAELNGRRIR 181
+ +
Sbjct: 61 -KYHNVGLSKCE 71
>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 = 53.0 bits (128), Expect = 1e-09
Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 15/93 (16%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRD--VILKN-------GFGFVEFEDYRDADDAVY 55
++IG L + E+ L +G I I+++ G+ F+ F + +D A+
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRGYGS 88
+NG+ L +TV + ++ +G G
Sbjct: 67 AMNGQYLCNRPITV------SYAFKKDSKGSGP 93
Score = 40.6 bits (96), Expect = 4e-05
Identities = 14/94 (14%), Positives = 28/94 (29%), Gaps = 6/94 (6%)
Query: 110 TRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGV------VEFESSSDM 163
+ + + NL + + L D G + R + G + F S
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 164 KKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
A++ ++ L R I + + S
Sbjct: 62 DAAIEAMNGQYLCNRPITVSYAFKKDSKGSGPSS 95
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 52.5 bits (127), Expect = 1e-09
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 9/76 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVYE 56
K+++GGL D++ + + +G++ D +L GFGFV FE + E
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59
Query: 57 LNGKSLLGERVTVEIA 72
++ + + V + A
Sbjct: 60 IHFHEINNKMVECKKA 75
Score = 31.7 bits (73), Expect = 0.038
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 6/66 (9%)
Query: 121 LSSRVSWQDLKDFMRQVGEVCYA----DAH-KRHRNEGVVEFESSSDMKKALDKLDNAEL 175
LS + +D+K + Q G+V A D RHR G V FES ++K ++ E+
Sbjct: 7 LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIHFHEI 65
Query: 176 NGRRIR 181
N + +
Sbjct: 66 NNKMVE 71
>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 = 52.5 bits (126), Expect = 2e-09
Identities = 12/72 (16%), Positives = 29/72 (40%), Gaps = 4/72 (5%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--KNGFGFVEFEDYRDADDAV--YELNGKS 61
++I LP V E ++ +G++ ++++ F+E A V Y
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPH 77
Query: 62 LLGERVTVEIAK 73
L + + ++ +
Sbjct: 78 LRNQPIYIQYSN 89
>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 = 51.9 bits (125), Expect = 3e-09
Identities = 18/79 (22%), Positives = 34/79 (43%), Gaps = 9/79 (11%)
Query: 2 VGTKVYIGGLPYGVRERDLEKFVKGYGR-------IRDVI--LKNGFGFVEFEDYRDADD 52
+ +++G L + E + + G IR+ + + G+ FVEF D A+
Sbjct: 8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEK 67
Query: 53 AVYELNGKSLLGERVTVEI 71
++++NGK L G
Sbjct: 68 CLHKINGKPLPGATPAKRF 86
Score = 33.8 bits (78), Expect = 0.009
Identities = 14/77 (18%), Positives = 26/77 (33%), Gaps = 10/77 (12%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGE------VCYADAHKRHRNEGVVEFESSSDMKKALDK 169
L + +L + + +GE + VEF + +K L K
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 170 LDNAELNG----RRIRL 182
++ L G +R +L
Sbjct: 72 INGKPLPGATPAKRFKL 88
>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 = 51.7 bits (124), Expect = 4e-09
Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 14/78 (17%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-------------GFGFVEFEDYRDAD 51
++Y+G +P+G+ E + F R+ + F F+EF +
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 52 DAVYELNGKSLLGERVTV 69
A+ +G G+ + +
Sbjct: 68 QAM-AFDGIIFQGQSLKI 84
Score = 47.4 bits (113), Expect = 1e-07
Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 11/83 (13%)
Query: 109 PTRSDHRLIVENLSSRVSWQDLKDFMRQV----------GEVCYADAHKRHRNEGVVEFE 158
P S RL V N+ ++ + + DF G A + +N +EF
Sbjct: 2 PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR 61
Query: 159 SSSDMKKALDKLDNAELNGRRIR 181
S + +A+ D G+ ++
Sbjct: 62 SVDETTQAM-AFDGIIFQGQSLK 83
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 52.3 bits (126), Expect = 4e-09
Identities = 26/102 (25%), Positives = 46/102 (45%), Gaps = 11/102 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVY 55
TK+++GGLPY + L K+ +G+G I + ++ G+GFV D A+ A
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRG 97
+ N + G + V +A ++ R + + P G
Sbjct: 78 DPNPI-IDGRKANVNLA--YLGAKPRSLQTGFAIGVSGPSSG 116
Score = 33.0 bits (76), Expect = 0.023
Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 10/90 (11%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAH-KRHRNEGVVEFESSSDMKKALDK 169
++ V L + L+ + G++ A D + R G V + ++A K
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC-K 77
Query: 170 LDNAELNGRRIR----LIEDKPRGGGRGRS 195
N ++GR+ + KPR G +
Sbjct: 78 DPNPIIDGRKANVNLAYLGAKPRSLQTGFA 107
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif,
RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 111
Score = 52.2 bits (125), Expect = 4e-09
Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 16/82 (19%)
Query: 6 VYIGGLPYGVRERDL----EKFVKGYGRIRDVILKN-----------GFGFVEFEDYRDA 50
V++ GL + + ++ E F K +G+I V++ N +V + DA
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGK-FGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76
Query: 51 DDAVYELNGKSLLGERVTVEIA 72
A+ +N + G + +
Sbjct: 77 LRAIQCVNNVVVDGRTLKASLG 98
Score = 35.2 bits (81), Expect = 0.004
Identities = 12/75 (16%), Positives = 31/75 (41%), Gaps = 11/75 (14%)
Query: 118 VENLSSRVSWQDL---KDFMRQVGEVC--------YADAHKRHRNEGVVEFESSSDMKKA 166
V LS R++ ++ ++ + G++ + V + S D +A
Sbjct: 20 VVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRA 79
Query: 167 LDKLDNAELNGRRIR 181
+ ++N ++GR ++
Sbjct: 80 IQCVNNVVVDGRTLK 94
>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 = 51.9 bits (124), Expect = 7e-09
Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 5/85 (5%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--GFGFVEFEDYRDADDAVYELNGKSLL 63
V GGL GV L ++ G + +++ + F + ++ A LNGK ++
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVV 89
Query: 64 ---GERVTVEIAKGIDRSQERGRRG 85
G+++T+ + G
Sbjct: 90 DDLGQKITLYLNFVEKVQWSGPSSG 114
Score = 29.1 bits (65), Expect = 0.60
Identities = 21/102 (20%), Positives = 40/102 (39%), Gaps = 13/102 (12%)
Query: 100 HDRDDRYGPPTRSDHRLIVEN--LSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEF 157
H+ + T+S L+V N L + VS L + + G V ++ +
Sbjct: 15 HEGIETVSYATQS---LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARY 70
Query: 158 ESSSDMKKALDKLDNAEL---NGRRIRL----IEDKPRGGGR 192
++ + K+A L+ E+ G++I L +E G
Sbjct: 71 RTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWSGPS 112
>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 = 51.3 bits (123), Expect = 8e-09
Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 9/89 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVYELN 58
V + G+P+ E D+ F G R+ V L NG G V+F +D +A+ + N
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRN 76
Query: 59 GKSLLGERVTVEIAKGIDRSQERGRRGYG 87
++ V V A G G
Sbjct: 77 RMLMIQRYVEVSPATERQWVAAGGHITSG 105
Score = 47.8 bits (114), Expect = 1e-07
Identities = 21/98 (21%), Positives = 36/98 (36%), Gaps = 4/98 (4%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMR--QVGEVCYA-DAHKRHRNEGVVEFESSSDMK 164
P D + V + D++DF +V V D R+ G+V+F S D
Sbjct: 11 PINPDDLYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTF 70
Query: 165 KALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRS 202
+AL + + + R + + R +S S
Sbjct: 71 EALKR-NRMLMIQRYVEVSPATERQWVAAGGHITSGPS 107
>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 = 51.5 bits (123), Expect = 8e-09
Identities = 13/72 (18%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--KNGFGFVEFEDYRDADDAV--YELNGKS 61
++I LP V E ++ +G++ ++++ F+E A+ V Y
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPV 93
Query: 62 LLGERVTVEIAK 73
L G+ + ++ +
Sbjct: 94 LRGQPIYIQFSN 105
Score = 37.2 bits (86), Expect = 0.001
Identities = 16/101 (15%), Positives = 33/101 (32%), Gaps = 8/101 (7%)
Query: 84 RGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA 143
+ S P G R G P+R + + L V+ ++ G+V
Sbjct: 7 HHHHSSGLVPRGSHMGDSRSA--GVPSR---VIHIRKLPIDVTEGEVISLGLPFGKVTNL 61
Query: 144 DAHKRHRNEGVVEFESSSDMKKALD--KLDNAELNGRRIRL 182
+ +N+ +E + ++ L G+ I +
Sbjct: 62 -LMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI 101
>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 = 50.9 bits (122), Expect = 9e-09
Identities = 14/88 (15%), Positives = 34/88 (38%), Gaps = 9/88 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
V + GLP+G + ++ +F G + + + G FV+F A+ A+ +
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KK 76
Query: 58 NGKSLLGERVTVEIAKGIDRSQERGRRG 85
+ + + + + + + G
Sbjct: 77 HKERIGHRYIEIFKSSRAEVRTSGPSSG 104
Score = 46.7 bits (111), Expect = 4e-07
Identities = 20/95 (21%), Positives = 32/95 (33%), Gaps = 6/95 (6%)
Query: 99 GHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA-----DAHKRHRNEG 153
G P T +D + + L S +++ F + V D R E
Sbjct: 1 GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60
Query: 154 VVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPR 188
V+F S +KAL K + R I + +
Sbjct: 61 FVQFASQEIAEKALKK-HKERIGHRYIEIFKSSRA 94
>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 = 51.4 bits (123), Expect = 1e-08
Identities = 20/100 (20%), Positives = 33/100 (33%), Gaps = 9/100 (9%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
G VY+ GLP+ + + F K + D I G GFVEF + D A+
Sbjct: 25 GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL 84
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPP 94
+ + + + V ++ P
Sbjct: 85 -CRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGPSS 123
Score = 47.5 bits (113), Expect = 2e-07
Identities = 23/127 (18%), Positives = 43/127 (33%), Gaps = 14/127 (11%)
Query: 85 GYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA- 143
G P + R P + + ++ L + + DF +++ V +
Sbjct: 1 GSSGSSGKSPSGQ----KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSI 56
Query: 144 ----DAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLI----EDKPRGGGRGRS 195
+ + EG VEF + +D K AL + + R I++ + R
Sbjct: 57 YIAYGPNGKATGEGFVEFRNEADYKAALCR-HKQYMGNRFIQVHPITKKGMLEKIDMIRK 115
Query: 196 RSSSSRS 202
R S S
Sbjct: 116 RLQSGPS 122
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 50.6 bits (121), Expect = 1e-08
Identities = 13/72 (18%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--KNGFGFVEFEDYRDADDAV--YELNGKS 61
++I LP V E ++ +G++ ++++ F+E A+ V Y
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPV 78
Query: 62 LLGERVTVEIAK 73
L G+ + ++ +
Sbjct: 79 LRGQPIYIQFSN 90
Score = 34.1 bits (78), Expect = 0.008
Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 6/77 (7%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKA 166
G P+R H + L V+ ++ G+V + +N+ +E +
Sbjct: 13 GVPSRVIH---IRKLPIDVTEGEVISLGLPFGKVTNL-LMLKGKNQAFIEMNTEEAANTM 68
Query: 167 LDKLDN--AELNGRRIR 181
++ + L G+ I
Sbjct: 69 VNYYTSVTPVLRGQPIY 85
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 50.5 bits (121), Expect = 1e-08
Identities = 18/91 (19%), Positives = 32/91 (35%), Gaps = 15/91 (16%)
Query: 2 VGTKVYIGGLPY------GVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDY 47
+ + G P V ++ L G++ ++ GF FVE
Sbjct: 5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSM 64
Query: 48 RDADDAVYELNGKSLLG-ERVTVEIAKGIDR 77
DA + +GK L R+ + K ++R
Sbjct: 65 NDAKKIIKSFHGKRLDLKHRLFLYTMKDVER 95
Score = 37.8 bits (88), Expect = 4e-04
Identities = 14/84 (16%), Positives = 31/84 (36%), Gaps = 8/84 (9%)
Query: 113 DHRLIVENLSSRVSWQDLKDFMRQVGEVCYA-----DAHKRHRNEGVVEFESSSDMKKAL 167
+ ++ + V + L + G+V +A + + VE S +D KK +
Sbjct: 12 NGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKII 71
Query: 168 DKLDNAELNGR---RIRLIEDKPR 188
L+ + + ++D R
Sbjct: 72 KSFHGKRLDLKHRLFLYTMKDVER 95
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 49.7 bits (119), Expect = 2e-08
Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 8/76 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-------GFGFVEFEDYRDADDAVYEL 57
VYI G P D++++++ G++ ++ ++ G FV F+ A V E
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ET 71
Query: 58 NGKSLLGERVTVEIAK 73
G+ + +
Sbjct: 72 PGQKYKETDLLILFKD 87
Score = 36.3 bits (84), Expect = 0.001
Identities = 11/71 (15%), Positives = 28/71 (39%), Gaps = 5/71 (7%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKLD 171
+ ++ + + D+K+++ G+V HK + V F+S KK + +
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ETP 72
Query: 172 NAELNGRRIRL 182
+ + +
Sbjct: 73 GQKYKETDLLI 83
>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 = 50.6 bits (121), Expect = 2e-08
Identities = 22/97 (22%), Positives = 40/97 (41%), Gaps = 15/97 (15%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKN-----GFGFVEFEDYRD 49
++Y+ L V+E+DL+ Y D+ L G F+ + +
Sbjct: 45 NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104
Query: 50 ADDAVYELNGKSLLGERVTVEIAKGID--RSQERGRR 84
A A+ E NG L G+ + V+ A+ + + G+R
Sbjct: 105 AAKALKEANGYVLFGKPMVVQFARSARPKQDPKEGKR 141
Score = 45.2 bits (107), Expect = 2e-06
Identities = 15/90 (16%), Positives = 32/90 (35%), Gaps = 10/90 (11%)
Query: 109 PTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK----------RHRNEGVVEFE 158
P + R+ V+NL+ V +DLK + + R + + +
Sbjct: 41 PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLP 100
Query: 159 SSSDMKKALDKLDNAELNGRRIRLIEDKPR 188
+ KAL + + L G+ + + +
Sbjct: 101 NEKAAAKALKEANGYVLFGKPMVVQFARSA 130
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 49.5 bits (119), Expect = 3e-08
Identities = 18/90 (20%), Positives = 36/90 (40%), Gaps = 10/90 (11%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVY 55
+ + + GLP+ E+DL+++ +G + V +K GFGFV F +Y +
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
+ + + G ++ G
Sbjct: 76 QRH--MIDGRWCDCKLPNSKQSQDSGPSSG 103
Score = 30.7 bits (70), Expect = 0.15
Identities = 19/87 (21%), Positives = 29/87 (33%), Gaps = 7/87 (8%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAH-KRHRNEGVVEFESSSDMKKALDKL 170
LIV L + + QDLK++ GEV D + G V F K + +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 171 DNAELNGRRIRLIEDKPRGGGRGRSRS 197
++GR + S
Sbjct: 78 H--MIDGRWCDCKLPNSKQSQDSGPSS 102
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 48.6 bits (117), Expect = 4e-08
Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 9/76 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVYE 56
K++IGGL + + L ++ +G +++ ++ GFGFV F D D +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 60
Query: 57 LNGKSLLGERVTVEIA 72
+ L + + ++A
Sbjct: 61 QSRHELDSKTIDPKVA 76
Score = 31.7 bits (73), Expect = 0.038
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 6/72 (8%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAH-KRHRNEGVVEFESSSDMKKALDK 169
++ + LS + + + L+++ Q GEV D KR R G V F + + K L
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 60
Query: 170 LDNAELNGRRIR 181
EL+ + I
Sbjct: 61 QSRHELDSKTID 72
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 49.2 bits (118), Expect = 4e-08
Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 9/89 (10%)
Query: 6 VYIGGLPYGVRERDL-EKFVKGYGRIRDV-ILKN------GFGFVEFEDYRDADDAVYEL 57
+++G L V + L E FVK Y R ++ + G+GFV+F D + A+ E
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 58 NGKSLLGER-VTVEIAKGIDRSQERGRRG 85
G LG + V + +A + G
Sbjct: 72 QGAVGLGSKPVRLSVAIPKASRVKPVESG 100
Score = 31.9 bits (73), Expect = 0.054
Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 6/81 (7%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKD-FMRQVGEVCYA----DAHKRHRNEGVVEFESSSD 162
+ ++ L V +L+ V L + F++ D + G V+F +
Sbjct: 4 GSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELE 63
Query: 163 MKKALDKLDNA-ELNGRRIRL 182
K+AL + A L + +RL
Sbjct: 64 QKRALTECQGAVGLGSKPVRL 84
>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 = 48.5 bits (116), Expect = 7e-08
Identities = 20/102 (19%), Positives = 34/102 (33%), Gaps = 4/102 (3%)
Query: 99 GHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEV---CYADAHKRHRNEGVV 155
G + + H + + L R + D+ +F + + R E V
Sbjct: 1 GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADV 60
Query: 156 EFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
EF + D A+ K D A + R + L + G S
Sbjct: 61 EFATHEDAVAAMAK-DKANMQHRYVELFLNSTAGTSGSGPSS 101
Score = 47.8 bits (114), Expect = 1e-07
Identities = 21/89 (23%), Positives = 32/89 (35%), Gaps = 7/89 (7%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN------GFGFVEFEDYRDADDAVYE 56
G V++ GLPY E D+ F +R I G VEF + DA A+
Sbjct: 15 GHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAM-A 73
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRG 85
+ ++ V + + S G
Sbjct: 74 KDKANMQHRYVELFLNSTAGTSGSGPSSG 102
>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 = 47.7 bits (114), Expect = 1e-07
Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 7/77 (9%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN------GFGFVEFEDYRDADDAVYE 56
V + G P+ V E+++ +F+ + I++N G+ FV+F + + A+ +
Sbjct: 10 CHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQAL-K 68
Query: 57 LNGKSLLGERVTVEIAK 73
N + + G + V K
Sbjct: 69 CNREYMGGRYIEVFREK 85
Score = 45.4 bits (108), Expect = 8e-07
Identities = 16/84 (19%), Positives = 36/84 (42%), Gaps = 4/84 (4%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVC---YADAHKRHRNEGVVEFESSSDM 163
G + H + + V+ +++ +F+ + V +AH V+F + ++
Sbjct: 4 GSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEV 63
Query: 164 KKALDKLDNAELNGRRIRLIEDKP 187
K+AL + + GR I + +K
Sbjct: 64 KQALKC-NREYMGGRYIEVFREKS 86
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif,
systemic lupus erythematosus, phosphoprotein, RNA
maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1
PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Length = 193
Score = 49.8 bits (118), Expect = 1e-07
Identities = 13/116 (11%), Positives = 35/116 (30%), Gaps = 5/116 (4%)
Query: 71 IAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDL 130
I + + +S+ + + ++ + + D+
Sbjct: 67 IVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDI 126
Query: 131 KDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
K+++ G+V HK + V F+S KK ++ + + +
Sbjct: 127 KEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLI 181
Score = 45.6 bits (107), Expect = 3e-06
Identities = 15/80 (18%), Positives = 32/80 (40%), Gaps = 8/80 (10%)
Query: 1 MVGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK-------NGFGFVEFEDYRDADDA 53
+ VYI G P D++++++ G++ ++ ++ G FV F+ A
Sbjct: 107 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF 166
Query: 54 VYELNGKSLLGERVTVEIAK 73
V E G+ + +
Sbjct: 167 V-ETPGQKYKETDLLILFKD 185
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 105
Score = 48.0 bits (115), Expect = 1e-07
Identities = 18/90 (20%), Positives = 33/90 (36%), Gaps = 9/90 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVY 55
K+++GGL + + L + YG + D ++ GFGFV+F+D +
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL- 75
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
+L G + + G
Sbjct: 76 ASRPHTLDGRNIDPKPCTPRGMQPSGPSSG 105
Score = 29.5 bits (67), Expect = 0.32
Identities = 23/105 (21%), Positives = 34/105 (32%), Gaps = 7/105 (6%)
Query: 99 GHDRDDRYGPPTRSDHR-LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAH-KRHRNE 152
G + L V L + + L+ + Q GEV D + R
Sbjct: 1 GSSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGF 60
Query: 153 GVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRS 197
G V+F+ + + L L+GR I PRG S
Sbjct: 61 GFVKFKDPNCVGTVL-ASRPHTLDGRNIDPKPCTPRGMQPSGPSS 104
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics,
RRM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 116
Score = 48.0 bits (115), Expect = 1e-07
Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 9/90 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVY 55
K++IGGL + E L + + +G++ D ++ GFGFV F + D A+
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM- 86
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
S+ G V + A + S G
Sbjct: 87 AARPHSIDGRVVEPKRAVAREESGSGPSSG 116
Score = 28.8 bits (65), Expect = 0.87
Identities = 19/88 (21%), Positives = 35/88 (39%), Gaps = 6/88 (6%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAH-KRHRNEGVVEFESSSDMKKALDK 169
+L + LS + + L+++ Q G++ D KR R G V F S +++ A+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-A 87
Query: 170 LDNAELNGRRIRLIEDKPRGGGRGRSRS 197
++GR + R S
Sbjct: 88 ARPHSIDGRVVEPKRAVAREESGSGPSS 115
>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 = 48.0 bits (114), Expect = 1e-07
Identities = 20/102 (19%), Positives = 35/102 (34%), Gaps = 11/102 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL----------KNGFGFVEFEDYRDADD 52
G V + GLP+ D++ F+ V ++G FVE E D
Sbjct: 17 GYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKL 76
Query: 53 AVYELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPP 94
A+ + + +S+ + V + + G S P
Sbjct: 77 AL-KKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPSS 117
Score = 40.3 bits (94), Expect = 8e-05
Identities = 21/93 (22%), Positives = 32/93 (34%), Gaps = 8/93 (8%)
Query: 97 GWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA-------DAHKRH 149
G GP + + + L S +D+++F+ R
Sbjct: 1 GSSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQ 60
Query: 150 RNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
E VE ES D+K AL K D + R I +
Sbjct: 61 SGEAFVELESEDDVKLALKK-DRESMGHRYIEV 92
>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 = 48.3 bits (115), Expect = 2e-07
Identities = 17/115 (14%), Positives = 32/115 (27%), Gaps = 7/115 (6%)
Query: 74 GIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLI-VENLSSRVSWQDLKD 132
G G + G ++ + + L + +++
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQ 61
Query: 133 FMRQVGEVCYA-----DAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
F + V D + E V+F S +KAL K + R I +
Sbjct: 62 FFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEV 115
Score = 48.3 bits (115), Expect = 2e-07
Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 9/79 (11%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
V + GLP+G + ++ +F G + + I G FV+F A+ A+
Sbjct: 42 DGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL 101
Query: 55 YELNGKSLLGERVTVEIAK 73
+ + + + V +
Sbjct: 102 -GKHKERIGHRYIEVFKSS 119
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 46.4 bits (111), Expect = 3e-07
Identities = 17/69 (24%), Positives = 35/69 (50%), Gaps = 12/69 (17%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAV- 54
K+++GGL + ++DL+ + +G + D +K GFGF+ F+D + +
Sbjct: 12 GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD 71
Query: 55 ---YELNGK 60
+ L+G+
Sbjct: 72 QKEHRLDGR 80
Score = 31.4 bits (72), Expect = 0.052
Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAH-KRHRNEGVVEFESSSDMKKALDK 169
++ V LS S +DLKD+ + GEV D + R R G + F+ ++ ++K LD+
Sbjct: 13 KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 170 LDNAELNGRRIR 181
++ L+GR I
Sbjct: 73 KEH-RLDGRVID 83
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 45.3 bits (108), Expect = 1e-06
Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 9/78 (11%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVY 55
K++IGGL + + L ++ +G +++ ++ GFGFV F D D +
Sbjct: 26 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL- 84
Query: 56 ELNGKSLLGERVTVEIAK 73
+ L + + ++A
Sbjct: 85 AQSRHELDSKTIDPKVAF 102
Score = 30.3 bits (69), Expect = 0.20
Identities = 21/81 (25%), Positives = 33/81 (40%), Gaps = 7/81 (8%)
Query: 107 GPPTRSDHR-LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAH-KRHRNEGVVEFESS 160
G S + + LS + + + L+++ Q GEV D KR R G V F
Sbjct: 18 GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
Query: 161 SDMKKALDKLDNAELNGRRIR 181
+ + K L EL+ + I
Sbjct: 78 AGVDKVL-AQSRHELDSKTID 97
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 45.6 bits (108), Expect = 1e-06
Identities = 16/94 (17%), Positives = 28/94 (29%), Gaps = 12/94 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL-----------KNGFGFVEFEDYRDADDAV 54
V + GLP+ ++ F + I G FV F A +A+
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQERGRRGYGS 88
+ L + + + + Q R S
Sbjct: 86 -RKHKDLLGKRYIELFRSTAAEVQQVLNRFSSAS 118
Score = 41.0 bits (96), Expect = 4e-05
Identities = 19/117 (16%), Positives = 33/117 (28%), Gaps = 9/117 (7%)
Query: 96 RGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA--------DAHK 147
G G + + + + L + +++ F Q +
Sbjct: 6 SGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDG 65
Query: 148 RHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRS 204
R + V F + AL K L R I L + +R SS+ S
Sbjct: 66 RPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFRSTAAEVQQVLNRFSSASGPS 121
>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 = 44.8 bits (106), Expect = 2e-06
Identities = 14/91 (15%), Positives = 23/91 (25%), Gaps = 11/91 (12%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL----------KNGFGFVEFEDYRDADD 52
+ GLP+ D+ F + G +E E +D
Sbjct: 11 VFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQK 70
Query: 53 AVYELNGKSLLGERVTVEIAKGIDRSQERGR 83
A+ E + + V V D
Sbjct: 71 AL-EKHRMYMGQRYVEVYEINNEDVDALMKS 100
Score = 38.3 bits (89), Expect = 3e-04
Identities = 13/82 (15%), Positives = 30/82 (36%), Gaps = 8/82 (9%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA-------DAHKRHRNEGVVEFESS 160
+ + L + +D+ +F + + R + ++E ES
Sbjct: 6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE 65
Query: 161 SDMKKALDKLDNAELNGRRIRL 182
D++KAL+K + R + +
Sbjct: 66 QDVQKALEK-HRMYMGQRYVEV 86
>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 = 42.6 bits (100), Expect = 1e-05
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 6 VYIGGLPY-GVRERDLEKFVKGYGRIRDVIL--KNGFGFVEFEDYRDADDAV--YELNGK 60
+++ LP+ G + + K + YG+I++ IL F+E E DA V
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKAL 87
Query: 61 SLLGERVTVEIAK 73
G V V++++
Sbjct: 88 WFQGRCVKVDLSE 100
>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 = 41.1 bits (96), Expect = 3e-05
Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 9/81 (11%)
Query: 3 GTKVYIGGLPYGVRERDLEKFV----KGYGRIRDVILK-----NGFGFVEFEDYRDADDA 53
G V + + Y + ++L++ + +G+++ V L V+ E+ +DA A
Sbjct: 9 GADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGA 68
Query: 54 VYELNGKSLLGERVTVEIAKG 74
V L+ + +++ V +A G
Sbjct: 69 VNSLHRYKIGSKKILVSLATG 89
>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 = 41.9 bits (98), Expect = 3e-05
Identities = 16/93 (17%), Positives = 31/93 (33%), Gaps = 11/93 (11%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL----------KNGFGFVEFEDYRDADD 52
G V + GLP+ D++ F+ ++G FVE D
Sbjct: 44 GFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKM 103
Query: 53 AVYELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
A+ + + +S+ + V + + G
Sbjct: 104 AL-KKDRESMGHRYIEVFKSHRTEMDWVLKHSG 135
Score = 39.2 bits (91), Expect = 2e-04
Identities = 23/119 (19%), Positives = 34/119 (28%), Gaps = 11/119 (9%)
Query: 74 GIDRSQERGRRGYGSYRAPPPRRGWGHDRD---DRYGPPTRSDHRLIVENLSSRVSWQDL 130
G G + G GP + + L S +D+
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDV 61
Query: 131 KDFMRQVGEVCYA-------DAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
++F+ A R E VE S D+K AL K D + R I +
Sbjct: 62 QNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKK-DRESMGHRYIEV 119
>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 = 40.2 bits (94), Expect = 5e-05
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 5/73 (6%)
Query: 6 VYIGGLPYGV-RERDLEKFVKGYGRIRDVIL--KNGFGFVEFEDYRDADDAV--YELNGK 60
V+I G L + V+ +G I + ++ K F+E DA AV Y
Sbjct: 18 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPA 77
Query: 61 SLLGERVTVEIAK 73
+ G+ V V +++
Sbjct: 78 LVFGKPVRVHLSQ 90
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 41.8 bits (97), Expect = 1e-04
Identities = 47/263 (17%), Positives = 80/263 (30%), Gaps = 8/263 (3%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVYEL 57
+++ + Y E L + + YG I+ + + G+ F+E+E RD A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 58 NGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLI 117
+GK + G RV V++ +G R RR G + R +R D R
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPG 224
Query: 118 VENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAELNG 177
L R +D + R+ + +R S S K+ + +
Sbjct: 225 PSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDK 284
Query: 178 RRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSV 237
R R R R R + S++
Sbjct: 285 DRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPE 344
Query: 238 SRSPSPSKTRKRSRSRSDSRARK 260
+ + R+RS R R
Sbjct: 345 EKGRDRDRERRRSHRSERERRRD 367
>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 = 40.5 bits (94), Expect = 1e-04
Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 4/70 (5%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL---KNGF-GFVEFEDYRDADDAVYELNGKS 61
+ + L Y V L + +G + +I N F +++ D A A L+G++
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 108
Query: 62 LLGERVTVEI 71
+ T+ I
Sbjct: 109 IYNACCTLRI 118
Score = 37.4 bits (86), Expect = 0.001
Identities = 15/69 (21%), Positives = 27/69 (39%), Gaps = 1/69 (1%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVC-YADAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
R+IVENL V+ L + G V K ++ + ++++ + A LD
Sbjct: 48 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 107
Query: 174 ELNGRRIRL 182
+ L
Sbjct: 108 NIYNACCTL 116
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 37.6 bits (87), Expect = 5e-04
Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 9/70 (12%)
Query: 2 VGTKVYIGGLPYGVRERDLEKF-----VKGYGRIRDVILKNGFGFVEFEDYRDADDAV-- 54
G V + GLP V + L + G G + G + F + DA+ +
Sbjct: 7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADAERVLAQ 66
Query: 55 --YELNGKSL 62
+EL+G L
Sbjct: 67 ADHELHGAQL 76
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 38.1 bits (88), Expect = 5e-04
Identities = 13/70 (18%), Positives = 27/70 (38%), Gaps = 4/70 (5%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL----KNGFGFVEFEDYRDADDAVYELNGKS 61
+ + L Y V L + +G + +I +++ D A A L+G++
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 90
Query: 62 LLGERVTVEI 71
+ T+ I
Sbjct: 91 IYNACCTLRI 100
Score = 36.9 bits (85), Expect = 0.001
Identities = 17/98 (17%), Positives = 31/98 (31%), Gaps = 4/98 (4%)
Query: 86 YGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA-D 144
G+ D + R+IVENL V+ L + G V
Sbjct: 4 SGNLALAASAAA--VDAGMAMAGQSPVL-RIIVENLFYPVTLDVLHQIFSKFGTVLKIIT 60
Query: 145 AHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
K ++ + ++++ + A LD + L
Sbjct: 61 FTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL 98
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 37.7 bits (87), Expect = 6e-04
Identities = 18/68 (26%), Positives = 30/68 (44%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
L ++N ++ L VG+V KR+ + +VEFES +KA L+ A+
Sbjct: 27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGAD 86
Query: 175 LNGRRIRL 182
+ L
Sbjct: 87 IYAGCCTL 94
Score = 36.2 bits (83), Expect = 0.002
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 3/69 (4%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--KNGF-GFVEFEDYRDADDAVYELNGKSL 62
+ I Y + L G+++ +++ +NG VEFE A A LNG +
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADI 87
Query: 63 LGERVTVEI 71
T++I
Sbjct: 88 YAGCCTLKI 96
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 37.2 bits (86), Expect = 7e-04
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 17 ERDLEKFVKGYGRIRDV-ILKN------GFGFVEFEDYRDADDAVYELNGKSLLGERVTV 69
E + + YG + ++ + N G +V+F DA+ AV +LN + G+ +
Sbjct: 41 EEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100
Query: 70 E 70
E
Sbjct: 101 E 101
Score = 26.4 bits (58), Expect = 4.4
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 155 VEFESSSDMKKALDKLDNAELNGRRIR 181
V+F D +KA+ L+N NG+ I
Sbjct: 73 VKFRREEDAEKAVIDLNNRWFNGQPIH 99
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 36.7 bits (84), Expect = 0.004
Identities = 14/85 (16%), Positives = 30/85 (35%), Gaps = 11/85 (12%)
Query: 1 MVGTKVYIGGLPYGV---------RERDLEKFVKGYGRIRDV--ILKNGFGFVEFEDYRD 49
+Y+GG+ + E + G I + + GFV+F+ +
Sbjct: 132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQAN 191
Query: 50 ADDAVYELNGKSLLGERVTVEIAKG 74
A+ A ++ ++LL +
Sbjct: 192 AEFAKEAMSNQTLLLPSDKEWDDRR 216
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 35.0 bits (80), Expect = 0.005
Identities = 11/62 (17%), Positives = 24/62 (38%), Gaps = 10/62 (16%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN----------GFGFVEFEDYRDADDAV 54
KV++GGLP + E ++ + +G + G+ F+ F++ +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69
Query: 55 YE 56
Sbjct: 70 DA 71
>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 = 37.0 bits (85), Expect = 0.006
Identities = 39/218 (17%), Positives = 67/218 (30%), Gaps = 80/218 (36%)
Query: 14 GVRERDLEKFVK-------GYGRIRDVILKNGFGFVEFEDYRDADDAVYELNG--KSLLG 64
+ + ++ +V ++ + L NG A + V ++G +SL G
Sbjct: 343 NLTQEQVQDYVNKTNSHLPAGKQVE-ISLVNG-----------AKNLV--VSGPPQSLYG 388
Query: 65 ERVTVEIAK---GIDRSQE--RGRRGYGSYR-----AP-------PPRRGWGHDRDDR-- 105
+T+ AK G+D+S+ R+ S R +P P D
Sbjct: 389 LNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNV 448
Query: 106 -----------YGPPTRSDHR----LIVENL-----SSRVSWQDLKDFMRQVGEVCYADA 145
Y SD R I E + V W+ F A
Sbjct: 449 SFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQF----------KA 498
Query: 146 HKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLI 183
H +++F L L + +G +R+I
Sbjct: 499 T--H----ILDFGPGGA--SGLGVLTHRNKDGTGVRVI 528
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 34.4 bits (78), Expect = 0.008
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 14 GVRERDLEKFVKGYGRIRDVIL---KNGFGFVEFEDYRDADDAVYELNGKS 61
G + L + ++ YG + +++L K G VEF + A+ AV G
Sbjct: 28 GYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVGLV 78
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 36.4 bits (83), Expect = 0.008
Identities = 30/184 (16%), Positives = 54/184 (29%), Gaps = 50/184 (27%)
Query: 26 GYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAKGIDRSQERGRRG 85
Y I V FV+ D +D D KS+L + I D R
Sbjct: 17 QYKDILSVFEDA---FVDNFDCKDVQDMP-----KSILSKEEIDHIIMSKDA-VSGTLRL 67
Query: 86 YGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSW--QDLKDFMRQ--VGEVC 141
+ + + + + E L + +K RQ +
Sbjct: 68 FWTLLS----------------KQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRM 111
Query: 142 YADAHKRHRNEG-------VVEFESSSDMKKALDKLDNAE---LNGRRIRLIEDKPRGGG 191
Y + R N+ V + +++AL +L A+ ++G G
Sbjct: 112 YIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDG-----------VLG 160
Query: 192 RGRS 195
G++
Sbjct: 161 SGKT 164
Score = 35.6 bits (81), Expect = 0.018
Identities = 23/193 (11%), Positives = 50/193 (25%), Gaps = 76/193 (39%)
Query: 46 DYRDADDAVYELNGKSLLGER----------VTVEIAKGIDRSQERGRRGYGSYR----- 90
D V +L+ SL+ ++ + +E+ ++ R Y
Sbjct: 400 IKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTF 459
Query: 91 -----APPPRRGW-----GH-----DRDDRY--------------------GPP------ 109
PP + GH + +R
Sbjct: 460 DSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGS 519
Query: 110 ---TRSDHRL----IVEN---LSSRVSWQDLKDFMRQVGEVCYADAHKR-------HRNE 152
T + I +N V+ + DF+ ++ E + +E
Sbjct: 520 ILNTLQQLKFYKPYICDNDPKYERLVN--AILDFLPKIEENLICSKYTDLLRIALMAEDE 577
Query: 153 GVVEFESSSDMKK 165
+ E E+ +++
Sbjct: 578 AIFE-EAHKQVQR 589
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 33.1 bits (75), Expect = 0.015
Identities = 12/65 (18%), Positives = 30/65 (46%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
L V NL + + + + +R++ + C ++ F + ++A +++N ++
Sbjct: 12 LYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSITGCSAILRFINQDSAERAQKRMENEDV 71
Query: 176 NGRRI 180
G RI
Sbjct: 72 FGNRI 76
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 32.7 bits (74), Expect = 0.024
Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 1/74 (1%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKA 166
G L+++NL++++ L+ Q G + + + ++ + + KA
Sbjct: 1 GAMAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGI-ALCKYTTREEANKA 59
Query: 167 LDKLDNAELNGRRI 180
L+N L I
Sbjct: 60 QMALNNCVLANTTI 73
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics,
joint center for struc genomics, JCSG, protein
structure initiative, PSI-biology; HET: MSE CIT; 0.95A
{Mus musculus} PDB: 2lq5_A
Length = 114
Score = 32.7 bits (75), Expect = 0.033
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 20 LEKFVKGYGRIRDVIL----KNGFGFVEFEDYRDADDAVYELNG 59
+E+ K +G + + + G +V+ A AV L+G
Sbjct: 35 IEECNK-HGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHG 77
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding
protein, RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 32.5 bits (74), Expect = 0.040
Identities = 13/64 (20%), Positives = 21/64 (32%), Gaps = 10/64 (15%)
Query: 17 ERDLEKFVKGYGRIRDVIL----------KNGFGFVEFEDYRDADDAVYELNGKSLLGER 66
D+ YG ++ + + G FVEF D A+ L G+
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRV 88
Query: 67 VTVE 70
V +
Sbjct: 89 VVTK 92
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 32.0 bits (73), Expect = 0.052
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 27 YGRIRDVIL----KNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAKGIDR 77
+G+IR ++L +G V F D +AD + L+G+ G ++T + G
Sbjct: 50 FGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTD 104
Score = 26.2 bits (58), Expect = 4.9
Identities = 12/55 (21%), Positives = 21/55 (38%), Gaps = 1/55 (1%)
Query: 128 QDLKDFMRQVGEVCYADAHKRHRNEGV-VEFESSSDMKKALDKLDNAELNGRRIR 181
+DL+ + G++ RH + V F + + LD GR+I
Sbjct: 41 EDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 95
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 30.7 bits (69), Expect = 0.15
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 3/65 (4%)
Query: 117 IVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAELN 176
+L + +DL GE+ + D R EG++ F+ + K+AL K +A
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWID-FVRGAKEGIILFKEKA--KEALGKAKDANNG 79
Query: 177 GRRIR 181
++R
Sbjct: 80 NLQLR 84
>3r45_A Histone H3-like centromeric protein A; histone fold, centromere,
CENP-A, histone chaperone, hjurp; 2.60A {Homo sapiens}
Length = 156
Score = 31.1 bits (69), Expect = 0.17
Identities = 17/68 (25%), Positives = 26/68 (38%)
Query: 191 GRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRS 250
G S+ + R RS K +PR RS S +P S+ + S +R+R
Sbjct: 2 GSSHHHHHHSQDPNSMGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSRRRQ 61
Query: 251 RSRSDSRA 258
+ R
Sbjct: 62 GWLKEIRK 69
>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA
dependent ATPase, RNA helicase; HET: ANP; 1.91A
{Saccharomyces cerevisiae S288C}
Length = 579
Score = 31.7 bits (72), Expect = 0.22
Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 2/78 (2%)
Query: 147 KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKS 206
+ ++ S K+ D D++E++ R + R R RS +
Sbjct: 502 IGKAMFEIRDYSSRDGNNKSYDYDDDSEISFRGNK--NYNNRSQNRDYDDEPFRRSNNNR 559
Query: 207 RSRSRSSKSRSPRSRSKS 224
RS SRS+ + SR+ +
Sbjct: 560 RSFSRSNDKNNYSSRNSN 577
>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 = 29.6 bits (66), Expect = 0.33
Identities = 11/72 (15%), Positives = 22/72 (30%), Gaps = 6/72 (8%)
Query: 116 LIVENLSSRVSWQD-----LKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKL 170
LI + V + + R + K + + F + A +L
Sbjct: 8 LIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKR-VRINFSNPLSAADARLRL 66
Query: 171 DNAELNGRRIRL 182
E G+ ++L
Sbjct: 67 HKTEFLGKEMKL 78
>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 = 30.9 bits (69), Expect = 0.38
Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 2/59 (3%)
Query: 9 GGLPYGVRERDLEKFVKGYGRIRDVILKNG--FGFVEFEDYRDADDAVYELNGKSLLGE 65
GGL GV L ++ G + +++ + F + ++ A LNGK ++ +
Sbjct: 26 GGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDD 84
>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P-
TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1
a.74.1.1 PDB: 2w2h_C
Length = 358
Score = 31.0 bits (69), Expect = 0.41
Identities = 10/73 (13%), Positives = 22/73 (30%), Gaps = 1/73 (1%)
Query: 184 EDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSP 243
E GG G S S + + ++ + +S+
Sbjct: 276 EKTSEQGGTGGGSGGGSGGGSGGGTSGGVPGQNTGGQEARP-NYHCQLCFLRSLGIDYLD 334
Query: 244 SKTRKRSRSRSDS 256
+ RK+++ R +
Sbjct: 335 ASLRKKNKQRLKA 347
>2nsz_A Programmed cell death protein 4; PDCD4, tumor suppressor,
translation, antitumor protein; 1.15A {Mus musculus}
SCOP: a.118.1.14 PDB: 2kzt_B 2hm8_A 2ggf_A
Length = 129
Score = 29.4 bits (66), Expect = 0.50
Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 7/64 (10%)
Query: 18 RDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAKGIDR 77
+ + VK I +LK ++ D +A+ + EL E V I ++
Sbjct: 1 QPVNHLVK---EIDM-LLKE---YLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLES 53
Query: 78 SQER 81
+ E
Sbjct: 54 TGES 57
>1xio_A Anabaena sensory rhodopsin; signaling protein, photoreceptor; HET:
RET PEE; 2.00A {Nostoc SP} SCOP: f.13.1.1
Length = 261
Score = 30.4 bits (68), Expect = 0.57
Identities = 10/62 (16%), Positives = 19/62 (30%), Gaps = 5/62 (8%)
Query: 26 GYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVE---IAKGIDRSQERG 82
+ + K GF F++ R+ +D+ + R Q+
Sbjct: 201 LFC-LLPFFSKVGFSFLDLHGLRNLNDSRQTTGD-RFAENTLQFVENITLFANSRRQQSR 258
Query: 83 RR 84
RR
Sbjct: 259 RR 260
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 29.8 bits (67), Expect = 0.77
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 32 DVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEI 71
++I+K FVEF + A+ LNG+ G +V E+
Sbjct: 173 EIIVKI---FVEFSIASETHKAIQALNGRWFAGRKVVAEV 209
Score = 27.1 bits (60), Expect = 5.7
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 155 VEFESSSDMKKALDKLDNAELNGRRIR 181
VEF +S+ KA+ L+ GR++
Sbjct: 180 VEFSIASETHKAIQALNGRWFAGRKVV 206
>3bzh_A Ubiquitin-conjugating enzyme E2 E1; structural genomics consortium,
ubiquitin-conjuga enzyme, ligase, SGC, UBL conjugation
pathway; 1.60A {Homo sapiens} PDB: 1y6l_A
Length = 194
Score = 29.0 bits (65), Expect = 1.2
Identities = 14/50 (28%), Positives = 26/50 (52%)
Query: 200 SRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKR 249
S S++ + S SS S + ++ ++ +P+K +SK S S + KR
Sbjct: 3 SDDDSRASTSSSSSSSSNQQTEKETNTPKKKESKVSMSKNSKLLSTSAKR 52
>2cp6_A Restin; microtubule binding, cytoskeleton associated protein,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
b.34.10.1
Length = 172
Score = 28.5 bits (63), Expect = 1.4
Identities = 10/53 (18%), Positives = 23/53 (43%)
Query: 195 SRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTR 247
+ + + + + + +S RSP + S S + S + SR+ ++T
Sbjct: 115 PAKAKANAVRRVMATTSASLKRSPSASSLSSMSSVASSVSSRPSRTGLLTETS 167
>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA
binding domain, poly(A polymerase, mitochondria,
transferase; 3.10A {Homo sapiens}
Length = 464
Score = 29.0 bits (64), Expect = 1.7
Identities = 8/56 (14%), Positives = 20/56 (35%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDK 169
R ++ + ++S ++ Q G + ++ VVEF + +
Sbjct: 53 QRTVLIHCPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNG 108
>2ion_A PDCD4, programmed cell death 4, PDCD4; alpha-helical, antitumor
protein; 1.57A {Mus musculus} SCOP: a.118.1.14 PDB:
2ios_A 2iol_A
Length = 152
Score = 28.3 bits (63), Expect = 1.8
Identities = 8/41 (19%), Positives = 16/41 (39%)
Query: 41 FVEFEDYRDADDAVYELNGKSLLGERVTVEIAKGIDRSQER 81
++ D +A+ + EL E V I ++ + E
Sbjct: 19 YLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGES 59
>1lxi_A Bone morphogenetic protein 7; cystine-knot growth factor,
hormone-growth factor complex; HET: NAG; 2.00A {Homo
sapiens} SCOP: g.17.1.2 PDB: 1lx5_A* 1bmp_A* 1m4u_L*
2qcw_A 2r53_A
Length = 139
Score = 28.1 bits (62), Expect = 2.0
Identities = 7/37 (18%), Positives = 17/37 (45%)
Query: 197 SSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSK 233
S+ S+ RS++RS++ ++ + S +
Sbjct: 1 STGSKQRSQNRSKTPKNQEALRMANVAENSSSDQRQA 37
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_C*
Length = 1342
Score = 28.9 bits (65), Expect = 2.3
Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 2/62 (3%)
Query: 23 FVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAKGIDRSQERG 82
++ + IL F V FE + EL + L GE + +I E+G
Sbjct: 209 ILRALNYTTEQILDLFFEKVIFE--IRDNKLQMELVPERLRGETASFDIEANGKVYVEKG 266
Query: 83 RR 84
RR
Sbjct: 267 RR 268
>2xag_B REST corepressor 1; amine oxidase, chromatin regulator, histone
inhibitor binding, methylation, nucleosome core,
oxidoreductase; HET: FAD TCF; 3.10A {Homo sapiens} PDB:
2xaf_B* 2xah_B* 2xaj_B* 2xaq_B* 2xas_B*
Length = 482
Score = 28.7 bits (62), Expect = 2.4
Identities = 14/81 (17%), Positives = 39/81 (48%)
Query: 182 LIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSP 241
++E P G+ R R++++ S S + + + +S + + + + + S + A + S +
Sbjct: 1 MVEKGPEVSGKRRGRNNAAASASAAAASAAASAACASPAATAASGAAASSASAAAASAAA 60
Query: 242 SPSKTRKRSRSRSDSRARKVS 262
+P+ + +S + + S
Sbjct: 61 APNNGQNKSLAAAAPNGNSSS 81
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 27.0 bits (60), Expect = 3.2
Identities = 11/34 (32%), Positives = 16/34 (47%)
Query: 38 GFGFVEFEDYRDADDAVYELNGKSLLGERVTVEI 71
FVEF + A+ LNG+ G +V E+
Sbjct: 72 VKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 105
>2r52_A BMP-6, bone morphogenetic protein 6; TGF-beta ligand,
chondrogenesis, cleavage on PAIR of basic residues,
cytokine, developmental protein; 2.50A {Homo sapiens}
Length = 143
Score = 26.9 bits (59), Expect = 4.6
Identities = 11/36 (30%), Positives = 21/36 (58%)
Query: 198 SSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSK 233
+S+ SR + +SR+RS++S+ S + S+ K
Sbjct: 4 TSASSRRRQQSRNRSTQSQDVARVSSASDYNSSELK 39
>2kcm_A Cold shock domain family protein; nucleic acid binding protein,
beta barrel, structural genomi 2, protein structure
initiative; NMR {Shewanella oneidensis}
Length = 74
Score = 25.7 bits (57), Expect = 5.1
Identities = 6/45 (13%), Positives = 15/45 (33%), Gaps = 11/45 (24%)
Query: 38 GFGFVEFEDYRDADD------AVYELNG-KSLL-GERVTVEIAKG 74
+GF++ + D + + + L+ G V +
Sbjct: 13 KYGFIQGD---DGESYFLHFSELLDKKDEGKLVKGSMVHFDPTPT 54
>3sbt_B A1 cistron-splicing factor AAR2; rnaseh like domain, VHS like
domain, U5 snRNP assembly; 1.80A {Saccharomyces
cerevisiae} PDB: 3sbs_A
Length = 363
Score = 27.0 bits (59), Expect = 6.5
Identities = 15/107 (14%), Positives = 27/107 (25%), Gaps = 4/107 (3%)
Query: 101 DRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFM-RQVGEVCYAD--AHKRHRNEGVVEF 157
+ D NL+ V ++ + + + Y D NE +
Sbjct: 97 KERQMMVSYPKIDEDDTWYNLTEFVQMDKIRKIVRKDENQFSYVDSSMTTVQENELLKSS 156
Query: 158 ESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRS 204
+ K D+ + I K R R +S
Sbjct: 157 LQKAGSKMEAKNEDDPAHSLNYTV-INFKSREAIRPGHEMEDFLDKS 202
>1dzl_A Late major capsid protein L1; icosahedral; 3.50A {Human
papillomavirus type 16} SCOP: b.121.6.1
Length = 505
Score = 27.1 bits (60), Expect = 6.7
Identities = 8/30 (26%), Positives = 14/30 (46%)
Query: 224 SGSPRKSKSKAKSVSRSPSPSKTRKRSRSR 253
P+ + K K+ + S S T KR + +
Sbjct: 475 KAKPKFTLGKRKATPTTSSTSTTAKRKKRK 504
>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and
PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A
{Schizosaccharomyces pombe} PDB: 3swn_A
Length = 94
Score = 25.6 bits (56), Expect = 6.7
Identities = 13/68 (19%), Positives = 29/68 (42%), Gaps = 4/68 (5%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
LI + + S + W +K G + D + + V E+++ + + + K L
Sbjct: 24 LIDKCIGSNL-WVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTE---KHSEMLL 79
Query: 176 NGRRIRLI 183
NG + ++
Sbjct: 80 NGNGMCML 87
>1jr3_D DNA polymerase III, delta subunit; processivity, processivity
clamp, clamp loader, AAA+ ATPase, transferase; HET:
DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20
PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A*
3gli_A*
Length = 343
Score = 26.7 bits (59), Expect = 7.3
Identities = 9/46 (19%), Positives = 14/46 (30%), Gaps = 3/46 (6%)
Query: 29 RIRDVILKNGFG---FVEFEDYRDADDAVYELNGKSLLGERVTVEI 71
+R V GF + D + SL R T+ +
Sbjct: 37 AVRQVAAAQGFEEHHTFSIDPNTDWNAIFSLCQAMSLFASRQTLLL 82
>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex,
PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM
site, SM fold, heteromeric heptameric ring; 3.60A {Homo
sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D
Length = 126
Score = 26.2 bits (57), Expect = 7.7
Identities = 10/54 (18%), Positives = 27/54 (50%)
Query: 170 LDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSK 223
L + N ++ +++K +G G GR +++ +++ +R R R + + +
Sbjct: 73 LPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGNIFQKRR 126
>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA
binding protein; NMR {Saccharomyces cerevisiae}
Length = 117
Score = 25.8 bits (56), Expect = 8.2
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 4/66 (6%)
Query: 120 NLSSRVSWQDLKDFMRQVGEVCYADAHKRH----RNEGVVEFESSSDMKKALDKLDNAEL 175
LS +VS + F+++ + D K N ++ F S K L L+ ++
Sbjct: 28 PLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQF 87
Query: 176 NGRRIR 181
G+ IR
Sbjct: 88 QGKVIR 93
>2ism_A Putative oxidoreductase; BL41XU spring-8, bladed beta-propellor,
glucose dehydrogenas structural genomics, NPPSFA; 1.90A
{Thermus thermophilus}
Length = 352
Score = 26.6 bits (59), Expect = 8.6
Identities = 8/29 (27%), Positives = 16/29 (55%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV 33
++ + G R +E + G+GR+R+V
Sbjct: 292 RLVLEGERGRWRVLRVETALSGFGRLREV 320
>1dyk_A Laminin alpha 2 chain; metal binding protein; 2.0A {Mus musculus}
SCOP: b.29.1.4 b.29.1.4 PDB: 1okq_A 1qu0_A
Length = 394
Score = 26.9 bits (59), Expect = 8.7
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 2 VGTKVYIGGLPYGVRERDLEKFVKGY-GRIRDVILKNGFGFVEFEDYRDADDAV 54
V++GG P G+ + L + G IR + L G G ++ A +
Sbjct: 332 TNDPVFVGGFPGGLNQFGL-TTNIRFRGCIRSLKLTKGTGKPLEVNFAKALELR 384
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
0.314 0.132 0.374
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: 3,964,785
Number of extensions: 245542
Number of successful extensions: 1379
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1004
Number of HSP's successfully gapped: 441
Length of query: 262
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 170
Effective length of database: 4,133,061
Effective search space: 702620370
Effective search space used: 702620370
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (25.3 bits)