RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2160
(773 letters)
>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 = 123 bits (311), Expect = 2e-33
Identities = 49/102 (48%), Positives = 74/102 (72%)
Query: 344 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQI 403
R ++E V+I+KN+F P F+ D ++ E ++DLR ECSK G ++K++L D+HP+GVA +
Sbjct: 10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASV 69
Query: 404 FFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETA 445
F++PE AD C + L+GRWFG RQITA+ WDG T Y+ ++
Sbjct: 70 SFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQSGPSS 111
Score = 123 bits (311), Expect = 2e-33
Identities = 49/102 (48%), Positives = 74/102 (72%)
Query: 629 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQI 688
R ++E V+I+KN+F P F+ D ++ E ++DLR ECSK G ++K++L D+HP+GVA +
Sbjct: 10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASV 69
Query: 689 FFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETA 730
F++PE AD C + L+GRWFG RQITA+ WDG T Y+ ++
Sbjct: 70 SFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQSGPSS 111
>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 = 119 bits (301), Expect = 3e-32
Identities = 27/91 (29%), Positives = 42/91 (46%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+N ++V L ++T E + ++ G++ + T Q I LYTD T KG+A
Sbjct: 8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 67
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERA 585
++ S A+ DG E G IKV A
Sbjct: 68 VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
Score = 117 bits (295), Expect = 1e-31
Identities = 26/88 (29%), Positives = 42/88 (47%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
++ ++V L ++T E + ++ G++ + T Q I LYTD T KG+A ++
Sbjct: 11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 70
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERA 300
S A+ DG E G IKV A
Sbjct: 71 DDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
Score = 31.1 bits (71), Expect = 0.30
Identities = 16/103 (15%), Positives = 34/103 (33%), Gaps = 23/103 (22%)
Query: 339 DKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKH-- 396
+ + I V+ L ++VT + + + + G +K +
Sbjct: 3 HHHHHHSHSDNNTIFVQGL------GENVT-----IESVADYFKQIGIIKTNKKTGQPMI 51
Query: 397 ----------PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+G A + F +P +A A + +G+ F I
Sbjct: 52 NLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIK 94
Score = 31.1 bits (71), Expect = 0.30
Identities = 16/103 (15%), Positives = 34/103 (33%), Gaps = 23/103 (22%)
Query: 624 DKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKH-- 681
+ + I V+ L ++VT + + + + G +K +
Sbjct: 3 HHHHHHSHSDNNTIFVQGL------GENVT-----IESVADYFKQIGIIKTNKKTGQPMI 51
Query: 682 ----------PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+G A + F +P +A A + +G+ F I
Sbjct: 52 NLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIK 94
>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 = 119 bits (301), Expect = 4e-32
Identities = 27/98 (27%), Positives = 47/98 (47%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+ +N+ +YV L +T ++ + ++CG+V + T Q I +Y D T KGDA
Sbjct: 10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 69
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGE 592
+Y + A+ DG + +G K+KV A+
Sbjct: 70 VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 107
Score = 116 bits (293), Expect = 4e-31
Identities = 29/110 (26%), Positives = 49/110 (44%), Gaps = 3/110 (2%)
Query: 198 GQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYT 257
G P D +++ +YV L +T ++ + ++CG+V + T Q I +Y
Sbjct: 1 GSSGSSGDP---DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYL 57
Query: 258 DPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGE 307
D T KGDA +Y + A+ DG + +G K+KV A+
Sbjct: 58 DKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 107
Score = 35.1 bits (81), Expect = 0.014
Identities = 23/105 (21%), Positives = 39/105 (37%), Gaps = 23/105 (21%)
Query: 337 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV------ 390
+ + S I V+ L + VT DL + +CG VK
Sbjct: 3 SGSSGDPDEDSDNSAIYVQGL------NDSVT-----LDDLADFFKQCGVVKMNKRTGQP 51
Query: 391 ---VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+ DK P+G A + +++P A A E +G+ F ++
Sbjct: 52 MIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLK 96
Score = 35.1 bits (81), Expect = 0.014
Identities = 23/105 (21%), Positives = 39/105 (37%), Gaps = 23/105 (21%)
Query: 622 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV------ 675
+ + S I V+ L + VT DL + +CG VK
Sbjct: 3 SGSSGDPDEDSDNSAIYVQGL------NDSVT-----LDDLADFFKQCGVVKMNKRTGQP 51
Query: 676 ---VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ DK P+G A + +++P A A E +G+ F ++
Sbjct: 52 MIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLK 96
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 115 bits (289), Expect = 1e-30
Identities = 27/93 (29%), Positives = 43/93 (46%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+ +N ++V L ++T E + ++ G++ + T Q I LYTD T KG+A
Sbjct: 2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAKF 587
++ S A+ DG E G IKV A
Sbjct: 62 VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATR 94
Score = 112 bits (282), Expect = 1e-29
Identities = 26/89 (29%), Positives = 42/89 (47%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
++ ++V L ++T E + ++ G++ + T Q I LYTD T KG+A ++
Sbjct: 6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65
Query: 274 KKESVDLALSILDGYEIRGKKIKVERAKF 302
S A+ DG E G IKV A
Sbjct: 66 DPPSAKAAIDWFDGKEFSGNPIKVSFATR 94
Score = 32.4 bits (74), Expect = 0.13
Identities = 17/98 (17%), Positives = 38/98 (38%), Gaps = 23/98 (23%)
Query: 344 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV---------VLHD 394
+ + + + I V+ L ++VT + + + + G +K + D
Sbjct: 2 QDNSDNNTIFVQGL------GENVT-----IESVADYFKQIGIIKTNKKTGQPMINLYTD 50
Query: 395 KH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+ +G A + F +P +A A + +G+ F I
Sbjct: 51 RETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIK 88
Score = 32.4 bits (74), Expect = 0.13
Identities = 17/98 (17%), Positives = 38/98 (38%), Gaps = 23/98 (23%)
Query: 629 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV---------VLHD 679
+ + + + I V+ L ++VT + + + + G +K + D
Sbjct: 2 QDNSDNNTIFVQGL------GENVT-----IESVADYFKQIGIIKTNKKTGQPMINLYTD 50
Query: 680 KH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ +G A + F +P +A A + +G+ F I
Sbjct: 51 RETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIK 88
>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 = 99.7 bits (249), Expect = 4e-25
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 1/84 (1%)
Query: 351 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEA 410
+ N+F+P +++V E + D+ EEC+K G V + + +G + A
Sbjct: 9 CFQLSNMFNPQT-EEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAA 67
Query: 411 ADACRELLNGRWFGQRQITAETWD 434
A A L+GRWF + ITA
Sbjct: 68 AIAAVNALHGRWFAGKMITAAYVP 91
Score = 99.7 bits (249), Expect = 4e-25
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 1/84 (1%)
Query: 636 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEA 695
+ N+F+P +++V E + D+ EEC+K G V + + +G + A
Sbjct: 9 CFQLSNMFNPQT-EEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAA 67
Query: 696 ADACRELLNGRWFGQRQITAETWD 719
A A L+GRWF + ITA
Sbjct: 68 AIAAVNALHGRWFAGKMITAAYVP 91
>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 = 96.6 bits (241), Expect = 3e-22
Identities = 54/429 (12%), Positives = 104/429 (24%), Gaps = 161/429 (37%)
Query: 192 EEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQM 251
EE + + + K+ + LP D+T +E +++ L VD
Sbjct: 6 EEIRKRLEHTERQFRN-------RRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKY-- 56
Query: 252 KIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDP 311
KG A T + E + A++ +R +++ V+
Sbjct: 57 -------------KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ----------- 92
Query: 312 KLKPKKKRKKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLIL 371
++++ V NL +T
Sbjct: 93 -----------------------------------PTDALLCVANL------PPSLT--- 108
Query: 372 EYQQDLREECSKCGHVKKVVL----HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQ 427
QQ E G +++ L +G + + ++A + L G+ G
Sbjct: 109 --QQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLG--- 163
Query: 428 ITAETWDGKTRYKIQETAEEREARLKKWETFLGKKIKVERAKFTMKGEAYDPKLKPKKKR 487
+ + V +
Sbjct: 164 --------------------------------PRTLYVHWT-------------DAGQLT 178
Query: 488 KKDLEKLKKAQENTKVYVSNLPLDLTQEEFV-EVMQKCGLVMKDVDTNQMKIKLYTDPYT 546
L + + V LP + + + +L
Sbjct: 179 PALL-------HSRCLCVDRLPPGFNDVDALCRALSAVHSP--------TFCQLACGQDG 223
Query: 547 KDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKK 606
+ KG A+ Y E + A DG + G ++V P +
Sbjct: 224 QL-KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC-------------APGPPGRS 269
Query: 607 DLEKLKKAQ 615
L L AQ
Sbjct: 270 MLAALIAAQ 278
Score = 84.6 bits (210), Expect = 3e-18
Identities = 58/390 (14%), Positives = 101/390 (25%), Gaps = 141/390 (36%)
Query: 327 KKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGH 386
+ K + + R R I+++ L DVT Q++ + S
Sbjct: 5 PEEIRKRLEHTERQFRNRRK-----ILIRGL------PGDVT-----NQEVHDLLSDYEL 48
Query: 387 VKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAE 446
V K G A + E A+A +
Sbjct: 49 KYCFVDKYK---GTAFVTLLNGEQAEAAINAFHQSRLR---------------------- 83
Query: 447 EREARLKKWETFLGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVS 506
+++ V+ + + V+
Sbjct: 84 -------------ERELSVQLQ-----------------------------PTDALLCVA 101
Query: 507 NLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLA 566
NLP LTQ++F E+++ G + + L T KG Y+KK+S A
Sbjct: 102 NLPPSLTQQQFEELVRPFGSLER--------CFLVYSERTGQSKGYGFAEYMKKDSAARA 153
Query: 567 LSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLFDWRPDKM 626
S L G + + + V + L
Sbjct: 154 KSDLLGKPLGPRTLYVHWT-------------DAGQLTPALL------------------ 182
Query: 627 RGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL---HDKHPE 683
S+ + V L P D D L S L D +
Sbjct: 183 ---HSRC---LCVDRL-PPGFNDVDA---------LCRALSAVHSPTFCQLACGQDGQLK 226
Query: 684 GVAQIFFKEPEAADACRELLNGRWFGQRQI 713
G A + ++ E A+ ++ +G G +
Sbjct: 227 GFAVLEYETAEMAEEAQQQADGLSLGGSHL 256
Score = 80.4 bits (199), Expect = 1e-16
Identities = 36/238 (15%), Positives = 74/238 (31%), Gaps = 76/238 (31%)
Query: 481 LKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKL 540
L P++ RK+ ++ + K+ + LP D+T +E +++ L VD
Sbjct: 3 LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKY------ 56
Query: 541 YTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKP 600
KG A T + E + A++ +R +++ V+
Sbjct: 57 ---------KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ--------------- 92
Query: 601 KKKRKKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQ 660
++++ V NL +T QQ
Sbjct: 93 -------------------------------PTDALLCVANL------PPSLT-----QQ 110
Query: 661 DLREECSKCGHVKKVVL----HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
E G +++ L +G + + ++A + L G+ G R +
Sbjct: 111 QFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLY 168
Score = 40.3 bits (95), Expect = 0.002
Identities = 18/105 (17%), Positives = 35/105 (33%), Gaps = 19/105 (18%)
Query: 612 KKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGH 671
+ K + + R R I+++ L DVT Q++ + S
Sbjct: 5 PEEIRKRLEHTERQFRNRRK-----ILIRGL------PGDVT-----NQEVHDLLSDYEL 48
Query: 672 VKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
V K G A + E A+A + +R+++ +
Sbjct: 49 KYCFVDKYK---GTAFVTLLNGEQAEAAINAFHQSRLRERELSVQ 90
>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 = 95.8 bits (239), Expect = 6e-22
Identities = 53/407 (13%), Positives = 103/407 (25%), Gaps = 139/407 (34%)
Query: 315 PKKKRKKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQ 374
P KR D A R + +V+ VKNL K Q
Sbjct: 10 PDSKRPLDEGSPAAAGLTSKKANEALTR--NRELTTVL-VKNL------PKSYN-----Q 55
Query: 375 QDLREECSKCGHVK--KVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAET 432
+ + CG + V K A+I F + A A +
Sbjct: 56 NKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKV----------- 104
Query: 433 WDGKTRYKIQETAEEREARLKKWETFLGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLE 492
+I V
Sbjct: 105 -------------------------VGQNEIIVSHLT----------------------- 116
Query: 493 KLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGD 552
++++N P TQ +++Q +V + +L + + +
Sbjct: 117 -------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSI-------RLPSLRFNTS-RRF 161
Query: 553 ALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLK 612
A KE + L+G +I G + + + K
Sbjct: 162 AYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS---------------NPLEKSKRTDSA 206
Query: 613 KAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHV 672
+ + I+++NL ++ + LRE G +
Sbjct: 207 TLEGR------------------EIMIRNL------STELLD----ENLLRESFEGFGSI 238
Query: 673 KKV-VLHDKHPEGVAQIF----FKEPEAADACRELLNGRWFGQRQIT 714
+K+ + + F+ ++A+ + +N G R+I+
Sbjct: 239 EKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREIS 284
Score = 85.0 bits (211), Expect = 3e-18
Identities = 53/416 (12%), Positives = 99/416 (23%), Gaps = 145/416 (34%)
Query: 177 EKSVDATAPMENPKAEEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVM 236
++ +D +P +K R E T V V NLP Q + +
Sbjct: 13 KRPLDEGSPAAAGLTSKKANEALTRNRE----------LTTVLVKNLPKSYNQNKVYKYF 62
Query: 237 QKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIK 296
+ CG + + + + K A + + + A++ + +I
Sbjct: 63 KHCGPI--------IHVDVADS--LKKNFRFARIEFARYDGALAAITKTHKV-VGQNEII 111
Query: 297 VERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKN 356
V L+ + N
Sbjct: 112 VSHLTEC----------------------------TLW-------------------MTN 124
Query: 357 LFDPALFDKDVTLILEYQQDLREECSKCGHVKKVV----LHDKHPEGVAQIFFKEPEAAD 412
T Q+++R+ V + L A I E A
Sbjct: 125 F------PPSYT-----QRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDAR 173
Query: 413 ACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLGKKIKVERAKFTM 472
C E LNG G + + +
Sbjct: 174 YCVEKLNGLKIE-----------------------------------GYTLVTKVS---- 194
Query: 473 KGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFV-EVMQKCGLVMKDV 531
K + ++ + NL +L E + E + G +
Sbjct: 195 -----------NPLEKSKRTDSATLE-GREIMIRNLSTELLDENLLRESFEGFGSI---- 238
Query: 532 DTNQMKIKLYTD-PYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
KI + A + K+S + AL ++ + ++I V A
Sbjct: 239 ----EKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLAD 289
Score = 67.7 bits (166), Expect = 2e-12
Identities = 35/275 (12%), Positives = 64/275 (23%), Gaps = 80/275 (29%)
Query: 466 ERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCG 525
+R K+ + +E T V V NLP Q + + + CG
Sbjct: 13 KRPLDEGS----PAAAGLTSKKANEALTRN--RELTTVLVKNLPKSYNQNKVYKYFKHCG 66
Query: 526 LVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 585
+ + + + K A + + + A++ + +I V
Sbjct: 67 PI--------IHVDVADS--LKKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIVSHL 115
Query: 586 KFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDP 645
L+ + N
Sbjct: 116 TEC----------------------------TLW-------------------MTNF--- 125
Query: 646 ALFDKDVTLILEYQQDLREECSKCGHVKKVV----LHDKHPEGVAQIFFKEPEAADACRE 701
T Q+++R+ V + L A I E A C E
Sbjct: 126 ---PPSYT-----QRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177
Query: 702 LLNGRWFGQRQITAETWDGKTRYKIQETAEEREAR 736
LNG + + + + E R
Sbjct: 178 KLNGLKIEGYTLVTK-VSNPLEKSKRTDSATLEGR 211
Score = 45.0 bits (107), Expect = 5e-05
Identities = 24/127 (18%), Positives = 35/127 (27%), Gaps = 17/127 (13%)
Query: 600 PKKKRKKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQ 659
P KR D A R + +V+ VKNL K Q
Sbjct: 10 PDSKRPLDEGSPAAAGLTSKKANEALTR--NRELTTVL-VKNL------PKSYN-----Q 55
Query: 660 QDLREECSKCGHVK--KVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAET 717
+ + CG + V K A+I F + A A + +I
Sbjct: 56 NKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQ-NEIIVSH 114
Query: 718 WDGKTRY 724
T +
Sbjct: 115 LTECTLW 121
>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 = 89.4 bits (222), Expect = 2e-21
Identities = 30/108 (27%), Positives = 53/108 (49%), Gaps = 18/108 (16%)
Query: 341 MRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHP--- 397
+R + S V++++N+ DP D D + ++ EEC K G V +V+++ +
Sbjct: 15 LRKQEST---VMVLRNMVDPKDIDDD------LEGEVTEECGKFGAVNRVIIYQEKQGEE 65
Query: 398 ---EGVAQIF--FKEPEAADACRELLNGRWFGQRQITAETWDGKTRYK 440
E + +IF F + LNGRWF R++ AE +D + R+
Sbjct: 66 EDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD-QERFD 112
Score = 89.4 bits (222), Expect = 2e-21
Identities = 30/108 (27%), Positives = 53/108 (49%), Gaps = 18/108 (16%)
Query: 626 MRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHP--- 682
+R + S V++++N+ DP D D + ++ EEC K G V +V+++ +
Sbjct: 15 LRKQEST---VMVLRNMVDPKDIDDD------LEGEVTEECGKFGAVNRVIIYQEKQGEE 65
Query: 683 ---EGVAQIF--FKEPEAADACRELLNGRWFGQRQITAETWDGKTRYK 725
E + +IF F + LNGRWF R++ AE +D + R+
Sbjct: 66 EDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD-QERFD 112
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 84.9 bits (210), Expect = 5e-20
Identities = 27/113 (23%), Positives = 52/113 (46%), Gaps = 15/113 (13%)
Query: 340 KMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-----D 394
M +K V++++N+ D+D+ + + +EEC K G V K V+
Sbjct: 2 AMGKCPTK---VVLLRNMVGAGEVDEDL------EVETKEECEKYGKVGKCVIFEIPGAP 52
Query: 395 KHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEE 447
+ F+ E+A LNGR+FG R + A ++ ++++ + AE+
Sbjct: 53 DDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYN-LDKFRVLDLAEQ 104
Score = 84.9 bits (210), Expect = 5e-20
Identities = 27/113 (23%), Positives = 52/113 (46%), Gaps = 15/113 (13%)
Query: 625 KMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-----D 679
M +K V++++N+ D+D+ + + +EEC K G V K V+
Sbjct: 2 AMGKCPTK---VVLLRNMVGAGEVDEDL------EVETKEECEKYGKVGKCVIFEIPGAP 52
Query: 680 KHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEE 732
+ F+ E+A LNGR+FG R + A ++ ++++ + AE+
Sbjct: 53 DDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYN-LDKFRVLDLAEQ 104
>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 = 83.7 bits (207), Expect = 1e-19
Identities = 23/96 (23%), Positives = 36/96 (37%), Gaps = 8/96 (8%)
Query: 351 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH------DKHPEGVAQIF 404
V+ + N+ P D E +D+R+ECSK G VK + + + G +
Sbjct: 7 VLCLMNMVLPEELL-DDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVE 65
Query: 405 FKEPEAADACRELLNGRWFGQRQITAETWDGKTRYK 440
F + L GR F R + + D Y
Sbjct: 66 FTSVFDCQKAMQGLTGRKFANRVVVTKYCD-PDSYH 100
Score = 83.7 bits (207), Expect = 1e-19
Identities = 23/96 (23%), Positives = 36/96 (37%), Gaps = 8/96 (8%)
Query: 636 VIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH------DKHPEGVAQIF 689
V+ + N+ P D E +D+R+ECSK G VK + + + G +
Sbjct: 7 VLCLMNMVLPEELL-DDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVE 65
Query: 690 FKEPEAADACRELLNGRWFGQRQITAETWDGKTRYK 725
F + L GR F R + + D Y
Sbjct: 66 FTSVFDCQKAMQGLTGRKFANRVVVTKYCD-PDSYH 100
>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 = 81.2 bits (201), Expect = 1e-17
Identities = 33/223 (14%), Positives = 66/223 (29%), Gaps = 41/223 (18%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
G + ++YV N+P +T+E ++ + Q K A
Sbjct: 1 GAMARRLYVGNIPFGITEEAMMDFFNAQMRL---GGLTQAPGNPVLAVQINQDKNFAFLE 57
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQE 331
+ + A++ DG +G+ +K+ R D + L E
Sbjct: 58 FRSVDETTQAMA-FDGIIFQGQSLKIRRP--------------------HDYQPLPGMSE 96
Query: 332 KLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVV 391
+ P + + + + L + ++E + G +K
Sbjct: 97 NPSVYVPGVVSTVVPDSAHKLFIGGL------PNYLN-----DDQVKELLTSFGPLKAFN 145
Query: 392 LHDKHPE-----GVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
L K G A + + D LNG G +++
Sbjct: 146 LV-KDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 187
Score = 77.0 bits (190), Expect = 3e-16
Identities = 32/218 (14%), Positives = 64/218 (29%), Gaps = 41/218 (18%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
++YV N+P +T+E ++ + Q K A + +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRL---GGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 562 SVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLFDW 621
A++ DG +G+ +K+ R D + L E +
Sbjct: 63 ETTQAMA-FDGIIFQGQSLKIRRP--------------------HDYQPLPGMSENPSVY 101
Query: 622 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKH 681
P + + + + L + ++E + G +K L K
Sbjct: 102 VPGVVSTVVPDSAHKLFIGGL------PNYLN-----DDQVKELLTSFGPLKAFNLV-KD 149
Query: 682 PE-----GVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
G A + + D LNG G +++
Sbjct: 150 SATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 187
Score = 72.0 bits (177), Expect = 1e-14
Identities = 35/241 (14%), Positives = 72/241 (29%), Gaps = 67/241 (27%)
Query: 354 VKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHP---------EGVAQIF 404
V N+ +T ++ + + + + + +P + A +
Sbjct: 9 VGNI------PFGIT-----EEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 57
Query: 405 FKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLGKKIK 464
F+ + +G F G+ +K
Sbjct: 58 FRSVDETTQAMAF-DGI-----------------------------------IFQGQSLK 81
Query: 465 VERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKC 524
+ R P + + + K+++ LP L ++ E++
Sbjct: 82 IRRPHD--YQPLPGMSENPSVYVPGVVSTVVPDSAH-KLFIGGLPNYLNDDQVKELLTSF 138
Query: 525 GLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVER 584
G + L D T KG A C Y+ D A++ L+G ++ KK+ V+R
Sbjct: 139 GPLKA--------FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 190
Query: 585 A 585
A
Sbjct: 191 A 191
Score = 59.7 bits (145), Expect = 2e-10
Identities = 23/114 (20%), Positives = 45/114 (39%), Gaps = 8/114 (7%)
Query: 187 ENPKAEEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDV 246
+ + + + + + K+++ LP L ++ E++ G +
Sbjct: 86 HDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKA-- 143
Query: 247 DTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 300
L D T KG A C Y+ D A++ L+G ++ KK+ V+RA
Sbjct: 144 ------FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191
>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 = 78.8 bits (195), Expect = 3e-17
Identities = 43/222 (19%), Positives = 74/222 (33%), Gaps = 65/222 (29%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
+T + V+ LP D+T E + + G + ++ D T G A +
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINT--------CRIMRDYKTGYSYGYAFVDFT 53
Query: 274 KKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKL 333
+ A+ +L+G +R K++KV A +P + KD L
Sbjct: 54 SEMDSQRAIKVLNGITVRNKRLKVSYA-------------RPGGESIKD--------TNL 92
Query: 334 FDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VL 392
+ V NL + +T L K G + + +L
Sbjct: 93 Y-------------------VTNL------PRTIT-----DDQLDTIFGKYGSIVQKNIL 122
Query: 393 HDK---HPEGVAQIFFKEPEAADACRELLNGRWF--GQRQIT 429
DK P GVA + + + E A LN G + ++
Sbjct: 123 RDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLS 164
Score = 78.8 bits (195), Expect = 3e-17
Identities = 44/222 (19%), Positives = 74/222 (33%), Gaps = 65/222 (29%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
NT + V+ LP D+T E + + G + ++ D T G A +
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINT--------CRIMRDYKTGYSYGYAFVDFT 53
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKL 618
+ A+ +L+G +R K++KV A +P + KD L
Sbjct: 54 SEMDSQRAIKVLNGITVRNKRLKVSYA-------------RPGGESIKD--------TNL 92
Query: 619 FDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VL 677
+ V NL + +T L K G + + +L
Sbjct: 93 Y-------------------VTNL------PRTIT-----DDQLDTIFGKYGSIVQKNIL 122
Query: 678 HDK---HPEGVAQIFFKEPEAADACRELLNGRWF--GQRQIT 714
DK P GVA + + + E A LN G + ++
Sbjct: 123 RDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLS 164
Score = 62.6 bits (153), Expect = 1e-11
Identities = 46/240 (19%), Positives = 77/240 (32%), Gaps = 83/240 (34%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKE 407
+IV L +D+T ++L G + ++ D + G A + F
Sbjct: 6 LIVNYL------PQDMT-----DRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTS 54
Query: 408 PEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLGKKIKVER 467
+ ++LNG T K++KV
Sbjct: 55 EMDSQRAIKVLNGI-----------------------------------TVRNKRLKVSY 79
Query: 468 AKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLV 527
A+ P + KD T +YV+NLP +T ++ + K G +
Sbjct: 80 AR-------------PGGESIKD----------TNLYVTNLPRTITDDQLDTIFGKYGSI 116
Query: 528 MKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRG--KKIKVERA 585
V N + D T +G A Y K+E A+S L+ G + + V A
Sbjct: 117 ---VQKNIL-----RDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 45.6 bits (109), Expect = 1e-05
Identities = 24/90 (26%), Positives = 39/90 (43%), Gaps = 10/90 (11%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+ T +YV+NLP +T ++ + K G + V N + D T +G A Y
Sbjct: 87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSI---VQKNIL-----RDKLTGRPRGVAFVRY 138
Query: 273 IKKESVDLALSILDGYEIRG--KKIKVERA 300
K+E A+S L+ G + + V A
Sbjct: 139 NKREEAQEAISALNNVIPEGGSQPLSVRLA 168
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 78.1 bits (193), Expect = 2e-16
Identities = 36/235 (15%), Positives = 80/235 (34%), Gaps = 54/235 (22%)
Query: 484 KKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTD 543
+ R ++ ++VYV ++ +L ++ + G + I + D
Sbjct: 12 QMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKS--------IDMSWD 63
Query: 544 PYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKK 603
T KG A Y E+ LAL ++ + G+ IKV R +
Sbjct: 64 SVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP-------------SNIGQ 110
Query: 604 RKKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLR 663
+ +++L E ++ + I V ++ +D++ D++
Sbjct: 111 AQPIIDQLA----------------EEARAFNRIYVASV------HQDLS-----DDDIK 143
Query: 664 EECSKCGHVKKVVLHDKHPE-----GVAQIFFKEPEAADACRELLNGRWFGQRQI 713
G +K L + P G I +++ +++ +N G + +
Sbjct: 144 SVFEAFGKIKSATLA-RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 197
Score = 76.2 bits (188), Expect = 8e-16
Identities = 35/221 (15%), Positives = 76/221 (34%), Gaps = 54/221 (24%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
++VYV ++ +L ++ + G + I + D T KG A Y
Sbjct: 26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKS--------IDMSWDSVTMKHKGFAFVEY 77
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEK 332
E+ LAL ++ + G+ IKV R + + +++L
Sbjct: 78 EVPEAAQLALEQMNSVMLGGRNIKVGRP-------------SNIGQAQPIIDQLA----- 119
Query: 333 LFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL 392
E ++ + I V ++ +D++ D++ G +K L
Sbjct: 120 -----------EEARAFNRIYVASV------HQDLS-----DDDIKSVFEAFGKIKSATL 157
Query: 393 HDKHPE-----GVAQIFFKEPEAADACRELLNGRWFGQRQI 428
+ P G I +++ +++ +N G + +
Sbjct: 158 A-RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 197
Score = 72.7 bits (179), Expect = 1e-14
Identities = 42/253 (16%), Positives = 87/253 (34%), Gaps = 72/253 (28%)
Query: 338 PDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKH 396
R S + V ++ ++ + +R+ + G +K + + D
Sbjct: 17 SAAQRQGALAIMSRVYVGSI------YYELG-----EDTIRQAFAPFGPIKSIDMSWDSV 65
Query: 397 ---PEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLK 453
+G A + ++ PEAA E +N G
Sbjct: 66 TMKHKGFAFVEYEVPEAAQLALEQMNSVMLG----------------------------- 96
Query: 454 KWETFLGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEN-TKVYVSNLPLDL 512
G+ IKV R + + +++L + ++YV+++ DL
Sbjct: 97 ------GRNIKVGRPS-------------NIGQAQPIIDQLAEEARAFNRIYVASVHQDL 137
Query: 513 TQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDG 572
+ ++ V + G + L DP T KG Y K +S A+S ++
Sbjct: 138 SDDDIKSVFEAFGKIKS--------ATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNL 189
Query: 573 YEIRGKKIKVERA 585
+++ G+ ++V +A
Sbjct: 190 FDLGGQYLRVGKA 202
Score = 56.6 bits (137), Expect = 3e-09
Identities = 21/107 (19%), Positives = 47/107 (43%), Gaps = 8/107 (7%)
Query: 194 KVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKI 253
+ + +P + + ++YV+++ DL+ ++ V + G +
Sbjct: 104 RPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKI--------KSA 155
Query: 254 KLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 300
L DP T KG Y K +S A+S ++ +++ G+ ++V +A
Sbjct: 156 TLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
>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 = 82.2 bits (202), Expect = 3e-16
Identities = 99/639 (15%), Positives = 192/639 (30%), Gaps = 186/639 (29%)
Query: 245 DVDTNQMKIKLYTD---PYTKDFKGDALCTYIKKESVDLALSILDGYE---IRGKKIKVE 298
D +T + + + Y D + F + C ++ D+ SIL E I K V
Sbjct: 8 DFETGEHQYQ-YKDILSVFEDAFVDNFDCKDVQ----DMPKSILSKEEIDHIIMSKDAVS 62
Query: 299 RAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLFDWRPDKMRGE---RSKNESVII-- 353
+ K ++ +K +E+ + + ++ E S + I
Sbjct: 63 GTLRLF----WTLLSKQEEMVQKFVEE---VLRINYKFLMSPIKTEQRQPSMMTRMYIEQ 115
Query: 354 VKNLF-DPALFDK-DVTLILEYQQDLREECSKCGHVKKVVLH------------------ 393
L+ D +F K +V+ + Y + LR+ + K V++
Sbjct: 116 RDRLYNDNQVFAKYNVSRLQPYLK-LRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSY 174
Query: 394 ---DKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQ-ETAEERE 449
K + + K + + E+L + D + K++ + +
Sbjct: 175 KVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL 234
Query: 450 ARL-------------------KKWETF-LGKKIKVERAKFTMKGEAYDPKLKPKKKRKK 489
RL K W F L KI + T R K
Sbjct: 235 RRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLT----T---------------RFK 275
Query: 490 DLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKC-GLVMKD-----VDTNQMKIKLY-- 541
+ A T + + + + LT +E ++ K +D + TN ++ +
Sbjct: 276 QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAE 335
Query: 542 -------TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRG--KKIKVERAKFTMKGE 592
T K D L ++ +L++L+ E R ++ V F
Sbjct: 336 SIRDGLATWDNWKHVNCDKL-----TTIIESSLNVLEPAEYRKMFDRLSV----FP---- 382
Query: 593 AYDPKLKPKKKRKKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKD- 651
+ L + W + K++ +++V L +L +K
Sbjct: 383 -PSAHIPTIL-----LSLI---------W------FDVIKSDVMVVVNKLHKYSLVEKQP 421
Query: 652 ---VTLILEYQQDLREECSKCG--HVKKVV----------LHDKHPEGVAQIFF------ 690
I +L+ + H + +V D P + Q F+
Sbjct: 422 KESTISIPSIYLELKVKLENEYALH-RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHH 480
Query: 691 ----KEPEAADACREL-LNGRWFGQRQITAET-WDGKT----------RYK--IQETAEE 732
+ PE R + L+ R+ Q+ T W+ YK I + +
Sbjct: 481 LKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPK 540
Query: 733 REARLKKWETFLEEEDKKKKEAGKGSIDEKESKELQAPL 771
E + FL + + I K + L+ L
Sbjct: 541 YERLVNAILDFL-------PKIEENLICSKYTDLLRIAL 572
>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 = 73.7 bits (181), Expect = 3e-16
Identities = 21/99 (21%), Positives = 35/99 (35%), Gaps = 18/99 (18%)
Query: 351 VIIVKNLFDPALFDKDVTLIL---------------EYQQDLREECSKCGHVKKVVLHDK 395
I + N++ L +++ E K G V+++ + D
Sbjct: 3 TIALLNIYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN 62
Query: 396 ---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
H G + F+ E A+ LN RWF + I AE
Sbjct: 63 LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101
Score = 73.7 bits (181), Expect = 3e-16
Identities = 21/99 (21%), Positives = 35/99 (35%), Gaps = 18/99 (18%)
Query: 636 VIIVKNLFDPALFDKDVTLIL---------------EYQQDLREECSKCGHVKKVVLHDK 680
I + N++ L +++ E K G V+++ + D
Sbjct: 3 TIALLNIYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN 62
Query: 681 ---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
H G + F+ E A+ LN RWF + I AE
Sbjct: 63 LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101
>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 = 75.7 bits (187), Expect = 4e-16
Identities = 48/221 (21%), Positives = 76/221 (34%), Gaps = 65/221 (29%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
T + V+ LP ++TQEEF + G + KL D T G YI
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIES--------CKLVRDKITGQSLGYGFVNYID 53
Query: 275 KESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLF 334
+ + A++ L+G ++ K IKV A +P +D L+
Sbjct: 54 PKDAEKAINTLNGLRLQTKTIKVSYA-------------RPSSASIRD--------ANLY 92
Query: 335 DWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLH 393
V L K +T Q++L + S+ G + +L
Sbjct: 93 -------------------VSGL------PKTMT-----QKELEQLFSQYGRIITSRILV 122
Query: 394 DK---HPEGVAQIFFKEPEAADACRELLNGRWF--GQRQIT 429
D+ GV I F + A+ + LNG+ IT
Sbjct: 123 DQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPIT 163
Score = 75.3 bits (186), Expect = 6e-16
Identities = 48/221 (21%), Positives = 76/221 (34%), Gaps = 65/221 (29%)
Query: 500 NTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 559
T + V+ LP ++TQEEF + G + KL D T G YI
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIES--------CKLVRDKITGQSLGYGFVNYID 53
Query: 560 KESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLF 619
+ + A++ L+G ++ K IKV A +P +D L+
Sbjct: 54 PKDAEKAINTLNGLRLQTKTIKVSYA-------------RPSSASIRD--------ANLY 92
Query: 620 DWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLH 678
V L K +T Q++L + S+ G + +L
Sbjct: 93 -------------------VSGL------PKTMT-----QKELEQLFSQYGRIITSRILV 122
Query: 679 DK---HPEGVAQIFFKEPEAADACRELLNGRWF--GQRQIT 714
D+ GV I F + A+ + LNG+ IT
Sbjct: 123 DQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPIT 163
Score = 58.4 bits (142), Expect = 4e-10
Identities = 41/244 (16%), Positives = 81/244 (33%), Gaps = 83/244 (34%)
Query: 348 NESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK---HPEGVAQI 403
+++ +IV L +++T Q++ R G ++ ++ DK G +
Sbjct: 1 SKTNLIVNYL------PQNMT-----QEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFV 49
Query: 404 FFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLGKKI 463
+ +P+ A+ LNG K I
Sbjct: 50 NYIDPKDAEKAINTLNGL-----------------------------------RLQTKTI 74
Query: 464 KVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQK 523
KV A+ P + + +YVS LP +TQ+E ++ +
Sbjct: 75 KVSYAR-------------PSSASIR----------DANLYVSGLPKTMTQKELEQLFSQ 111
Query: 524 CGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRG--KKIK 581
G + + + + D T +G + K+ + A+ L+G + G + I
Sbjct: 112 YGRI---ITSRIL-----VDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPIT 163
Query: 582 VERA 585
V+ A
Sbjct: 164 VKFA 167
Score = 45.3 bits (108), Expect = 1e-05
Identities = 20/90 (22%), Positives = 39/90 (43%), Gaps = 10/90 (11%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+YVS LP +TQ+E ++ + G + + + + D T +G +
Sbjct: 86 IRDANLYVSGLPKTMTQKELEQLFSQYGRI---ITSRIL-----VDQVTGVSRGVGFIRF 137
Query: 273 IKKESVDLALSILDGYEIRG--KKIKVERA 300
K+ + A+ L+G + G + I V+ A
Sbjct: 138 DKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
Score = 34.1 bits (79), Expect = 0.086
Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 15/85 (17%)
Query: 633 NESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK---HPEGVAQI 688
+++ +IV L +++T Q++ R G ++ ++ DK G +
Sbjct: 1 SKTNLIVNYL------PQNMT-----QEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFV 49
Query: 689 FFKEPEAADACRELLNGRWFGQRQI 713
+ +P+ A+ LNG + I
Sbjct: 50 NYIDPKDAEKAINTLNGLRLQTKTI 74
>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 = 77.0 bits (189), Expect = 5e-16
Identities = 39/245 (15%), Positives = 76/245 (31%), Gaps = 47/245 (19%)
Query: 343 GERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQ 402
G SV++V NL +P + VT Q L G V++V + A
Sbjct: 28 GLAGAGNSVLLVSNL-NP----ERVT-----PQSLFILFGVYGDVQRVKILFNKK-ENAL 76
Query: 403 IFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLGKK 462
+ + A LNG + I + +E E++
Sbjct: 77 VQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQG------------- 123
Query: 463 IKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQ 522
+ Y + K+ + +++SN+P +++E+ +
Sbjct: 124 ----------LTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFS 173
Query: 523 KCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEI-RGKKIK 581
G V+K + + + AL E AL L +++ ++
Sbjct: 174 SNGGVVK------------GFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLR 221
Query: 582 VERAK 586
V +K
Sbjct: 222 VSFSK 226
Score = 59.2 bits (143), Expect = 6e-10
Identities = 37/210 (17%), Positives = 73/210 (34%), Gaps = 30/210 (14%)
Query: 212 GEESTKVYVSNL-PLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 270
G ++ + VSNL P +T + + G V + +K+ + K +AL
Sbjct: 31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQR--------VKILFNK-----KENALV 77
Query: 271 TYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQ 330
LA+S L+G+++ GK I++ T+ + ++ + + +
Sbjct: 78 QMADGNQAQLAMSHLNGHKLHGKPIRI-----TLSKHQNVQLPREGQEDQGLTKDYGNSP 132
Query: 331 EKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV 390
F K + + + N+ V+ ++DL+ S G V K
Sbjct: 133 LHRFKKPGSKNFQNIFPPSATLHLSNI------PPSVS-----EEDLKVLFSSNGGVVKG 181
Query: 391 VLHDKHPEGVAQIFFKEPEAADACRELLNG 420
+ +A I E A L+
Sbjct: 182 FKFFQKDRKMALIQMGSVEEAVQALIDLHN 211
Score = 58.9 bits (142), Expect = 8e-10
Identities = 37/207 (17%), Positives = 72/207 (34%), Gaps = 30/207 (14%)
Query: 500 NTKVYVSNL-PLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
N+ + VSNL P +T + + G V + +K+ + K +AL
Sbjct: 34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQR--------VKILFNK-----KENALVQMA 80
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKL 618
LA+S L+G+++ GK I++ T+ + ++ + + +
Sbjct: 81 DGNQAQLAMSHLNGHKLHGKPIRI-----TLSKHQNVQLPREGQEDQGLTKDYGNSPLHR 135
Query: 619 FDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH 678
F K + + + N+ V+ ++DL+ S G V K
Sbjct: 136 FKKPGSKNFQNIFPPSATLHLSNI------PPSVS-----EEDLKVLFSSNGGVVKGFKF 184
Query: 679 DKHPEGVAQIFFKEPEAADACRELLNG 705
+ +A I E A L+
Sbjct: 185 FQKDRKMALIQMGSVEEAVQALIDLHN 211
Score = 48.8 bits (116), Expect = 2e-06
Identities = 21/129 (16%), Positives = 47/129 (36%), Gaps = 17/129 (13%)
Query: 178 KSVDATAPMENPKAEEKVVPGQK----RKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFV 233
++V + + K +KP + +I S +++SN+P +++E+
Sbjct: 110 QNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLK 169
Query: 234 EVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEI-RG 292
+ G V+K + + + AL E AL L +++
Sbjct: 170 VLFSSNGGVVK------------GFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGEN 217
Query: 293 KKIKVERAK 301
++V +K
Sbjct: 218 HHLRVSFSK 226
Score = 47.3 bits (112), Expect = 6e-06
Identities = 22/107 (20%), Positives = 36/107 (33%), Gaps = 11/107 (10%)
Query: 628 GERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQ 687
G SV++V NL +P + VT Q L G V++V + A
Sbjct: 28 GLAGAGNSVLLVSNL-NP----ERVT-----PQSLFILFGVYGDVQRVKILFNKK-ENAL 76
Query: 688 IFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEERE 734
+ + A LNG + I + +E E++
Sbjct: 77 VQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQG 123
>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 = 73.2 bits (179), Expect = 7e-15
Identities = 35/243 (14%), Positives = 74/243 (30%), Gaps = 43/243 (17%)
Query: 348 NESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKE 407
+ V++V L D + + D + G+V+KV P G A + +
Sbjct: 3 DSPVLMVYGL-DQSKMNCD---------RVFNVFCLYGNVEKVKFMKSKP-GAAMVEMAD 51
Query: 408 PEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLGKKIKVER 467
A D LN + +++ Q ++ + + K R
Sbjct: 52 GYAVDRAITHLNNNFMFGQKM-------NVCVSKQPAIMPGQSYGLEDGSCSYKDFSESR 104
Query: 468 AKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLV 527
+ + K + + ++ N PL++T+E F E+ + G+
Sbjct: 105 --------------NNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVK 150
Query: 528 MKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKF 587
+ + L + K L L+ Y+++ +
Sbjct: 151 --------RPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP---Y 199
Query: 588 TMK 590
T+K
Sbjct: 200 TLK 202
Score = 62.8 bits (152), Expect = 3e-11
Identities = 34/225 (15%), Positives = 65/225 (28%), Gaps = 32/225 (14%)
Query: 212 GEESTKVYVSNL-PLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 270
G +S + V L + + V G V K+K + K G A+
Sbjct: 1 GADSPVLMVYGLDQSKMNCDRVFNVFCLYGNV--------EKVK-----FMKSKPGAAMV 47
Query: 271 TYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQ 330
+VD A++ L+ + G+K+ V +K L+ KD + + +
Sbjct: 48 EMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNR 107
Query: 331 EKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV 390
F + +V+ N +VT +++ E C + G +
Sbjct: 108 ---FSTPEQAAKNRIQHPSNVLHFFNA------PLEVT-----EENFFEICDELGVKRPT 153
Query: 391 VL----HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
+ + + A LN
Sbjct: 154 SVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP 198
Score = 47.8 bits (113), Expect = 3e-06
Identities = 19/105 (18%), Positives = 36/105 (34%), Gaps = 11/105 (10%)
Query: 201 RKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPY 260
PE I S ++ N PL++T+E F E+ + G+ +
Sbjct: 109 STPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRP--------TSVKVFSG 160
Query: 261 TKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMK 305
+ L + K L L+ Y+++ +T+K
Sbjct: 161 KSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP---YTLK 202
Score = 43.9 bits (103), Expect = 6e-05
Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 11/81 (13%)
Query: 633 NESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKE 692
+ V++V L D + + D + G+V+KV P G A + +
Sbjct: 3 DSPVLMVYGL-DQSKMNCD---------RVFNVFCLYGNVEKVKFMKSKP-GAAMVEMAD 51
Query: 693 PEAADACRELLNGRWFGQRQI 713
A D LN + +++
Sbjct: 52 GYAVDRAITHLNNNFMFGQKM 72
>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 = 70.7 bits (173), Expect = 5e-14
Identities = 40/238 (16%), Positives = 75/238 (31%), Gaps = 47/238 (19%)
Query: 350 SVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPE 409
SV++V NL +P + VT Q L G V++V + A + +
Sbjct: 4 SVLLVSNL-NP----ERVT-----PQSLFILFGVYGDVQRVKILFNKK-ENALVQMADGN 52
Query: 410 AADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLGKKIKVERAK 469
A LNG + I T K + + + L K
Sbjct: 53 QAQLAMSHLNGHKLHGKPIRI-TL-SKHQNVQLPREGQEDQGLTK--------------- 95
Query: 470 FTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMK 529
Y + K+ + +++SN+P +++E+ + G V+K
Sbjct: 96 ------DYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK 149
Query: 530 DVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEI-RGKKIKVERAK 586
+ + + AL E AL L +++ ++V +K
Sbjct: 150 GF------------KFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK 195
Score = 58.4 bits (141), Expect = 7e-10
Identities = 39/207 (18%), Positives = 73/207 (35%), Gaps = 30/207 (14%)
Query: 500 NTKVYVSNL-PLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
N+ + VSNL P +T + + G V + +K+ + K +AL
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQR--------VKILFNK-----KENALVQMA 49
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKL 618
LA+S L+G+++ GK I++ +K + + + + KD +
Sbjct: 50 DGNQAQLAMSHLNGHKLHGKPIRITLSKH--QNVQLPREGQEDQGLTKDYGNSPLHR--- 104
Query: 619 FDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH 678
F K + + + N+ V+ ++DL+ S G V K
Sbjct: 105 FKKPGSKNFQNIFPPSATLHLSNI------PPSVS-----EEDLKVLFSSNGGVVKGFKF 153
Query: 679 DKHPEGVAQIFFKEPEAADACRELLNG 705
+ +A I E A L+
Sbjct: 154 FQKDRKMALIQMGSVEEAVQALIDLHN 180
Score = 57.6 bits (139), Expect = 1e-09
Identities = 38/207 (18%), Positives = 73/207 (35%), Gaps = 30/207 (14%)
Query: 215 STKVYVSNL-PLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
++ + VSNL P +T + + G V + +K+ + K +AL
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQR--------VKILFNK-----KENALVQMA 49
Query: 274 KKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKL 333
LA+S L+G+++ GK I++ +K + + + + KD +
Sbjct: 50 DGNQAQLAMSHLNGHKLHGKPIRITLSKH--QNVQLPREGQEDQGLTKDYGNSPLHR--- 104
Query: 334 FDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH 393
F K + + + N+ V+ ++DL+ S G V K
Sbjct: 105 FKKPGSKNFQNIFPPSATLHLSNI------PPSVS-----EEDLKVLFSSNGGVVKGFKF 153
Query: 394 DKHPEGVAQIFFKEPEAADACRELLNG 420
+ +A I E A L+
Sbjct: 154 FQKDRKMALIQMGSVEEAVQALIDLHN 180
Score = 48.4 bits (115), Expect = 2e-06
Identities = 22/132 (16%), Positives = 48/132 (36%), Gaps = 15/132 (11%)
Query: 173 SKVEEKSVDATAPMENPKAEEKVVPGQKR--KPEPPKWFDIGEESTKVYVSNLPLDLTQE 230
SK + + + ++ R KP + +I S +++SN+P +++E
Sbjct: 76 SKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEE 135
Query: 231 EFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEI 290
+ + G V+K + + + AL E AL L +++
Sbjct: 136 DLKVLFSSNGGVVKGF------------KFFQKDRKMALIQMGSVEEAVQALIDLHNHDL 183
Query: 291 -RGKKIKVERAK 301
++V +K
Sbjct: 184 GENHHLRVSFSK 195
Score = 42.2 bits (99), Expect = 2e-04
Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 11/79 (13%)
Query: 635 SVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPE 694
SV++V NL +P + VT Q L G V++V + A + +
Sbjct: 4 SVLLVSNL-NP----ERVT-----PQSLFILFGVYGDVQRVKILFNKK-ENALVQMADGN 52
Query: 695 AADACRELLNGRWFGQRQI 713
A LNG + I
Sbjct: 53 QAQLAMSHLNGHKLHGKPI 71
>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 = 69.6 bits (171), Expect = 7e-14
Identities = 29/216 (13%), Positives = 67/216 (31%), Gaps = 66/216 (30%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQKCG-----LVMKDVDTNQMKIKLYTDPYTKDFKGDA 268
++ K++V +P ++++ E+ ++ G V++D N + K
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGC-----------C 50
Query: 269 LCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKK 328
T+ +++ A + L ++ + KP K + + +
Sbjct: 51 FVTFYTRKAALEAQNALHNMKVLPGMHHPIQM-------------KPADSEKNNAVEDR- 96
Query: 329 AQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK 388
KLF + + K T + D+R S G ++
Sbjct: 97 ---KLF-------------------IGMI------SKKCT-----ENDIRVMFSSFGQIE 123
Query: 389 KV-VLHDK--HPEGVAQIFFKEPEAADACRELLNGR 421
+ +L G A + F A + ++
Sbjct: 124 ECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159
Score = 68.8 bits (169), Expect = 1e-13
Identities = 29/216 (13%), Positives = 66/216 (30%), Gaps = 66/216 (30%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCG-----LVMKDVDTNQMKIKLYTDPYTKDFKGDA 553
+ K++V +P ++++ E+ ++ G V++D N + K
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGC-----------C 50
Query: 554 LCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKK 613
T+ +++ A + L ++ + KP K + + +
Sbjct: 51 FVTFYTRKAALEAQNALHNMKVLPGMHHPIQM-------------KPADSEKNNAVEDR- 96
Query: 614 AQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK 673
KLF + + K T + D+R S G ++
Sbjct: 97 ---KLF-------------------IGMI------SKKCT-----ENDIRVMFSSFGQIE 123
Query: 674 KV-VLHDK--HPEGVAQIFFKEPEAADACRELLNGR 706
+ +L G A + F A + ++
Sbjct: 124 ECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159
Score = 49.9 bits (120), Expect = 4e-07
Identities = 32/243 (13%), Positives = 69/243 (28%), Gaps = 83/243 (34%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPE-----GVAQIFF 405
+ V + + + ++DLRE + G V ++ VL D+ G + F
Sbjct: 6 MFVGQV------PRTWS-----EKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
Query: 406 KEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLGKKIKV 465
+AA + L+ K+
Sbjct: 55 YTRKAALEAQNALH----------------------------------------NMKV-- 72
Query: 466 ERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCG 525
P + + D EK A E+ K+++ + T+ + + G
Sbjct: 73 -----------LPGMHHPIQMKPADSEK-NNAVEDRKLFIGMISKKCTENDIRVMFSSFG 120
Query: 526 LVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEI---RGKKIKV 582
+ + ++ P +G A T+ + A+ + + + V
Sbjct: 121 QI---EECRILR-----GP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV 171
Query: 583 ERA 585
+ A
Sbjct: 172 KFA 174
>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 = 68.4 bits (168), Expect = 2e-13
Identities = 33/220 (15%), Positives = 62/220 (28%), Gaps = 59/220 (26%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
+ ++YV N+P +T+E ++ + Q K A +
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRL---GGLTQAPGNPVLAVQINQDKNFAFLEFR 59
Query: 274 KKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKL 333
+ A++ DG +G+ +K+ R Y P KL
Sbjct: 60 SVDETTQAMA-FDGIIFQGQSLKIRRPH------DYQPLPGAH---------------KL 97
Query: 334 FDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH 393
F + L + ++E + G +K L
Sbjct: 98 F-------------------IGGL------PNYLN-----DDQVKELLTSFGPLKAFNLV 127
Query: 394 -DKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
D +G A + + D LNG G +++
Sbjct: 128 KDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167
Score = 66.9 bits (164), Expect = 5e-13
Identities = 33/217 (15%), Positives = 61/217 (28%), Gaps = 59/217 (27%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
++YV N+P +T+E ++ + Q K A + +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRL---GGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 562 SVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLFDW 621
A++ DG +G+ +K+ R Y P KLF
Sbjct: 63 ETTQAMA-FDGIIFQGQSLKIRRPH------DYQPLPGAH---------------KLF-- 98
Query: 622 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-DK 680
+ L + ++E + G +K L D
Sbjct: 99 -----------------IGGL------PNYLN-----DDQVKELLTSFGPLKAFNLVKDS 130
Query: 681 H---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+G A + + D LNG G +++
Sbjct: 131 ATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167
Score = 60.7 bits (148), Expect = 6e-11
Identities = 38/241 (15%), Positives = 70/241 (29%), Gaps = 87/241 (36%)
Query: 354 VKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQI-------F-- 404
V N+ +T ++ + + + + + +P QI F
Sbjct: 9 VGNI------PFGIT-----EEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 57
Query: 405 FKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLGKKIK 464
F+ + +G F G+ +K
Sbjct: 58 FRSVDETTQAMAF-DGI-----------------------------------IFQGQSLK 81
Query: 465 VERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKC 524
+ R Y P K +++ LP L ++ E++
Sbjct: 82 IRRPH------DYQPLPGAHK-----------------LFIGGLPNYLNDDQVKELLTSF 118
Query: 525 GLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVER 584
G + L D T KG A C Y+ D A++ L+G ++ KK+ V+R
Sbjct: 119 GPLKA--------FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170
Query: 585 A 585
A
Sbjct: 171 A 171
Score = 59.2 bits (144), Expect = 2e-10
Identities = 35/174 (20%), Positives = 66/174 (37%), Gaps = 27/174 (15%)
Query: 138 PKVDDDFLARYQMSYGFIEQPNTVDEKKPSADLVQSK----------VEEKSV-DATAPM 186
+ ++ + + F Q + + V + +E +SV + T M
Sbjct: 14 FGITEEAMMDF-----FNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 68
Query: 187 ENPKAEEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDV 246
+ + GQ K P + + K+++ LP L ++ E++ G +
Sbjct: 69 ---AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKA-- 123
Query: 247 DTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 300
L D T KG A C Y+ D A++ L+G ++ KK+ V+RA
Sbjct: 124 ------FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
>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 = 67.2 bits (165), Expect = 4e-13
Identities = 36/219 (16%), Positives = 71/219 (32%), Gaps = 60/219 (27%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
++ +++ NL + + E + + D+ + D T +
Sbjct: 8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAK-NDL-----AV---VDVRTGTNRKFGY 58
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKA 614
+ E ++ AL L G ++ G +IK+E+ K + +K +A
Sbjct: 59 VDFESAEDLEKALE-LTGLKVFGNEIKLEKP-------------KGRDSKK------VRA 98
Query: 615 QEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKK 674
L KNL ++T + +L+E + +
Sbjct: 99 ARTLL-------------------AKNL------SFNIT-----EDELKEVFEDALEI-R 127
Query: 675 VVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
+V D +G+A I FK A+ E G R +
Sbjct: 128 LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 166
Score = 66.9 bits (164), Expect = 5e-13
Identities = 36/216 (16%), Positives = 69/216 (31%), Gaps = 60/216 (27%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+++ NL + + E + + D+ + D T + +
Sbjct: 11 TTPFNLFIGNLNPNKSVAELKVAISELFAK-NDL-----AV---VDVRTGTNRKFGYVDF 61
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEK 332
E ++ AL L G ++ G +IK+E+ K + +K +A
Sbjct: 62 ESAEDLEKALE-LTGLKVFGNEIKLEKP-------------KGRDSKK------VRAART 101
Query: 333 LFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL 392
L KNL ++T + +L+E + ++V
Sbjct: 102 LL-------------------AKNL------SFNIT-----EDELKEVFEDALEI-RLVS 130
Query: 393 HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
D +G+A I FK A+ E G R +
Sbjct: 131 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 166
Score = 65.7 bits (161), Expect = 1e-12
Identities = 32/247 (12%), Positives = 64/247 (25%), Gaps = 84/247 (34%)
Query: 343 GERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKH---PEG 399
G S + + NL + + + +L+ S+ + + D
Sbjct: 7 GSESTTPFNLFIGNL------NPNKS-----VAELKVAISELFAKNDLAVVDVRTGTNRK 55
Query: 400 VAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFL 459
+ F+ E + EL G
Sbjct: 56 FGYVDFESAEDLEKALEL-TGL-----------------------------------KVF 79
Query: 460 GKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVE 519
G +IK+E+ K + +K + NL ++T++E E
Sbjct: 80 GNEIKLEKPK-------------GRDSKKVR--------AARTLLAKNLSFNITEDELKE 118
Query: 520 VMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKK 579
V + + + KG A + + + L G EI G+
Sbjct: 119 VFEDALEIRLVSQDGKS-------------KGIAYIEFKSEADAEKNLEEKQGAEIDGRS 165
Query: 580 IKVERAK 586
+ +
Sbjct: 166 VSLYYTG 172
Score = 54.5 bits (132), Expect = 8e-09
Identities = 16/108 (14%), Positives = 34/108 (31%), Gaps = 19/108 (17%)
Query: 194 KVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKI 253
K+ + R + + + NL ++T++E EV + + +
Sbjct: 84 KLEKPKGRDSKKV------RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKS-- 135
Query: 254 KLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
KG A + + + L G EI G+ + +
Sbjct: 136 -----------KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 172
>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 = 65.0 bits (159), Expect = 5e-13
Identities = 18/109 (16%), Positives = 40/109 (36%), Gaps = 9/109 (8%)
Query: 478 DPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMK 537
R+ + ++ V+ L + + + G V
Sbjct: 3 SGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKV--------RD 54
Query: 538 IKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+++ +D ++ KG A + + +SV LA+ L G + G I V+ ++
Sbjct: 55 VRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ 102
Score = 64.3 bits (157), Expect = 1e-12
Identities = 19/114 (16%), Positives = 43/114 (37%), Gaps = 14/114 (12%)
Query: 188 NPKAEEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVD 247
+ + + V P + ++ V+ L + + + G V
Sbjct: 3 SGSSGKSPVREPVDNLSPEE-----RDARTVFCMQLAARIRPRDLEDFFSAVGKV----- 52
Query: 248 TNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
+++ +D ++ KG A + + +SV LA+ L G + G I V+ ++
Sbjct: 53 ---RDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ 102
Score = 35.8 bits (83), Expect = 0.011
Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 374 QQDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+DL + S G V+ V ++ D+ +G+A + F E ++ L G+ I
Sbjct: 39 PRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPII 97
Score = 35.8 bits (83), Expect = 0.011
Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 659 QQDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+DL + S G V+ V ++ D+ +G+A + F E ++ L G+ I
Sbjct: 39 PRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPII 97
>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 = 63.4 bits (155), Expect = 1e-12
Identities = 24/93 (25%), Positives = 40/93 (43%), Gaps = 8/93 (8%)
Query: 208 WFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGD 267
+ + VYVSNLP LT + + K G V+K + + D T+ KG
Sbjct: 9 SGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVK--------VTIMKDKDTRKSKGV 60
Query: 268 ALCTYIKKESVDLALSILDGYEIRGKKIKVERA 300
A ++ K+S ++ ++ G+ IK A
Sbjct: 61 AFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93
Score = 59.9 bits (146), Expect = 2e-11
Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 8/85 (9%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
+ VYVSNLP LT + + K G V+K + + D T+ KG A ++ K
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVK--------VTIMKDKDTRKSKGVAFILFLDK 68
Query: 561 ESVDLALSILDGYEIRGKKIKVERA 585
+S ++ ++ G+ IK A
Sbjct: 69 DSAQNCTRAINNKQLFGRVIKASIA 93
Score = 42.6 bits (101), Expect = 2e-05
Identities = 27/96 (28%), Positives = 40/96 (41%), Gaps = 15/96 (15%)
Query: 338 PDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKH 396
M G + ++S + V NL +T DL SK G V KV ++ DK
Sbjct: 5 SSGMSGGLAPSKSTVYVSNL------PFSLT-----NNDLYRIFSKYGKVVKVTIMKDKD 53
Query: 397 ---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+GVA I F + ++A C +N + R I
Sbjct: 54 TRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIK 89
Score = 42.6 bits (101), Expect = 2e-05
Identities = 27/96 (28%), Positives = 40/96 (41%), Gaps = 15/96 (15%)
Query: 623 PDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKH 681
M G + ++S + V NL +T DL SK G V KV ++ DK
Sbjct: 5 SSGMSGGLAPSKSTVYVSNL------PFSLT-----NNDLYRIFSKYGKVVKVTIMKDKD 53
Query: 682 ---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+GVA I F + ++A C +N + R I
Sbjct: 54 TRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIK 89
>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 = 4e-12
Identities = 41/219 (18%), Positives = 75/219 (34%), Gaps = 59/219 (26%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+YV +L D+T+ E G ++ I++ D T+ G A +
Sbjct: 13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILS--------IRVCRDMITRRSLGYAYVNF 64
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEK 332
+ + AL ++ I+GK +++ ++ DP
Sbjct: 65 QQPADAERALDTMNFDVIKGKPVRIMWSQR-------DPS-------------------- 97
Query: 333 LFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK--KV 390
R I +KNL DK + + L + S G++ KV
Sbjct: 98 -----------LRKSGVGNIFIKNL------DKSID-----NKALYDTFSAFGNILSCKV 135
Query: 391 VLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
V + +G + F+ EAA+ E +NG R++
Sbjct: 136 VCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 174
Score = 65.0 bits (159), Expect = 6e-12
Identities = 41/218 (18%), Positives = 75/218 (34%), Gaps = 59/218 (27%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
+YV +L D+T+ E G ++ I++ D T+ G A +
Sbjct: 14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILS--------IRVCRDMITRRSLGYAYVNFQ 65
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKL 618
+ + AL ++ I+GK +++ ++ DP
Sbjct: 66 QPADAERALDTMNFDVIKGKPVRIMWSQR-------DPS--------------------- 97
Query: 619 FDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK--KVV 676
R I +KNL DK + + L + S G++ KVV
Sbjct: 98 ----------LRKSGVGNIFIKNL------DKSID-----NKALYDTFSAFGNILSCKVV 136
Query: 677 LHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ +G + F+ EAA+ E +NG R++
Sbjct: 137 CDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 174
Score = 48.4 bits (116), Expect = 2e-06
Identities = 39/276 (14%), Positives = 82/276 (29%), Gaps = 94/276 (34%)
Query: 342 RGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK---HP 397
S + + V +L DVT + L E+ S G + + V D
Sbjct: 8 PSAPSYPMASLYVGDL------HPDVT-----EAMLYEKFSPAGPILSIRVCRDMITRRS 56
Query: 398 EGVAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWET 457
G A + F++P A+ + +N
Sbjct: 57 LGYAYVNFQQPADAERALDTMNFDVIK--------------------------------- 83
Query: 458 FLGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEF 517
GK +++ ++ P ++ +++ NL + +
Sbjct: 84 --GKPVRIMWSQR-----------DPSLRKSGV----------GNIFIKNLDKSIDNKAL 120
Query: 518 VEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRG 577
+ G ++ K+ D KG + +E+ + A+ ++G +
Sbjct: 121 YDTFSAFGNILS--------CKVVCDENGS--KGYGFVHFETQEAAERAIEKMNGMLLND 170
Query: 578 KKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKK 613
+K+ V R K +K+R+ +L K
Sbjct: 171 RKVFVGRF-------------KSRKEREAELGARAK 193
Score = 38.0 bits (89), Expect = 0.005
Identities = 18/113 (15%), Positives = 41/113 (36%), Gaps = 23/113 (20%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
+++ NL + + + G ++ K+ D KG + +
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILS--------CKVVCDENGS--KGYGFVHFETQ 153
Query: 276 ESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKK 328
E+ + A+ ++G + +K+ V R K +K+R+ +L K
Sbjct: 154 EAAERAIEKMNGMLLNDRKVFVGRF-------------KSRKEREAELGARAK 193
Score = 35.7 bits (83), Expect = 0.029
Identities = 18/91 (19%), Positives = 33/91 (36%), Gaps = 15/91 (16%)
Query: 627 RGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK---HP 682
S + + V +L DVT + L E+ S G + + V D
Sbjct: 8 PSAPSYPMASLYVGDL------HPDVT-----EAMLYEKFSPAGPILSIRVCRDMITRRS 56
Query: 683 EGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
G A + F++P A+ + +N + +
Sbjct: 57 LGYAYVNFQQPADAERALDTMNFDVIKGKPV 87
>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 = 62.8 bits (153), Expect = 4e-12
Identities = 28/126 (22%), Positives = 51/126 (40%), Gaps = 16/126 (12%)
Query: 461 KKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEV 520
++ +K T P + KK+++K VYV N+ T ++
Sbjct: 4 PCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDK-------RSVYVGNVDYGSTAQDLEAH 56
Query: 521 MQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKI 580
CG + +I + D ++ KG A + ++ SVD A++ +D RG+ I
Sbjct: 57 FSSCGSI--------NRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTI 107
Query: 581 KVERAK 586
KV +
Sbjct: 108 KVLPKR 113
Score = 61.7 bits (150), Expect = 1e-11
Identities = 26/122 (21%), Positives = 46/122 (37%), Gaps = 13/122 (10%)
Query: 184 APMENPKAEEKVVPGQKRKPEPPKWFDIGEE----STKVYVSNLPLDLTQEEFVEVMQKC 239
A + + PP+ E+ VYV N+ T ++ C
Sbjct: 1 AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60
Query: 240 GLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVER 299
G + +I + D ++ KG A + ++ SVD A++ +D RG+ IKV
Sbjct: 61 GSI--------NRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKVLP 111
Query: 300 AK 301
+
Sbjct: 112 KR 113
Score = 36.6 bits (85), Expect = 0.006
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 374 QQDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
QDL S CG + ++ +L DK HP+G A I F E + DA ++ F R I
Sbjct: 50 AQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIK 108
Score = 36.6 bits (85), Expect = 0.006
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 659 QQDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
QDL S CG + ++ +L DK HP+G A I F E + DA ++ F R I
Sbjct: 50 AQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIK 108
>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 = 61.4 bits (150), Expect = 5e-12
Identities = 25/89 (28%), Positives = 40/89 (44%), Gaps = 9/89 (10%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
++ +YV N+ T EE CG V ++ + D ++ KG A +
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSV--------NRVTILCDKFSGHPKGFAYIEF 55
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
KESV +L+ LD RG++IKV +
Sbjct: 56 SDKESVRTSLA-LDESLFRGRQIKVIPKR 83
Score = 59.8 bits (146), Expect = 2e-11
Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 9/88 (10%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
+ +YV N+ T EE CG V ++ + D ++ KG A +
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSV--------NRVTILCDKFSGHPKGFAYIEFS 56
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAK 586
KESV +L+ LD RG++IKV +
Sbjct: 57 DKESVRTSLA-LDESLFRGRQIKVIPKR 83
Score = 37.9 bits (89), Expect = 0.001
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 5/60 (8%)
Query: 374 QQDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
++L CG V +V +L DK HP+G A I F + E+ L+ F RQI
Sbjct: 20 AEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLFRGRQIK 78
Score = 37.9 bits (89), Expect = 0.001
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 5/60 (8%)
Query: 659 QQDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
++L CG V +V +L DK HP+G A I F + E+ L+ F RQI
Sbjct: 20 AEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLFRGRQIK 78
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 61.3 bits (149), Expect = 9e-12
Identities = 17/116 (14%), Positives = 37/116 (31%), Gaps = 21/116 (18%)
Query: 500 NTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 559
+V + L ++ + ++ +K G V + +++ P T+ G A +
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEE--------VEILLHPRTRKHLGLARVLFTS 57
Query: 560 KESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQ 615
+ L + G I + D K ++R K E +
Sbjct: 58 TRGAKETVKNLHLTSVMGNIIHAQ----------LDIK---GQQRMKYYELIVNGS 100
Score = 61.3 bits (149), Expect = 1e-11
Identities = 17/116 (14%), Positives = 37/116 (31%), Gaps = 21/116 (18%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
+V + L ++ + ++ +K G V + +++ P T+ G A +
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEE--------VEILLHPRTRKHLGLARVLFTS 57
Query: 275 KESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQ 330
+ L + G I + D K ++R K E +
Sbjct: 58 TRGAKETVKNLHLTSVMGNIIHAQ----------LDIK---GQQRMKYYELIVNGS 100
Score = 51.2 bits (123), Expect = 3e-08
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 375 QDLREECSKCGHVKKVVLHDKHPE-----GVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
L++ C K G V++V + HP G+A++ F A + L+ I
Sbjct: 21 TFLKDMCRKYGEVEEVEIL-LHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIH 79
Query: 430 AE 431
A+
Sbjct: 80 AQ 81
Score = 51.2 bits (123), Expect = 3e-08
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 660 QDLREECSKCGHVKKVVLHDKHPE-----GVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
L++ C K G V++V + HP G+A++ F A + L+ I
Sbjct: 21 TFLKDMCRKYGEVEEVEIL-LHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIH 79
Query: 715 AE 716
A+
Sbjct: 80 AQ 81
>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 = 64.5 bits (157), Expect = 1e-11
Identities = 28/104 (26%), Positives = 51/104 (49%), Gaps = 14/104 (13%)
Query: 339 DKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH----- 393
D + +V++++N+ DP D D+ + ++ EEC K G V +V+++
Sbjct: 114 DANLAGSAMESTVMVLRNMVDPKDIDDDL------EGEVTEECGKFGAVNRVIIYQEKQG 167
Query: 394 -DKHPEGVAQIF--FKEPEAADACRELLNGRWFGQRQITAETWD 434
++ E + +IF F + LNGRWF R++ AE +D
Sbjct: 168 EEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD 211
Score = 64.5 bits (157), Expect = 1e-11
Identities = 28/104 (26%), Positives = 51/104 (49%), Gaps = 14/104 (13%)
Query: 624 DKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH----- 678
D + +V++++N+ DP D D+ + ++ EEC K G V +V+++
Sbjct: 114 DANLAGSAMESTVMVLRNMVDPKDIDDDL------EGEVTEECGKFGAVNRVIIYQEKQG 167
Query: 679 -DKHPEGVAQIF--FKEPEAADACRELLNGRWFGQRQITAETWD 719
++ E + +IF F + LNGRWF R++ AE +D
Sbjct: 168 EEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD 211
>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 = 62.1 bits (151), Expect = 1e-11
Identities = 20/122 (16%), Positives = 49/122 (40%), Gaps = 8/122 (6%)
Query: 180 VDATAPMENPKAEEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKC 239
V P +++ Q++ P + + + V+ +P + + + ++ ++
Sbjct: 7 VSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERY 66
Query: 240 GLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVER 299
G + +K+ D T+ +G + S A++ L+G+ I K++KV
Sbjct: 67 GPIES--------VKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL 118
Query: 300 AK 301
A
Sbjct: 119 AA 120
Score = 53.6 bits (129), Expect = 9e-09
Identities = 16/90 (17%), Positives = 38/90 (42%), Gaps = 8/90 (8%)
Query: 497 AQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 556
+ V+ +P + + + ++ ++ G + +K+ D T+ +G
Sbjct: 39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIES--------VKIVCDRETRQSRGYGFVK 90
Query: 557 YIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ S A++ L+G+ I K++KV A
Sbjct: 91 FQSGSSAQQAIAGLNGFNILNKRLKVALAA 120
>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 = 59.7 bits (145), Expect = 2e-11
Identities = 21/87 (24%), Positives = 33/87 (37%), Gaps = 15/87 (17%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
S+ + V NLP D +E ++++ L VD N K A T +
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRN---------------KRTAFVTLLN 49
Query: 275 KESVDLALSILDGYEIRGKKIKVERAK 301
E A+ + Y RGK + V+
Sbjct: 50 GEQAQNAIQMFHQYSFRGKDLIVQLQP 76
Score = 58.6 bits (142), Expect = 4e-11
Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 15/87 (17%)
Query: 500 NTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 559
++ + V NLP D +E ++++ L VD N K A T +
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRN---------------KRTAFVTLLN 49
Query: 560 KESVDLALSILDGYEIRGKKIKVERAK 586
E A+ + Y RGK + V+
Sbjct: 50 GEQAQNAIQMFHQYSFRGKDLIVQLQP 76
Score = 33.9 bits (78), Expect = 0.029
Identities = 13/86 (15%), Positives = 27/86 (31%), Gaps = 14/86 (16%)
Query: 346 SKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFF 405
S S I+VKNL +D Q++ + + + A +
Sbjct: 2 SSGSSGILVKNL------PQDSN-----CQEVHDLLKDYD---LKYCYVDRNKRTAFVTL 47
Query: 406 KEPEAADACRELLNGRWFGQRQITAE 431
E A ++ + F + + +
Sbjct: 48 LNGEQAQNAIQMFHQYSFRGKDLIVQ 73
Score = 33.9 bits (78), Expect = 0.029
Identities = 13/86 (15%), Positives = 27/86 (31%), Gaps = 14/86 (16%)
Query: 631 SKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFF 690
S S I+VKNL +D Q++ + + + A +
Sbjct: 2 SSGSSGILVKNL------PQDSN-----CQEVHDLLKDYD---LKYCYVDRNKRTAFVTL 47
Query: 691 KEPEAADACRELLNGRWFGQRQITAE 716
E A ++ + F + + +
Sbjct: 48 LNGEQAQNAIQMFHQYSFRGKDLIVQ 73
>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 = 59.2 bits (144), Expect = 4e-11
Identities = 23/87 (26%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
S VY+ ++P D T+E+ +++ G V+ +K+ DP T KG A +
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVIN--------LKMMFDPQTGRSKGYAFIEFRD 53
Query: 275 KESVDLALSILDGYEIRGKKIKVERAK 301
ES A+ L+GY++ + +K +
Sbjct: 54 LESSASAVRNLNGYQLGSRFLKCGYSS 80
Score = 56.9 bits (138), Expect = 2e-10
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 8/86 (9%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
VY+ ++P D T+E+ +++ G V+ +K+ DP T KG A +
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVIN--------LKMMFDPQTGRSKGYAFIEFRDL 54
Query: 561 ESVDLALSILDGYEIRGKKIKVERAK 586
ES A+ L+GY++ + +K +
Sbjct: 55 ESSASAVRNLNGYQLGSRFLKCGYSS 80
Score = 33.7 bits (78), Expect = 0.034
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 375 QDLREECSKCGHVKKVVL-HDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+ + + CS G V + + D +G A I F++ E++ + LNG G R +
Sbjct: 17 EQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLK 75
Score = 33.7 bits (78), Expect = 0.034
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 660 QDLREECSKCGHVKKVVL-HDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ + + CS G V + + D +G A I F++ E++ + LNG G R +
Sbjct: 17 EQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLK 75
>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 = 58.5 bits (142), Expect = 6e-11
Identities = 14/89 (15%), Positives = 34/89 (38%), Gaps = 8/89 (8%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
T + V N+P ++ +E ++ ++ V L + G+A+
Sbjct: 12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSV-------CLKYNEKGM-PTGEAMVA 63
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERA 300
+ ++ A+ L+ I +K+K+
Sbjct: 64 FESRDEATAAVIDLNDRPIGSRKVKLSGP 92
Score = 57.3 bits (139), Expect = 2e-10
Identities = 14/87 (16%), Positives = 34/87 (39%), Gaps = 8/87 (9%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
T + V N+P ++ +E ++ ++ V L + G+A+ +
Sbjct: 14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSV-------CLKYNEKGM-PTGEAMVAFE 65
Query: 559 KKESVDLALSILDGYEIRGKKIKVERA 585
++ A+ L+ I +K+K+
Sbjct: 66 SRDEATAAVIDLNDRPIGSRKVKLSGP 92
Score = 35.7 bits (83), Expect = 0.007
Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 17/85 (20%)
Query: 349 ESVIIVKNL-FDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPE----GVAQI 403
+VI V+N+ F V+ ++ + + V + + G A +
Sbjct: 15 PTVIKVQNMPFT-------VS-----IDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62
Query: 404 FFKEPEAADACRELLNGRWFGQRQI 428
F+ + A A LN R G R++
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKV 87
Score = 35.7 bits (83), Expect = 0.007
Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 17/85 (20%)
Query: 634 ESVIIVKNL-FDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPE----GVAQI 688
+VI V+N+ F V+ ++ + + V + + G A +
Sbjct: 15 PTVIKVQNMPFT-------VS-----IDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62
Query: 689 FFKEPEAADACRELLNGRWFGQRQI 713
F+ + A A LN R G R++
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKV 87
>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 = 60.2 bits (146), Expect = 8e-11
Identities = 21/105 (20%), Positives = 43/105 (40%), Gaps = 8/105 (7%)
Query: 482 KPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 541
+ + R + E+ K +++ +YV NL T+E+ E+ K G + KI +
Sbjct: 21 RDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI--------KKIIMG 72
Query: 542 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
D K G Y + + A+ ++G + + I+ +
Sbjct: 73 LDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA 117
Score = 60.2 bits (146), Expect = 8e-11
Identities = 20/103 (19%), Positives = 41/103 (39%), Gaps = 8/103 (7%)
Query: 199 QKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTD 258
Q + + + + ++S +YV NL T+E+ E+ K G + KI + D
Sbjct: 23 QHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI--------KKIIMGLD 74
Query: 259 PYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
K G Y + + A+ ++G + + I+ +
Sbjct: 75 KMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA 117
Score = 42.1 bits (99), Expect = 1e-04
Identities = 22/108 (20%), Positives = 40/108 (37%), Gaps = 16/108 (14%)
Query: 327 KKAQEKLFDWRPDKMRGERSKNESVII-VKNLFDPALFDKDVTLILEYQQDLREECSKCG 385
+ +Q + +R D E+ +S + V NL T ++ + E SK G
Sbjct: 16 ELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNL------SFYTT-----EEQIYELFSKSG 64
Query: 386 HVKKVVL----HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+KK+++ K G + + A+ +NG R I
Sbjct: 65 DIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIR 112
Score = 42.1 bits (99), Expect = 1e-04
Identities = 22/108 (20%), Positives = 40/108 (37%), Gaps = 16/108 (14%)
Query: 612 KKAQEKLFDWRPDKMRGERSKNESVII-VKNLFDPALFDKDVTLILEYQQDLREECSKCG 670
+ +Q + +R D E+ +S + V NL T ++ + E SK G
Sbjct: 16 ELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNL------SFYTT-----EEQIYELFSKSG 64
Query: 671 HVKKVVL----HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+KK+++ K G + + A+ +NG R I
Sbjct: 65 DIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIR 112
>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 = 57.7 bits (140), Expect = 1e-10
Identities = 14/90 (15%), Positives = 34/90 (37%), Gaps = 8/90 (8%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
T + V N+P ++ +E ++ ++ V L + G+A+
Sbjct: 12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSV-------CLKYNEKGM-PTGEAMVA 63
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ ++ A+ L+ I +K+K+
Sbjct: 64 FESRDEATAAVIDLNDRPIGSRKVKLVLGS 93
Score = 56.5 bits (137), Expect = 3e-10
Identities = 14/88 (15%), Positives = 34/88 (38%), Gaps = 8/88 (9%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
T + V N+P ++ +E ++ ++ V L + G+A+ +
Sbjct: 14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSV-------CLKYNEKGM-PTGEAMVAFE 65
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAK 586
++ A+ L+ I +K+K+
Sbjct: 66 SRDEATAAVIDLNDRPIGSRKVKLVLGS 93
Score = 35.3 bits (82), Expect = 0.010
Identities = 17/86 (19%), Positives = 31/86 (36%), Gaps = 17/86 (19%)
Query: 348 NESVIIVKNL-FDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL----HDKHPEGVAQ 402
++I V+N+ F V+ ++ + + V P G A
Sbjct: 14 GPTIIKVQNMPFT-------VS-----IDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61
Query: 403 IFFKEPEAADACRELLNGRWFGQRQI 428
+ F+ + A A LN R G R++
Sbjct: 62 VAFESRDEATAAVIDLNDRPIGSRKV 87
Score = 35.3 bits (82), Expect = 0.010
Identities = 17/86 (19%), Positives = 31/86 (36%), Gaps = 17/86 (19%)
Query: 633 NESVIIVKNL-FDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL----HDKHPEGVAQ 687
++I V+N+ F V+ ++ + + V P G A
Sbjct: 14 GPTIIKVQNMPFT-------VS-----IDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61
Query: 688 IFFKEPEAADACRELLNGRWFGQRQI 713
+ F+ + A A LN R G R++
Sbjct: 62 VAFESRDEATAAVIDLNDRPIGSRKV 87
>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 = 58.0 bits (141), Expect = 1e-10
Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 8/89 (8%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
V+V N+P + T+E+ ++ + G V+ +L D T KG C Y
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVS--------FRLVYDRETGKPKGYGFCEY 57
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
+E+ A+ L+G E G+ ++V+ A
Sbjct: 58 QDQETALSAMRNLNGREFSGRALRVDNAA 86
Score = 55.7 bits (135), Expect = 7e-10
Identities = 23/89 (25%), Positives = 42/89 (47%), Gaps = 8/89 (8%)
Query: 498 QENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 557
+ V+V N+P + T+E+ ++ + G V+ +L D T KG C Y
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVS--------FRLVYDRETGKPKGYGFCEY 57
Query: 558 IKKESVDLALSILDGYEIRGKKIKVERAK 586
+E+ A+ L+G E G+ ++V+ A
Sbjct: 58 QDQETALSAMRNLNGREFSGRALRVDNAA 86
Score = 29.1 bits (66), Expect = 1.6
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 374 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
++ L++ S+ G V +++D+ P+G +++ E A + LNGR F R +
Sbjct: 22 EEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALR 81
Score = 29.1 bits (66), Expect = 1.6
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 659 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
++ L++ S+ G V +++D+ P+G +++ E A + LNGR F R +
Sbjct: 22 EEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALR 81
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 57.5 bits (139), Expect = 2e-10
Identities = 20/105 (19%), Positives = 35/105 (33%), Gaps = 15/105 (14%)
Query: 197 PGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 256
G PP + + VYV NLP D + +++ G V +
Sbjct: 3 SGSSGPGSPPG--EGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTW-------- 52
Query: 257 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ + A Y + A+S L G + ++V A+
Sbjct: 53 -----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 92
Score = 54.1 bits (130), Expect = 3e-09
Identities = 18/90 (20%), Positives = 31/90 (34%), Gaps = 13/90 (14%)
Query: 497 AQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 556
A VYV NLP D + +++ G V + + + A
Sbjct: 16 APLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTW-------------QGPRRRAFLH 62
Query: 557 YIKKESVDLALSILDGYEIRGKKIKVERAK 586
Y + A+S L G + ++V A+
Sbjct: 63 YPDSAAAQQAVSCLQGLRLGTDTLRVALAR 92
Score = 29.0 bits (65), Expect = 1.7
Identities = 12/57 (21%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 375 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
DL+ + G V + L + P A + + + AA L G G +
Sbjct: 34 SDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVA 89
Score = 29.0 bits (65), Expect = 1.7
Identities = 12/57 (21%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 660 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
DL+ + G V + L + P A + + + AA L G G +
Sbjct: 34 SDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVA 89
>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 = 57.2 bits (139), Expect = 2e-10
Identities = 19/90 (21%), Positives = 40/90 (44%), Gaps = 8/90 (8%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
+ + V NL + + V +K G V + + +P+TK +G A
Sbjct: 10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGD--------VYIPREPHTKAPRGFAFVR 61
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ + A + +DG E+ G++++V+ A+
Sbjct: 62 FHDRRDAQDAEAAMDGAELDGRELRVQVAR 91
Score = 56.1 bits (136), Expect = 6e-10
Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 8/87 (9%)
Query: 500 NTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 559
+ V NL + + V +K G V + + +P+TK +G A +
Sbjct: 13 MITLKVDNLTYRTSPDSLRRVFEKYGRVGD--------VYIPREPHTKAPRGFAFVRFHD 64
Query: 560 KESVDLALSILDGYEIRGKKIKVERAK 586
+ A + +DG E+ G++++V+ A+
Sbjct: 65 RRDAQDAEAAMDGAELDGRELRVQVAR 91
Score = 36.0 bits (84), Expect = 0.007
Identities = 14/60 (23%), Positives = 22/60 (36%), Gaps = 4/60 (6%)
Query: 374 QQDLREECSKCGHVKKVVL-HDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
LR K G V V + + H P G A + F + A ++G R++
Sbjct: 27 PDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR 86
Score = 36.0 bits (84), Expect = 0.007
Identities = 14/60 (23%), Positives = 22/60 (36%), Gaps = 4/60 (6%)
Query: 659 QQDLREECSKCGHVKKVVL-HDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
LR K G V V + + H P G A + F + A ++G R++
Sbjct: 27 PDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR 86
>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 = 57.6 bits (140), Expect = 2e-10
Identities = 34/168 (20%), Positives = 56/168 (33%), Gaps = 63/168 (37%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK--KVVLHDKHPEGVAQIFFKEPE 409
I +KNL DK + + L + S G++ KVV + +G + F+ E
Sbjct: 8 IFIKNL------DKSID-----NKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQE 56
Query: 410 AADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLGKKIKVERAK 469
AA+ E +NG +K+ V R
Sbjct: 57 AAERAIEKMNGMLLN-----------------------------------DRKVFVGRF- 80
Query: 470 FTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEF 517
K +K+R+ +L +A+E T VY+ N T+
Sbjct: 81 ------------KSRKEREAELG--ARAKEFTNVYIKNFGPGSTRAAA 114
Score = 44.2 bits (105), Expect = 1e-05
Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 13/80 (16%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK--KVVLHDKHPEGVAQIFFKEPE 694
I +KNL DK + + L + S G++ KVV + +G + F+ E
Sbjct: 8 IFIKNL------DKSID-----NKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQE 56
Query: 695 AADACRELLNGRWFGQRQIT 714
AA+ E +NG R++
Sbjct: 57 AAERAIEKMNGMLLNDRKVF 76
Score = 41.9 bits (99), Expect = 6e-05
Identities = 19/120 (15%), Positives = 44/120 (36%), Gaps = 23/120 (19%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
S +++ NL + + + G ++ K+ D KG +
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILS--------CKVVCDENGS--KGYGFVHFET 54
Query: 275 KESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLF 334
+E+ + A+ ++G + +K+ V R K +K+R+ +L K ++
Sbjct: 55 QEAAERAIEKMNGMLLNDRKVFVGRF-------------KSRKEREAELGARAKEFTNVY 101
Score = 41.1 bits (97), Expect = 1e-04
Identities = 18/119 (15%), Positives = 43/119 (36%), Gaps = 23/119 (19%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
+++ NL + + + G ++ K+ D KG + +
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILS--------CKVVCDENGS--KGYGFVHFETQ 55
Query: 561 ESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLF 619
E+ + A+ ++G + +K+ V R K +K+R+ +L K ++
Sbjct: 56 EAAERAIEKMNGMLLNDRKVFVGRF-------------KSRKEREAELGARAKEFTNVY 101
Score = 31.8 bits (73), Expect = 0.22
Identities = 9/39 (23%), Positives = 14/39 (35%)
Query: 194 KVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEF 232
V + RK + +E T VY+ N T+
Sbjct: 76 FVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRAAA 114
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 58.2 bits (141), Expect = 2e-10
Identities = 26/118 (22%), Positives = 47/118 (39%), Gaps = 14/118 (11%)
Query: 184 APMENPKAEEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVM 243
A M + + R P E T + V NL + + V +K G V
Sbjct: 22 ASMTGGQQMGRGSMSYGRPPPDV------EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVG 75
Query: 244 KDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ + D YTK+ +G A + K + A+ +DG + G++++V+ A+
Sbjct: 76 D--------VYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 125
Score = 55.5 bits (134), Expect = 2e-09
Identities = 21/105 (20%), Positives = 43/105 (40%), Gaps = 8/105 (7%)
Query: 482 KPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 541
+ + + T + V NL + + V +K G V + +
Sbjct: 29 QMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGD--------VYIP 80
Query: 542 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
D YTK+ +G A + K + A+ +DG + G++++V+ A+
Sbjct: 81 RDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 125
Score = 38.2 bits (89), Expect = 0.002
Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 4/60 (6%)
Query: 374 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
LR K G V V + D++ G A + F + A+ + ++G R++
Sbjct: 61 PDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR 120
Score = 38.2 bits (89), Expect = 0.002
Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 4/60 (6%)
Query: 659 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
LR K G V V + D++ G A + F + A+ + ++G R++
Sbjct: 61 PDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR 120
>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 = 57.8 bits (140), Expect = 3e-10
Identities = 20/124 (16%), Positives = 41/124 (33%), Gaps = 8/124 (6%)
Query: 178 KSVDATAPMENPKAEEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQ 237
P + A R + + + V L L T+ + EV
Sbjct: 9 HHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFS 68
Query: 238 KCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKV 297
K G + + + D ++ +G A + + A +G E+ G++I+V
Sbjct: 69 KYGPIAD--------VSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120
Query: 298 ERAK 301
+ +
Sbjct: 121 DFSI 124
Score = 54.0 bits (130), Expect = 7e-09
Identities = 18/105 (17%), Positives = 40/105 (38%), Gaps = 8/105 (7%)
Query: 482 KPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 541
+ + + + N + V L L T+ + EV K G + + +
Sbjct: 28 QQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIAD--------VSIV 79
Query: 542 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
D ++ +G A + + A +G E+ G++I+V+ +
Sbjct: 80 YDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSI 124
Score = 39.3 bits (92), Expect = 8e-04
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 374 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
++DLRE SK G + V +++D+ G A ++F+ + A +E NG R+I
Sbjct: 60 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 119
Score = 39.3 bits (92), Expect = 8e-04
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 659 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
++DLRE SK G + V +++D+ G A ++F+ + A +E NG R+I
Sbjct: 60 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 119
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 56.5 bits (137), Expect = 3e-10
Identities = 24/101 (23%), Positives = 39/101 (38%), Gaps = 9/101 (8%)
Query: 201 RKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPY 260
+ E K+++S LP T+EE E+ + G V ++L T+
Sbjct: 3 SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKD--------LRLVTNR- 53
Query: 261 TKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
KG A Y + A+ +DG I+ IKV +
Sbjct: 54 AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISN 94
Score = 55.0 bits (133), Expect = 1e-09
Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 9/88 (10%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
E K+++S LP T+EE E+ + G V ++L T+ KG A Y
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKD--------LRLVTNR-AGKPKGLAYVEYE 66
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAK 586
+ A+ +DG I+ IKV +
Sbjct: 67 NESQASQAVMKMDGMTIKENIIKVAISN 94
Score = 40.0 bits (94), Expect = 2e-04
Identities = 16/96 (16%), Positives = 35/96 (36%), Gaps = 14/96 (14%)
Query: 337 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK 395
R S + + + L T +++L E C G VK + ++ ++
Sbjct: 5 SSGVFRYSTSLEKHKLFISGL------PFSCT-----KEELEEICKAHGTVKDLRLVTNR 53
Query: 396 --HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
P+G+A + ++ A ++G + I
Sbjct: 54 AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIK 89
Score = 40.0 bits (94), Expect = 2e-04
Identities = 16/96 (16%), Positives = 35/96 (36%), Gaps = 14/96 (14%)
Query: 622 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK 680
R S + + + L T +++L E C G VK + ++ ++
Sbjct: 5 SSGVFRYSTSLEKHKLFISGL------PFSCT-----KEELEEICKAHGTVKDLRLVTNR 53
Query: 681 --HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
P+G+A + ++ A ++G + I
Sbjct: 54 AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIK 89
>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 = 58.3 bits (142), Expect = 4e-10
Identities = 33/216 (15%), Positives = 61/216 (28%), Gaps = 62/216 (28%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
+YV NL +T++ + Q G + IK+ D A Y +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIAN--------IKIMIDK-NNKNVNYAFVEYHQSHD 53
Query: 278 VDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLFDWR 337
++AL L+G +I +K+ A ++ D LF
Sbjct: 54 ANIALQTLNGKQIENNIVKINWA-------------FQSQQSSSD------DTFNLF--- 91
Query: 338 PDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK--KVVLHDK 395
V +L + +V + LR V+ +
Sbjct: 92 ----------------VGDL------NVNVD-----DETLRNAFKDFPSYLSGHVMWDMQ 124
Query: 396 --HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
G + F + A + + G+ R +
Sbjct: 125 TGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR 160
Score = 58.3 bits (142), Expect = 4e-10
Identities = 33/216 (15%), Positives = 61/216 (28%), Gaps = 62/216 (28%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
+YV NL +T++ + Q G + IK+ D A Y +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIAN--------IKIMIDK-NNKNVNYAFVEYHQSHD 53
Query: 563 VDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLFDWR 622
++AL L+G +I +K+ A ++ D LF
Sbjct: 54 ANIALQTLNGKQIENNIVKINWA-------------FQSQQSSSD------DTFNLF--- 91
Query: 623 PDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK--KVVLHDK 680
V +L + +V + LR V+ +
Sbjct: 92 ----------------VGDL------NVNVD-----DETLRNAFKDFPSYLSGHVMWDMQ 124
Query: 681 --HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
G + F + A + + G+ R +
Sbjct: 125 TGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR 160
Score = 44.1 bits (105), Expect = 3e-05
Identities = 28/237 (11%), Positives = 70/237 (29%), Gaps = 78/237 (32%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK--HPEGVAQIFFKEP 408
+ V NL DK +T + L++ G + + ++ DK A + + +
Sbjct: 3 LYVGNL------DKAIT-----EDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQS 51
Query: 409 EAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLGKKIKVERA 468
A+ + LNG+ +K+ A
Sbjct: 52 HDANIALQTLNGK-----------------------------------QIENNIVKINWA 76
Query: 469 KFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVM 528
++ D + ++V +L +++ E + +
Sbjct: 77 F-------------QSQQSSSD--------DTFNLFVGDLNVNVDDETLRNAFKDFPSYL 115
Query: 529 KDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 585
+ D T +G ++ ++ A+ + G ++ G+ +++ A
Sbjct: 116 S--------GHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
Score = 36.7 bits (86), Expect = 0.009
Identities = 10/88 (11%), Positives = 35/88 (39%), Gaps = 8/88 (9%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+++ ++V +L +++ E + + + D T +G ++
Sbjct: 85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLS--------GHVMWDMQTGSSRGYGFVSF 136
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERA 300
++ A+ + G ++ G+ +++ A
Sbjct: 137 TSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>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 = 59.7 bits (144), Expect = 4e-10
Identities = 24/133 (18%), Positives = 42/133 (31%), Gaps = 6/133 (4%)
Query: 169 DLVQSKVEEKSVDATAPMENPKAEEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLT 228
D V S V + P + + +Y+ NL T
Sbjct: 22 DDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTT 81
Query: 229 QEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGY 288
E+ E + G+ D+ ++IK + + KG AL + S + +L
Sbjct: 82 DEDLTEAVHSLGVN--DI----LEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKR 135
Query: 289 EIRGKKIKVERAK 301
E+ G+ V
Sbjct: 136 ELHGQNPVVTPVN 148
Score = 52.4 bits (125), Expect = 1e-07
Identities = 19/88 (21%), Positives = 35/88 (39%), Gaps = 6/88 (6%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
+ +Y+ NL T E+ E + G+ D+ ++IK + + KG AL
Sbjct: 67 KRIALYIGNLTWWTTDEDLTEAVHSLGVN--DI----LEIKFFENRANGQSKGFALVGVG 120
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAK 586
+ S + +L E+ G+ V
Sbjct: 121 SEASSKKLMDLLPKRELHGQNPVVTPVN 148
Score = 39.3 bits (91), Expect = 0.003
Identities = 9/61 (14%), Positives = 19/61 (31%), Gaps = 6/61 (9%)
Query: 375 QDLREECSKCGHVKKV---VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
+DL E G + ++ +G A + ++ +LL R +
Sbjct: 83 EDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNP 142
Query: 429 T 429
Sbjct: 143 V 143
Score = 39.3 bits (91), Expect = 0.003
Identities = 9/61 (14%), Positives = 19/61 (31%), Gaps = 6/61 (9%)
Query: 660 QDLREECSKCGHVKKV---VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
+DL E G + ++ +G A + ++ +LL R +
Sbjct: 83 EDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNP 142
Query: 714 T 714
Sbjct: 143 V 143
>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 = 60.1 bits (146), Expect = 5e-10
Identities = 37/243 (15%), Positives = 70/243 (28%), Gaps = 87/243 (35%)
Query: 480 KLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCG-----LVMKDVDTN 534
K K EK + +++V NLP D+T+E+F + ++ G + +D
Sbjct: 4 FTIDIKSFLKPGEK--TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD---- 57
Query: 535 QMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAY 594
+G + ++A + LDG ++ + +++ A
Sbjct: 58 ---------------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA--------- 93
Query: 595 DPKLKPKKKRKKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTL 654
+ VKNL V+
Sbjct: 94 ----------------------------------THGAA---LTVKNL------SPVVS- 109
Query: 655 ILEYQQDLREECSKCGHVKKV-VLHDKH--PEGVAQIFFKEPEAAD-ACRELLNGRWFGQ 710
+ L + S+ G V+K V+ D G + F A A +G +
Sbjct: 110 ----NELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLT 165
Query: 711 RQI 713
Sbjct: 166 TTP 168
Score = 59.3 bits (144), Expect = 7e-10
Identities = 36/241 (14%), Positives = 68/241 (28%), Gaps = 90/241 (37%)
Query: 202 KPEPPKWFDIGEE-----STKVYVSNLPLDLTQEEFVEVMQKCG-----LVMKDVDTNQM 251
K F E +++V NLP D+T+E+F + ++ G + +D
Sbjct: 4 FTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------ 57
Query: 252 KIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDP 311
+G + ++A + LDG ++ + +++ A
Sbjct: 58 -------------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA----------- 93
Query: 312 KLKPKKKRKKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLIL 371
+ VKNL V+
Sbjct: 94 --------------------------------THGAA---LTVKNL------SPVVS--- 109
Query: 372 EYQQDLREECSKCGHVKKV-VLHDKH--PEGVAQIFFKEPEAAD-ACRELLNGRWFGQRQ 427
+ L + S+ G V+K V+ D G + F A A +G +
Sbjct: 110 --NELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTT 167
Query: 428 I 428
Sbjct: 168 P 168
Score = 40.8 bits (96), Expect = 9e-04
Identities = 36/291 (12%), Positives = 71/291 (24%), Gaps = 103/291 (35%)
Query: 327 KKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGH 386
K F +K +R + + V NL D+T ++D + + G
Sbjct: 4 FTIDIKSFLKPGEKTYTQRCR----LFVGNL------PTDIT-----EEDFKRLFERYGE 48
Query: 387 VKKVVLH-DKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETA 445
+V ++ D+ G I + A+ + L+G
Sbjct: 49 PSEVFINRDR---GFGFIRLESRTLAEIAKAELDGTILK--------------------- 84
Query: 446 EEREARLKKWETFLGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYV 505
+ +++ A + V
Sbjct: 85 --------------SRPLRIR-----------------------------FATHGAALTV 101
Query: 506 SNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDL 565
NL ++ E + + G V K + D + G + K
Sbjct: 102 KNLSPVVSNELLEQAFSQFGPV--------EKAVVVVDDRGRA-TGKGFVEFAAKPPARK 152
Query: 566 ALSIL-DGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQ 615
AL DG + + + ++ EKL +
Sbjct: 153 ALERCGDGAFLLTTTPRPVIVEP----------MEQFDDEDGLPEKLMQKT 193
Score = 31.6 bits (72), Expect = 0.88
Identities = 17/117 (14%), Positives = 31/117 (26%), Gaps = 20/117 (17%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
+ V NL ++ E + + G V K + D + G +
Sbjct: 96 GAALTVKNLSPVVSNELLEQAFSQFGPV--------EKAVVVVDDRGRA-TGKGFVEFAA 146
Query: 275 KESVDLALSIL-DGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQ 330
K AL DG + + + ++ EKL +
Sbjct: 147 KPPARKALERCGDGAFLLTTTPRPVIVEP----------MEQFDDEDGLPEKLMQKT 193
>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 = 55.7 bits (135), Expect = 5e-10
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 9/88 (10%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
E V+V NL + +E E+ + G + K + + D K K +
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTK--------VTICKDREGKP-KSFGFVCF 64
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERA 300
ESV A+++L+G + G+ I V
Sbjct: 65 KHPESVSYAIALLNGIRLYGRPINVSGP 92
Score = 54.9 bits (133), Expect = 1e-09
Identities = 20/91 (21%), Positives = 38/91 (41%), Gaps = 9/91 (9%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+ + + V+V NL + +E E+ + G + K + + D K K
Sbjct: 11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTK--------VTICKDREGKP-KSFGF 61
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERA 585
+ ESV A+++L+G + G+ I V
Sbjct: 62 VCFKHPESVSYAIALLNGIRLYGRPINVSGP 92
Score = 43.4 bits (103), Expect = 1e-05
Identities = 24/93 (25%), Positives = 37/93 (39%), Gaps = 18/93 (19%)
Query: 341 MRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEG 399
M + + + + V NL + V ++ L E + G + KV + D+ EG
Sbjct: 8 MFPAQEEADRTVFVGNL------EARVR-----EEILYELFLQAGPLTKVTICKDR--EG 54
Query: 400 VAQIF----FKEPEAADACRELLNGRWFGQRQI 428
+ F FK PE+ LLNG R I
Sbjct: 55 KPKSFGFVCFKHPESVSYAIALLNGIRLYGRPI 87
Score = 43.4 bits (103), Expect = 1e-05
Identities = 24/93 (25%), Positives = 37/93 (39%), Gaps = 18/93 (19%)
Query: 626 MRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEG 684
M + + + + V NL + V ++ L E + G + KV + D+ EG
Sbjct: 8 MFPAQEEADRTVFVGNL------EARVR-----EEILYELFLQAGPLTKVTICKDR--EG 54
Query: 685 VAQIF----FKEPEAADACRELLNGRWFGQRQI 713
+ F FK PE+ LLNG R I
Sbjct: 55 KPKSFGFVCFKHPESVSYAIALLNGIRLYGRPI 87
>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 = 55.7 bits (135), Expect = 7e-10
Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 8/89 (8%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+++ + V+NL D + + E+ + G + + I L D T KG A ++
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFGSISR--------IYLAKDKTTGQSKGFAFISF 64
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
++E A++ + G+ + VE AK
Sbjct: 65 HRREDAARAIAGVSGFGYDHLILNVEWAK 93
Score = 55.3 bits (134), Expect = 1e-09
Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 8/92 (8%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
++A +N + V+NL D + + E+ + G + + I L D T KG A
Sbjct: 10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISR--------IYLAKDKTTGQSKGFAF 61
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
++ ++E A++ + G+ + VE AK
Sbjct: 62 ISFHRREDAARAIAGVSGFGYDHLILNVEWAK 93
Score = 38.0 bits (89), Expect = 0.001
Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 4/62 (6%)
Query: 374 QQDLREECSKCGHVKKVVLH-DKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+ DL+E G + ++ L DK +G A I F E A ++G + +
Sbjct: 29 ETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN 88
Query: 430 AE 431
E
Sbjct: 89 VE 90
Score = 38.0 bits (89), Expect = 0.001
Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 4/62 (6%)
Query: 659 QQDLREECSKCGHVKKVVLH-DKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ DL+E G + ++ L DK +G A I F E A ++G + +
Sbjct: 29 ETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN 88
Query: 715 AE 716
E
Sbjct: 89 VE 90
>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 = 56.6 bits (137), Expect = 7e-10
Identities = 22/112 (19%), Positives = 43/112 (38%), Gaps = 12/112 (10%)
Query: 190 KAEEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTN 249
+ + V +P P + E ++V+ + + T+E+ + + G +
Sbjct: 1 REDYDSVEQDGDEPGPQR----SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKN----- 51
Query: 250 QMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
I L D T KG L Y + A+ L+G ++ G+ I V+
Sbjct: 52 ---IHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 100
Score = 53.9 bits (130), Expect = 6e-09
Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 8/91 (8%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 555
++ E ++V+ + + T+E+ + + G + I L D T KG L
Sbjct: 18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKN--------IHLNLDRRTGYLKGYTLV 69
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKVERAK 586
Y + A+ L+G ++ G+ I V+
Sbjct: 70 EYETYKEAQAAMEGLNGQDLMGQPISVDWCF 100
Score = 30.8 bits (70), Expect = 0.55
Identities = 18/97 (18%), Positives = 43/97 (44%), Gaps = 15/97 (15%)
Query: 337 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL-HDK 395
D+ +RS ++ V + ++ T ++D+ ++ ++ G +K + L D+
Sbjct: 10 DGDEPGPQRSVEGWILFVTGV------HEEAT-----EEDIHDKFAEYGEIKNIHLNLDR 58
Query: 396 H---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+G + ++ + A A E LNG+ + I+
Sbjct: 59 RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS 95
Score = 30.8 bits (70), Expect = 0.55
Identities = 18/97 (18%), Positives = 43/97 (44%), Gaps = 15/97 (15%)
Query: 622 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL-HDK 680
D+ +RS ++ V + ++ T ++D+ ++ ++ G +K + L D+
Sbjct: 10 DGDEPGPQRSVEGWILFVTGV------HEEAT-----EEDIHDKFAEYGEIKNIHLNLDR 58
Query: 681 H---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+G + ++ + A A E LNG+ + I+
Sbjct: 59 RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS 95
>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 = 56.8 bits (137), Expect = 1e-09
Identities = 25/149 (16%), Positives = 52/149 (34%), Gaps = 11/149 (7%)
Query: 153 GFIEQPNTVDEKKPSADLVQSKVEEKSVDATAPMENPKAEEKVVPGQKRKPEPPKWFDIG 212
+ T +A+ V + + + + V +
Sbjct: 11 TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVE-- 68
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
T + V NL + + V +K G V + + D YTK+ +G A +
Sbjct: 69 -GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGD--------VYIPRDRYTKESRGFAFVRF 119
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
K + A+ +DG + G++++V+ A+
Sbjct: 120 HDKRDAEDAMDAMDGAVLDGRELRVQMAR 148
Score = 52.1 bits (125), Expect = 5e-08
Identities = 22/109 (20%), Positives = 43/109 (39%), Gaps = 8/109 (7%)
Query: 478 DPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMK 537
K + + T + V NL + + V +K G V
Sbjct: 48 ATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGD-------- 99
Query: 538 IKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ + D YTK+ +G A + K + A+ +DG + G++++V+ A+
Sbjct: 100 VYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 148
Score = 34.0 bits (78), Expect = 0.077
Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 4/60 (6%)
Query: 374 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
LR K G V V + D++ G A + F + A+ + ++G R++
Sbjct: 84 PDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR 143
Score = 34.0 bits (78), Expect = 0.077
Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 4/60 (6%)
Query: 659 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
LR K G V V + D++ G A + F + A+ + ++G R++
Sbjct: 84 PDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR 143
>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 = 55.0 bits (133), Expect = 1e-09
Identities = 22/92 (23%), Positives = 43/92 (46%), Gaps = 14/92 (15%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
K + ++++V NLP D+T+EE ++ +K G ++ ++ D KG
Sbjct: 10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKA--------GEVFIHKD------KGFGF 55
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ ++A LD +RGK+++V A
Sbjct: 56 IRLETRTLAEIAKVELDNMPLRGKQLRVRFAC 87
Score = 53.0 bits (128), Expect = 6e-09
Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 14/88 (15%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
+ ++++V NLP D+T+EE ++ +K G ++ ++ D KG
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEKYGKA--------GEVFIHKD------KGFGFIRLE 59
Query: 274 KKESVDLALSILDGYEIRGKKIKVERAK 301
+ ++A LD +RGK+++V A
Sbjct: 60 TRTLAEIAKVELDNMPLRGKQLRVRFAC 87
Score = 36.9 bits (86), Expect = 0.003
Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 15/86 (17%)
Query: 344 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-DKHPEGVAQ 402
+ S + V NL D+T ++++R+ K G +V +H DK G
Sbjct: 10 KTFTQRSRLFVGNL------PPDIT-----EEEMRKLFEKYGKAGEVFIHKDK---GFGF 55
Query: 403 IFFKEPEAADACRELLNGRWFGQRQI 428
I + A+ + L+ +Q+
Sbjct: 56 IRLETRTLAEIAKVELDNMPLRGKQL 81
Score = 36.9 bits (86), Expect = 0.003
Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 15/86 (17%)
Query: 629 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-DKHPEGVAQ 687
+ S + V NL D+T ++++R+ K G +V +H DK G
Sbjct: 10 KTFTQRSRLFVGNL------PPDIT-----EEEMRKLFEKYGKAGEVFIHKDK---GFGF 55
Query: 688 IFFKEPEAADACRELLNGRWFGQRQI 713
I + A+ + L+ +Q+
Sbjct: 56 IRLETRTLAEIAKVELDNMPLRGKQL 81
>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 = 54.5 bits (132), Expect = 1e-09
Identities = 15/88 (17%), Positives = 31/88 (35%), Gaps = 8/88 (9%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
S+ +Y+ L T ++ V++ Q G ++ K D T KG +
Sbjct: 4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVS--------TKAILDKTTNKCKGYGFVDFD 55
Query: 274 KKESVDLALSILDGYEIRGKKIKVERAK 301
+ A++ L ++ + K
Sbjct: 56 SPSAAQKAVTALKASGVQAQMAKQSGPS 83
Score = 53.3 bits (129), Expect = 3e-09
Identities = 14/88 (15%), Positives = 31/88 (35%), Gaps = 8/88 (9%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
++ +Y+ L T ++ V++ Q G ++ K D T KG +
Sbjct: 4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVS--------TKAILDKTTNKCKGYGFVDFD 55
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAK 586
+ A++ L ++ + K
Sbjct: 56 SPSAAQKAVTALKASGVQAQMAKQSGPS 83
Score = 32.9 bits (76), Expect = 0.054
Identities = 13/58 (22%), Positives = 19/58 (32%), Gaps = 4/58 (6%)
Query: 375 QDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
QDL + C G + + DK +G + F P AA L +
Sbjct: 20 QDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA 77
Score = 32.9 bits (76), Expect = 0.054
Identities = 13/58 (22%), Positives = 19/58 (32%), Gaps = 4/58 (6%)
Query: 660 QDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
QDL + C G + + DK +G + F P AA L +
Sbjct: 20 QDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA 77
>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 = 55.0 bits (133), Expect = 1e-09
Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 8/89 (8%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+ VYV L +++ E+ + G V+ + D T +G +
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVN--------THMPKDRVTGQHQGYGFVEF 64
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
+ +E D A+ I+D ++ GK I+V +A
Sbjct: 65 LSEEDADYAIKIMDMIKLYGKPIRVNKAS 93
Score = 53.8 bits (130), Expect = 3e-09
Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 8/88 (9%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
++ VYV L +++ E+ + G V+ + D T +G ++
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVN--------THMPKDRVTGQHQGYGFVEFL 65
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAK 586
+E D A+ I+D ++ GK I+V +A
Sbjct: 66 SEEDADYAIKIMDMIKLYGKPIRVNKAS 93
Score = 33.0 bits (76), Expect = 0.075
Identities = 15/90 (16%), Positives = 31/90 (34%), Gaps = 15/90 (16%)
Query: 344 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK---HPEG 399
++ + V L D+ V+ + L E + G V + D+ +G
Sbjct: 10 SERNQDATVYVGGL------DEKVS-----EPLLWELFLQAGPVVNTHMPKDRVTGQHQG 58
Query: 400 VAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+ F E AD ++++ + I
Sbjct: 59 YGFVEFLSEEDADYAIKIMDMIKLYGKPIR 88
Score = 33.0 bits (76), Expect = 0.075
Identities = 15/90 (16%), Positives = 31/90 (34%), Gaps = 15/90 (16%)
Query: 629 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK---HPEG 684
++ + V L D+ V+ + L E + G V + D+ +G
Sbjct: 10 SERNQDATVYVGGL------DEKVS-----EPLLWELFLQAGPVVNTHMPKDRVTGQHQG 58
Query: 685 VAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ F E AD ++++ + I
Sbjct: 59 YGFVEFLSEEDADYAIKIMDMIKLYGKPIR 88
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 55.0 bits (133), Expect = 1e-09
Identities = 19/88 (21%), Positives = 36/88 (40%), Gaps = 8/88 (9%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
E ++V+ + + T+E+ + + G + I L D T KG L Y
Sbjct: 22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKN--------IHLNLDRRTGYLKGYTLVEYE 73
Query: 274 KKESVDLALSILDGYEIRGKKIKVERAK 301
+ A+ L+G ++ G+ I V+
Sbjct: 74 TYKEAQAAMEGLNGQDLMGQPISVDWCF 101
Score = 53.8 bits (130), Expect = 4e-09
Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 8/91 (8%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 555
++ E ++V+ + + T+E+ + + G + I L D T KG L
Sbjct: 19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKN--------IHLNLDRRTGYLKGYTLV 70
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKVERAK 586
Y + A+ L+G ++ G+ I V+
Sbjct: 71 EYETYKEAQAAMEGLNGQDLMGQPISVDWCF 101
Score = 32.6 bits (75), Expect = 0.092
Identities = 18/97 (18%), Positives = 44/97 (45%), Gaps = 15/97 (15%)
Query: 337 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-DK 395
D+ +RS ++ V + ++ T ++D+ ++ ++ G +K + L+ D+
Sbjct: 11 DGDEPGPQRSVEGWILFVTGV------HEEAT-----EEDIHDKFAEYGEIKNIHLNLDR 59
Query: 396 H---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+G + ++ + A A E LNG+ + I+
Sbjct: 60 RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS 96
Score = 32.6 bits (75), Expect = 0.092
Identities = 18/97 (18%), Positives = 44/97 (45%), Gaps = 15/97 (15%)
Query: 622 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-DK 680
D+ +RS ++ V + ++ T ++D+ ++ ++ G +K + L+ D+
Sbjct: 11 DGDEPGPQRSVEGWILFVTGV------HEEAT-----EEDIHDKFAEYGEIKNIHLNLDR 59
Query: 681 H---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+G + ++ + A A E LNG+ + I+
Sbjct: 60 RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS 96
>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 = 55.0 bits (133), Expect = 1e-09
Identities = 22/98 (22%), Positives = 43/98 (43%), Gaps = 14/98 (14%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
E V++ NL D +E EV+Q+ G + +++ P T+ KG A
Sbjct: 10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDL--------KYVRVVLHPDTEHSKGCAF 61
Query: 555 CTYIKKESVDLALSILD------GYEIRGKKIKVERAK 586
++ +E+ L+ G ++ G+++KV+ A
Sbjct: 62 AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAV 99
Score = 54.3 bits (131), Expect = 3e-09
Identities = 22/95 (23%), Positives = 43/95 (45%), Gaps = 14/95 (14%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
E V++ NL D +E EV+Q+ G + +++ P T+ KG A +
Sbjct: 13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDL--------KYVRVVLHPDTEHSKGCAFAQF 64
Query: 273 IKKESVDLALSILD------GYEIRGKKIKVERAK 301
+ +E+ L+ G ++ G+++KV+ A
Sbjct: 65 MTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAV 99
Score = 33.5 bits (77), Expect = 0.052
Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 10/66 (15%)
Query: 374 QQDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLN------GRWF 423
++ L E + G +K V V+ H +G A F EAA C + G
Sbjct: 29 EEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL 88
Query: 424 GQRQIT 429
RQ+
Sbjct: 89 DGRQLK 94
Score = 33.5 bits (77), Expect = 0.052
Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 10/66 (15%)
Query: 659 QQDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLN------GRWF 708
++ L E + G +K V V+ H +G A F EAA C + G
Sbjct: 29 EEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL 88
Query: 709 GQRQIT 714
RQ+
Sbjct: 89 DGRQLK 94
>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 = 54.4 bits (131), Expect = 2e-09
Identities = 14/83 (16%), Positives = 31/83 (37%), Gaps = 4/83 (4%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
++YV N+P +T+E ++ + + K A + +
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPV---LAVQINQDKNFAFLEFRSVD 64
Query: 277 SVDLALSILDGYEIRGKKIKVER 299
A++ DG +G+ +K+ R
Sbjct: 65 ETTQAMA-FDGIIFQGQSLKIRR 86
Score = 54.4 bits (131), Expect = 2e-09
Identities = 14/83 (16%), Positives = 31/83 (37%), Gaps = 4/83 (4%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
++YV N+P +T+E ++ + + K A + +
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPV---LAVQINQDKNFAFLEFRSVD 64
Query: 562 SVDLALSILDGYEIRGKKIKVER 584
A++ DG +G+ +K+ R
Sbjct: 65 ETTQAMA-FDGIIFQGQSLKIRR 86
>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 = 54.8 bits (132), Expect = 2e-09
Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 10/94 (10%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDP-YTKDFKGDAL 554
+ N ++++ +P +EE +E + K + DV +Y +G A
Sbjct: 4 GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDV-------IVYASAADKMKNRGFAF 56
Query: 555 CTYIKKESVDLALSIL--DGYEIRGKKIKVERAK 586
Y + +A L ++ G +I V+ A+
Sbjct: 57 VEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAE 90
Score = 51.7 bits (124), Expect = 3e-08
Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 10/92 (10%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDP-YTKDFKGDALCT 271
+ ++++ +P +EE +E + K + DV +Y +G A
Sbjct: 6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDV-------IVYASAADKMKNRGFAFVE 58
Query: 272 YIKKESVDLALSIL--DGYEIRGKKIKVERAK 301
Y + +A L ++ G +I V+ A+
Sbjct: 59 YESHRAAAMARRKLMPGRIQLWGHQIAVDWAE 90
>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 = 54.6 bits (132), Expect = 2e-09
Identities = 23/103 (22%), Positives = 38/103 (36%), Gaps = 8/103 (7%)
Query: 199 QKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTD 258
+ E E ++V+++ + ++E E G + I L D
Sbjct: 10 NEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKN--------IHLNLD 61
Query: 259 PYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
T KG AL Y + A L+G EI G+ I+V+
Sbjct: 62 RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF 104
Score = 53.1 bits (128), Expect = 8e-09
Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 8/92 (8%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+++ E ++V+++ + ++E E G + I L D T KG AL
Sbjct: 21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKN--------IHLNLDRRTGFSKGYAL 72
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
Y + A L+G EI G+ I+V+
Sbjct: 73 VEYETHKQALAAKEALNGAEIMGQTIQVDWCF 104
Score = 28.4 bits (64), Expect = 3.4
Identities = 14/59 (23%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 374 QQDLREECSKCGHVKKVVLH-DKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
+ +++E+ G +K + L+ D+ +G A + ++ + A A +E LNG + I
Sbjct: 40 EDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI 98
Score = 28.4 bits (64), Expect = 3.4
Identities = 14/59 (23%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 659 QQDLREECSKCGHVKKVVLH-DKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
+ +++E+ G +K + L+ D+ +G A + ++ + A A +E LNG + I
Sbjct: 40 EDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI 98
>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 = 54.1 bits (131), Expect = 2e-09
Identities = 19/89 (21%), Positives = 38/89 (42%), Gaps = 8/89 (8%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
S +++V NL ++E+ ++ G + + + D TK KG A T+
Sbjct: 6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSE--------LHYPIDSLTKKPKGFAFVTF 57
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
+ E A + +DG +G+ + V +
Sbjct: 58 MFPEHAVKAYAEVDGQVFQGRMLHVLPST 86
Score = 54.1 bits (131), Expect = 3e-09
Identities = 18/92 (19%), Positives = 39/92 (42%), Gaps = 8/92 (8%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+ + +++V NL ++E+ ++ G + + + D TK KG A
Sbjct: 3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSE--------LHYPIDSLTKKPKGFAF 54
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
T++ E A + +DG +G+ + V +
Sbjct: 55 VTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST 86
Score = 37.6 bits (88), Expect = 0.002
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 374 QQDLREECSKCGHVKKVVL-HDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
++DL + S G + ++ D P+G A + F PE A ++G+ F R +
Sbjct: 22 EEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLH 81
Score = 37.6 bits (88), Expect = 0.002
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 659 QQDLREECSKCGHVKKVVL-HDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
++DL + S G + ++ D P+G A + F PE A ++G+ F R +
Sbjct: 22 EEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLH 81
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 54.0 bits (130), Expect = 3e-09
Identities = 21/88 (23%), Positives = 37/88 (42%), Gaps = 11/88 (12%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 555
K Q K+ + N+P L E ++ + G+V + ++ TD T
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVV-ESC------EQVNTDSET----AVVNV 59
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKVE 583
TY K+ AL L+G+++ +KV
Sbjct: 60 TYSSKDQARQALDKLNGFQLENFTLKVA 87
Score = 53.2 bits (128), Expect = 4e-09
Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 11/87 (12%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
+ K+ + N+P L E ++ + G+V + ++ TD T T
Sbjct: 12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVV-ESC------EQVNTDSET----AVVNVT 60
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVE 298
Y K+ AL L+G+++ +KV
Sbjct: 61 YSSKDQARQALDKLNGFQLENFTLKVA 87
Score = 40.9 bits (96), Expect = 1e-04
Identities = 9/87 (10%), Positives = 26/87 (29%), Gaps = 12/87 (13%)
Query: 343 GERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEGVA 401
+ + + ++N+ + + L + G V+ ++ V
Sbjct: 9 VPKRQRIRKLQIRNI------PPHLQ-----WEVLDSLLVQYGVVESCEQVNTDSETAVV 57
Query: 402 QIFFKEPEAADACRELLNGRWFGQRQI 428
+ + + A + LNG +
Sbjct: 58 NVTYSSKDQARQALDKLNGFQLENFTL 84
Score = 40.9 bits (96), Expect = 1e-04
Identities = 9/87 (10%), Positives = 26/87 (29%), Gaps = 12/87 (13%)
Query: 628 GERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEGVA 686
+ + + ++N+ + + L + G V+ ++ V
Sbjct: 9 VPKRQRIRKLQIRNI------PPHLQ-----WEVLDSLLVQYGVVESCEQVNTDSETAVV 57
Query: 687 QIFFKEPEAADACRELLNGRWFGQRQI 713
+ + + A + LNG +
Sbjct: 58 NVTYSSKDQARQALDKLNGFQLENFTL 84
>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 = 53.4 bits (129), Expect = 4e-09
Identities = 17/89 (19%), Positives = 35/89 (39%), Gaps = 8/89 (8%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+ + + V L L T+ + EV K G + + + D ++ +G A +
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIAD--------VSIVYDQQSRRSRGFAFVYF 64
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
+ A +G E+ G++I+V
Sbjct: 65 ENVDDAKEAKERANGMELDGRRIRVSGPS 93
Score = 52.2 bits (126), Expect = 9e-09
Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 8/90 (8%)
Query: 497 AQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 556
N + V L L T+ + EV K G + + + D ++ +G A
Sbjct: 12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIAD--------VSIVYDQQSRRSRGFAFVY 63
Query: 557 YIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ + A +G E+ G++I+V
Sbjct: 64 FENVDDAKEAKERANGMELDGRRIRVSGPS 93
Score = 38.3 bits (90), Expect = 9e-04
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 374 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
++DLRE SK G + V +++D+ G A ++F+ + A +E NG R+I
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
Score = 38.3 bits (90), Expect = 9e-04
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 659 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
++DLRE SK G + V +++D+ G A ++F+ + A +E NG R+I
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 54.1 bits (130), Expect = 4e-09
Identities = 21/112 (18%), Positives = 42/112 (37%), Gaps = 11/112 (9%)
Query: 474 GEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDT 533
G ++ + K + ++ + NLP + ++ ++ ++ L
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE------ 55
Query: 534 NQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 585
++ T+DF G + +E + AL L+ E RG I VER
Sbjct: 56 -----TTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD 102
Score = 54.1 bits (130), Expect = 4e-09
Identities = 21/104 (20%), Positives = 40/104 (38%), Gaps = 17/104 (16%)
Query: 197 PGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 256
P + P + ++ + NLP + ++ ++ ++ L +
Sbjct: 16 PRGSHMSKLPA------KRYRITMKNLPEGCSWQDLKDLARENSLE-----------TTF 58
Query: 257 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 300
+ T+DF G + +E + AL L+ E RG I VER
Sbjct: 59 SSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD 102
Score = 29.8 bits (67), Expect = 1.2
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 1/58 (1%)
Query: 375 QDLREECSKCG-HVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
QDL++ + ++ + +G + F E E LN F IT E
Sbjct: 43 QDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVE 100
Score = 29.8 bits (67), Expect = 1.2
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 1/58 (1%)
Query: 660 QDLREECSKCG-HVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
QDL++ + ++ + +G + F E E LN F IT E
Sbjct: 43 QDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVE 100
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 53.4 bits (129), Expect = 4e-09
Identities = 23/104 (22%), Positives = 41/104 (39%), Gaps = 16/104 (15%)
Query: 198 GQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYT 257
G K P E YV NLP + Q + + + + ++L
Sbjct: 4 GSSGKELPT------EPPYTAYVGNLPFNTVQGDIDAIFKDLSIR---------SVRLVR 48
Query: 258 DPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
D T FKG + + +S+ AL+ DG + + ++V+ A+
Sbjct: 49 DKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVDIAE 91
Score = 50.7 bits (122), Expect = 4e-08
Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 10/85 (11%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
YV NLP + Q + + + + ++L D T FKG + + +
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLSIR---------SVRLVRDKDTDKFKGFCYVEFDEVD 67
Query: 562 SVDLALSILDGYEIRGKKIKVERAK 586
S+ AL+ DG + + ++V+ A+
Sbjct: 68 SLKEALT-YDGALLGDRSLRVDIAE 91
>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 = 52.9 bits (128), Expect = 4e-09
Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 8/90 (8%)
Query: 497 AQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 556
A +YV L ++ + G + I++ D T+ +G A
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITD--------IQIPLDYETEKHRGFAFVE 55
Query: 557 YIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ E A+ ++ E+ G+ I+V AK
Sbjct: 56 FELAEDAAAAIDNMNESELFGRTIRVNLAK 85
Score = 52.9 bits (128), Expect = 4e-09
Identities = 17/89 (19%), Positives = 33/89 (37%), Gaps = 8/89 (8%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+YV L ++ + G + I++ D T+ +G A +
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITD--------IQIPLDYETEKHRGFAFVEF 56
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
E A+ ++ E+ G+ I+V AK
Sbjct: 57 ELAEDAAAAIDNMNESELFGRTIRVNLAK 85
Score = 32.1 bits (74), Expect = 0.084
Identities = 17/91 (18%), Positives = 30/91 (32%), Gaps = 15/91 (16%)
Query: 343 GERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKH---PE 398
G + + V+ V L ++V + L G + + + D
Sbjct: 1 GSMATTKRVLYVGGL------AEEVD-----DKVLHAAFIPFGDITDIQIPLDYETEKHR 49
Query: 399 GVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
G A + F+ E A A + +N R I
Sbjct: 50 GFAFVEFELAEDAAAAIDNMNESELFGRTIR 80
Score = 32.1 bits (74), Expect = 0.084
Identities = 17/91 (18%), Positives = 30/91 (32%), Gaps = 15/91 (16%)
Query: 628 GERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKH---PE 683
G + + V+ V L ++V + L G + + + D
Sbjct: 1 GSMATTKRVLYVGGL------AEEVD-----DKVLHAAFIPFGDITDIQIPLDYETEKHR 49
Query: 684 GVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
G A + F+ E A A + +N R I
Sbjct: 50 GFAFVEFELAEDAAAAIDNMNESELFGRTIR 80
>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 = 53.4 bits (129), Expect = 5e-09
Identities = 22/106 (20%), Positives = 40/106 (37%), Gaps = 17/106 (16%)
Query: 197 PGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 256
G P ++ NLP D+T+E E + + ++L
Sbjct: 3 SGSSGSRLPK------SPPYTAFLGNLPYDVTEESIKEFFRGLNIS---------AVRLP 47
Query: 257 TDPYTKD-FKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
+P + KG + +S+ ALS L+ + K+I+V+ A
Sbjct: 48 REPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVAD 92
Score = 51.5 bits (124), Expect = 2e-08
Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 11/86 (12%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKD-FKGDALCTYIKK 560
++ NLP D+T+E E + + ++L +P + KG +
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLNIS---------AVRLPREPSNPERLKGFGYAEFEDL 67
Query: 561 ESVDLALSILDGYEIRGKKIKVERAK 586
+S+ ALS L+ + K+I+V+ A
Sbjct: 68 DSLLSALS-LNEESLGNKRIRVDVAD 92
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 54.9 bits (132), Expect = 5e-09
Identities = 25/123 (20%), Positives = 46/123 (37%), Gaps = 6/123 (4%)
Query: 179 SVDATAPMENPKAEEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQK 238
+ P + E P K + + VYV + T ++ ++V++
Sbjct: 19 YFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRS 78
Query: 239 CGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVE 298
G+ DV +++K + KG A + SV L +L G + G+K+ V
Sbjct: 79 IGVY--DV----VELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR 132
Query: 299 RAK 301
A
Sbjct: 133 PAT 135
Score = 47.6 bits (113), Expect = 1e-06
Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 6/87 (6%)
Query: 500 NTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 559
VYV + T ++ ++V++ G+ DV +++K + KG A
Sbjct: 55 RAAVYVGSFSWWTTDQQLIQVIRSIGVY--DV----VELKFAENRANGQSKGYAEVVVAS 108
Query: 560 KESVDLALSILDGYEIRGKKIKVERAK 586
+ SV L +L G + G+K+ V A
Sbjct: 109 ENSVHKLLELLPGKVLNGEKVDVRPAT 135
Score = 35.7 bits (82), Expect = 0.018
Identities = 10/61 (16%), Positives = 20/61 (32%), Gaps = 6/61 (9%)
Query: 375 QDLREECSKCGHVKKV---VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
Q L + G V ++ +G A++ + ELL G+ ++
Sbjct: 70 QQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKV 129
Query: 429 T 429
Sbjct: 130 D 130
Score = 35.7 bits (82), Expect = 0.018
Identities = 10/61 (16%), Positives = 20/61 (32%), Gaps = 6/61 (9%)
Query: 660 QDLREECSKCGHVKKV---VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
Q L + G V ++ +G A++ + ELL G+ ++
Sbjct: 70 QQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKV 129
Query: 714 T 714
Sbjct: 130 D 130
>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 = 52.6 bits (127), Expect = 8e-09
Identities = 21/106 (19%), Positives = 40/106 (37%), Gaps = 17/106 (16%)
Query: 197 PGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 256
R P ++ NLP D+T+E E + + ++L
Sbjct: 7 HHHHRSRLPK------SPPYTAFLGNLPYDVTEESIKEFFRGLNIS---------AVRLP 51
Query: 257 TDPYTKD-FKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
+P + KG + +S+ ALS L+ + ++I+V+ A
Sbjct: 52 REPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNRRIRVDVAD 96
Score = 50.3 bits (121), Expect = 6e-08
Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 11/86 (12%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKD-FKGDALCTYIKK 560
++ NLP D+T+E E + + ++L +P + KG +
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLNIS---------AVRLPREPSNPERLKGFGYAEFEDL 71
Query: 561 ESVDLALSILDGYEIRGKKIKVERAK 586
+S+ ALS L+ + ++I+V+ A
Sbjct: 72 DSLLSALS-LNEESLGNRRIRVDVAD 96
>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 = 53.1 bits (128), Expect = 8e-09
Identities = 21/105 (20%), Positives = 38/105 (36%), Gaps = 8/105 (7%)
Query: 197 PGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 256
++YV +L ++T++ + + G + I+L
Sbjct: 8 HSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIES--------IQLM 59
Query: 257 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
D T KG T+ E AL L+G+E+ G+ +KV
Sbjct: 60 MDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVT 104
Score = 51.2 bits (123), Expect = 3e-08
Identities = 21/86 (24%), Positives = 38/86 (44%), Gaps = 8/86 (9%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
++YV +L ++T++ + + G + I+L D T KG T+
Sbjct: 27 MRLYVGSLHFNITEDMLRGIFEPFGRIES--------IQLMMDSETGRSKGYGFITFSDS 78
Query: 561 ESVDLALSILDGYEIRGKKIKVERAK 586
E AL L+G+E+ G+ +KV
Sbjct: 79 ECAKKALEQLNGFELAGRPMKVGHVT 104
Score = 30.4 bits (69), Expect = 0.59
Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 4/60 (6%)
Query: 374 QQDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+ LR G ++ + ++ D +G I F + E A E LNG R +
Sbjct: 40 EDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK 99
Score = 30.4 bits (69), Expect = 0.59
Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 4/60 (6%)
Query: 659 QQDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ LR G ++ + ++ D +G I F + E A E LNG R +
Sbjct: 40 EDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK 99
>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 = 52.8 bits (127), Expect = 9e-09
Identities = 11/92 (11%), Positives = 35/92 (38%), Gaps = 9/92 (9%)
Query: 209 FDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDA 268
D+ +++N+P +T+ + ++ ++ + + + D + G A
Sbjct: 9 GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENA-------VHVLVDNNGQ-GLGQA 60
Query: 269 LCTYIKKESVDLALSILDGYEIRGKKIKVERA 300
L + ++ + L ++ G++ V
Sbjct: 61 LVQFKNEDDARKSER-LHRKKLNGREAFVHVV 91
Score = 50.9 bits (122), Expect = 5e-08
Identities = 10/91 (10%), Positives = 33/91 (36%), Gaps = 9/91 (9%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+++N+P +T+ + ++ ++ + + + D + G AL
Sbjct: 10 DVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENA-------VHVLVDNNGQ-GLGQAL 61
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERA 585
+ ++ + L ++ G++ V
Sbjct: 62 VQFKNEDDARKSER-LHRKKLNGREAFVHVV 91
>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 = 52.2 bits (126), Expect = 1e-08
Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 8/89 (8%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
S+ +YV +L ++T++ + + G + I L D T KG T+
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDN--------IVLMKDSDTGRSKGYGFITF 54
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
E AL L+G+E+ G+ ++V
Sbjct: 55 SDSECARRALEQLNGFELAGRPMRVGHVT 83
Score = 51.0 bits (123), Expect = 3e-08
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 8/88 (9%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
++ +YV +L ++T++ + + G + I L D T KG T+
Sbjct: 4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDN--------IVLMKDSDTGRSKGYGFITFS 55
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAK 586
E AL L+G+E+ G+ ++V
Sbjct: 56 DSECARRALEQLNGFELAGRPMRVGHVT 83
Score = 31.8 bits (73), Expect = 0.17
Identities = 14/60 (23%), Positives = 22/60 (36%), Gaps = 4/60 (6%)
Query: 374 QQDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+ LR G + + ++ D +G I F + E A E LNG R +
Sbjct: 19 EDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMR 78
Score = 31.8 bits (73), Expect = 0.17
Identities = 14/60 (23%), Positives = 22/60 (36%), Gaps = 4/60 (6%)
Query: 659 QQDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ LR G + + ++ D +G I F + E A E LNG R +
Sbjct: 19 EDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMR 78
>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 = 52.3 bits (126), Expect = 1e-08
Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
G ++YV NLP D+ ++ +V K G + +D+D +K A
Sbjct: 19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAI-RDID-----LKNRRGG-----PPFAFVE 67
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ + A+ DGY+ G +++VE +
Sbjct: 68 FEDPRDAEDAVYGRDGYDYDGYRLRVEFPR 97
Score = 51.2 bits (123), Expect = 3e-08
Identities = 20/90 (22%), Positives = 36/90 (40%), Gaps = 11/90 (12%)
Query: 497 AQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 556
+ ++YV NLP D+ ++ +V K G + I L F A
Sbjct: 19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRD--------IDLKNRRGGPPF---AFVE 67
Query: 557 YIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ + A+ DGY+ G +++VE +
Sbjct: 68 FEDPRDAEDAVYGRDGYDYDGYRLRVEFPR 97
Score = 48.1 bits (115), Expect = 4e-07
Identities = 18/96 (18%), Positives = 37/96 (38%), Gaps = 12/96 (12%)
Query: 337 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL-HDK 395
+RG N+ I V NL D+ +D+ + K G ++ + L + +
Sbjct: 10 GGGVIRGPAGNNDCRIYVGNL------PPDIR-----TKDIEDVFYKYGAIRDIDLKNRR 58
Query: 396 HPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
A + F++P A+ +G + ++ E
Sbjct: 59 GGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE 94
Score = 48.1 bits (115), Expect = 4e-07
Identities = 18/96 (18%), Positives = 37/96 (38%), Gaps = 12/96 (12%)
Query: 622 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL-HDK 680
+RG N+ I V NL D+ +D+ + K G ++ + L + +
Sbjct: 10 GGGVIRGPAGNNDCRIYVGNL------PPDIR-----TKDIEDVFYKYGAIRDIDLKNRR 58
Query: 681 HPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
A + F++P A+ +G + ++ E
Sbjct: 59 GGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE 94
>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 = 52.4 bits (126), Expect = 2e-08
Identities = 27/120 (22%), Positives = 46/120 (38%), Gaps = 19/120 (15%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
E + +Y+ NLP +T EE ++ K G + + I++ P T+ A Y
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ--------IRVGNTPETRGT---AYVVY 54
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEK 332
A+ L G+ + + + V + K KK E+LK +EK
Sbjct: 55 EDIFDAKNAVDHLSGFNVSNRYLVVLYYN--------ANRAFQKMDTKKKEEQLKLLKEK 106
Score = 52.0 bits (125), Expect = 2e-08
Identities = 27/120 (22%), Positives = 46/120 (38%), Gaps = 19/120 (15%)
Query: 498 QENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 557
+ N +Y+ NLP +T EE ++ K G + + I++ P T+ A Y
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ--------IRVGNTPETRGT---AYVVY 54
Query: 558 IKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEK 617
A+ L G+ + + + V + K KK E+LK +EK
Sbjct: 55 EDIFDAKNAVDHLSGFNVSNRYLVVLYYN--------ANRAFQKMDTKKKEEQLKLLKEK 106
Score = 39.3 bits (92), Expect = 5e-04
Identities = 16/116 (13%), Positives = 45/116 (38%), Gaps = 12/116 (10%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL-HDKHPEGVAQIFFKEPEA 695
+ ++NL +T +++ + K G ++++ + + G A + +++
Sbjct: 11 LYIRNL------PYKIT-----AEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFD 59
Query: 696 ADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLEEEDKKK 751
A + L+G R + ++ ++ +T ++ E E + D K
Sbjct: 60 AKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK 115
Score = 38.5 bits (90), Expect = 0.001
Identities = 16/106 (15%), Positives = 44/106 (41%), Gaps = 14/106 (13%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL-HDKHPEGVAQIFFKEPEA 410
+ ++NL +T +++ + K G ++++ + + G A + +++
Sbjct: 11 LYIRNL------PYKIT-----AEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFD 59
Query: 411 ADACRELLNGRWFGQRQITAETWDGKTRYKIQETA--EEREARLKK 454
A + L+G R + ++ ++ +T EE+ LK+
Sbjct: 60 AKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKE 105
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 52.9 bits (127), Expect = 2e-08
Identities = 16/88 (18%), Positives = 32/88 (36%), Gaps = 8/88 (9%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+YV L ++ + G + I++ D T+ +G A +
Sbjct: 61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITD--------IQIPLDYETEKHRGFAFVEF 112
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERA 300
E A+ ++ E+ G+ I+V A
Sbjct: 113 ELAEDAAAAIDNMNESELFGRTIRVNLA 140
Score = 52.5 bits (126), Expect = 2e-08
Identities = 17/111 (15%), Positives = 34/111 (30%), Gaps = 8/111 (7%)
Query: 475 EAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTN 534
+ A +YV L ++ + G +
Sbjct: 38 CVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITD----- 92
Query: 535 QMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 585
I++ D T+ +G A + E A+ ++ E+ G+ I+V A
Sbjct: 93 ---IQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
Score = 34.0 bits (78), Expect = 0.053
Identities = 17/98 (17%), Positives = 30/98 (30%), Gaps = 15/98 (15%)
Query: 336 WRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHD 394
G + + V+ V L ++V + L G + + + D
Sbjct: 50 SGGSGGSGGSATTKRVLYVGGL------AEEVD-----DKVLHAAFIPFGDITDIQIPLD 98
Query: 395 K---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
G A + F+ E A A + +N R I
Sbjct: 99 YETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR 136
Score = 34.0 bits (78), Expect = 0.053
Identities = 17/98 (17%), Positives = 30/98 (30%), Gaps = 15/98 (15%)
Query: 621 WRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHD 679
G + + V+ V L ++V + L G + + + D
Sbjct: 50 SGGSGGSGGSATTKRVLYVGGL------AEEVD-----DKVLHAAFIPFGDITDIQIPLD 98
Query: 680 K---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
G A + F+ E A A + +N R I
Sbjct: 99 YETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR 136
>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 = 51.8 bits (125), Expect = 2e-08
Identities = 17/89 (19%), Positives = 33/89 (37%), Gaps = 8/89 (8%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+YV L ++ + G + I++ D T+ +G A +
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITD--------IQIPLDYETEKHRGFAFVEF 61
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
E A+ ++ E+ G+ I+V AK
Sbjct: 62 ELAEDAAAAIDNMNESELFGRTIRVNLAK 90
Score = 51.5 bits (124), Expect = 2e-08
Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 8/90 (8%)
Query: 497 AQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 556
A +YV L ++ + G + I++ D T+ +G A
Sbjct: 9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITD--------IQIPLDYETEKHRGFAFVE 60
Query: 557 YIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ E A+ ++ E+ G+ I+V AK
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRVNLAK 90
Score = 30.7 bits (70), Expect = 0.39
Identities = 16/90 (17%), Positives = 29/90 (32%), Gaps = 15/90 (16%)
Query: 344 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKH---PEG 399
+ + V+ V L ++V + L G + + + D G
Sbjct: 7 GMATTKRVLYVGGL------AEEVD-----DKVLHAAFIPFGDITDIQIPLDYETEKHRG 55
Query: 400 VAQIFFKEPEAADACRELLNGRWFGQRQIT 429
A + F+ E A A + +N R I
Sbjct: 56 FAFVEFELAEDAAAAIDNMNESELFGRTIR 85
Score = 30.7 bits (70), Expect = 0.39
Identities = 16/90 (17%), Positives = 29/90 (32%), Gaps = 15/90 (16%)
Query: 629 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKH---PEG 684
+ + V+ V L ++V + L G + + + D G
Sbjct: 7 GMATTKRVLYVGGL------AEEVD-----DKVLHAAFIPFGDITDIQIPLDYETEKHRG 55
Query: 685 VAQIFFKEPEAADACRELLNGRWFGQRQIT 714
A + F+ E A A + +N R I
Sbjct: 56 FAFVEFELAEDAAAAIDNMNESELFGRTIR 85
>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 = 51.5 bits (124), Expect = 2e-08
Identities = 17/98 (17%), Positives = 33/98 (33%), Gaps = 13/98 (13%)
Query: 489 KDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKD 548
+D KK + + NL ++T++E EV + + +
Sbjct: 5 EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGK------------- 51
Query: 549 FKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
KG A + + + L G EI G+ + +
Sbjct: 52 SKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 89
Score = 51.1 bits (123), Expect = 3e-08
Identities = 16/98 (16%), Positives = 31/98 (31%), Gaps = 13/98 (13%)
Query: 204 EPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKD 263
E P + + NL ++T++E EV + + +
Sbjct: 5 EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGK------------- 51
Query: 264 FKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
KG A + + + L G EI G+ + +
Sbjct: 52 SKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 89
Score = 30.3 bits (69), Expect = 0.47
Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 1/55 (1%)
Query: 374 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
+ +L+E ++ V D +G+A I FK A+ E G R +
Sbjct: 30 EDELKEVFEDALEIRLVS-QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 83
Score = 30.3 bits (69), Expect = 0.47
Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 1/55 (1%)
Query: 659 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
+ +L+E ++ V D +G+A I FK A+ E G R +
Sbjct: 30 EDELKEVFEDALEIRLVS-QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 83
>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 = 53.3 bits (128), Expect = 2e-08
Identities = 23/103 (22%), Positives = 38/103 (36%), Gaps = 8/103 (7%)
Query: 199 QKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTD 258
+ E E ++V+++ + ++E E G + I L D
Sbjct: 56 NEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKN--------IHLNLD 107
Query: 259 PYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
T KG AL Y + A L+G EI G+ I+V+
Sbjct: 108 RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF 150
Score = 51.8 bits (124), Expect = 7e-08
Identities = 22/91 (24%), Positives = 38/91 (41%), Gaps = 8/91 (8%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 555
++ E ++V+++ + ++E E G + I L D T KG AL
Sbjct: 68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKN--------IHLNLDRRTGFSKGYALV 119
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKVERAK 586
Y + A L+G EI G+ I+V+
Sbjct: 120 EYETHKQALAAKEALNGAEIMGQTIQVDWCF 150
Score = 31.3 bits (71), Expect = 0.57
Identities = 22/136 (16%), Positives = 54/136 (39%), Gaps = 16/136 (11%)
Query: 298 ERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLFDWRPDKMRG-ERSKNESVIIVKN 356
++ +K +A K + E + + + + G +RS ++ V +
Sbjct: 20 DQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTS 79
Query: 357 LFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-DKH---PEGVAQIFFKEPEAAD 412
+ ++ + +++E+ G +K + L+ D+ +G A + ++ + A
Sbjct: 80 I------HEEAQ-----EDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 128
Query: 413 ACRELLNGRWFGQRQI 428
A +E LNG + I
Sbjct: 129 AAKEALNGAEIMGQTI 144
Score = 31.3 bits (71), Expect = 0.57
Identities = 22/136 (16%), Positives = 54/136 (39%), Gaps = 16/136 (11%)
Query: 583 ERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLFDWRPDKMRG-ERSKNESVIIVKN 641
++ +K +A K + E + + + + G +RS ++ V +
Sbjct: 20 DQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTS 79
Query: 642 LFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-DKH---PEGVAQIFFKEPEAAD 697
+ ++ + +++E+ G +K + L+ D+ +G A + ++ + A
Sbjct: 80 I------HEEAQ-----EDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 128
Query: 698 ACRELLNGRWFGQRQI 713
A +E LNG + I
Sbjct: 129 AAKEALNGAEIMGQTI 144
>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 = 51.1 bits (123), Expect = 3e-08
Identities = 17/89 (19%), Positives = 40/89 (44%), Gaps = 8/89 (8%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+ K++V L D ++ +V K G + + + + D T+ +G T+
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISE--------VVVVKDRETQRSRGFGFVTF 61
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
+ A+ ++G + G++I+V++A
Sbjct: 62 ENIDDAKDAMMAMNGKSVDGRQIRVDQAG 90
Score = 50.3 bits (121), Expect = 6e-08
Identities = 18/90 (20%), Positives = 41/90 (45%), Gaps = 8/90 (8%)
Query: 497 AQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 556
A + K++V L D ++ +V K G + + + + D T+ +G T
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISE--------VVVVKDRETQRSRGFGFVT 60
Query: 557 YIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ + A+ ++G + G++I+V++A
Sbjct: 61 FENIDDAKDAMMAMNGKSVDGRQIRVDQAG 90
Score = 34.9 bits (81), Expect = 0.015
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 374 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+Q L + SK G + +V V+ D+ G + F+ + A +NG+ RQI
Sbjct: 26 EQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIR 85
Score = 34.9 bits (81), Expect = 0.015
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 659 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+Q L + SK G + +V V+ D+ G + F+ + A +NG+ RQI
Sbjct: 26 EQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIR 85
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 52.9 bits (127), Expect = 3e-08
Identities = 21/119 (17%), Positives = 42/119 (35%), Gaps = 20/119 (16%)
Query: 194 KVVPGQKRKPEPPKWF-----------DIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLV 242
+ P + KP P KW + E K+ VSNL ++ + E+ + G +
Sbjct: 56 RPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTL 115
Query: 243 MKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
K + D + G A + ++ A+ G + G+ + ++
Sbjct: 116 --------KKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA 165
Score = 50.6 bits (121), Expect = 2e-07
Identities = 19/112 (16%), Positives = 39/112 (34%), Gaps = 13/112 (11%)
Query: 479 PKLKPKKKRKKDLEKLKKAQEN----TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTN 534
PK P K + + E K+ VSNL ++ + E+ + G +
Sbjct: 63 PKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTL------- 115
Query: 535 QMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
K + D + G A + ++ A+ G + G+ + ++
Sbjct: 116 -KKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA 165
Score = 47.9 bits (114), Expect = 2e-06
Identities = 20/117 (17%), Positives = 40/117 (34%), Gaps = 23/117 (19%)
Query: 340 KMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-DK--H 396
GE + + ++V NL D V+ D++E ++ G +KK + D+
Sbjct: 79 CGGGEGVETGAKLLVSNL------DFGVS-----DADIQELFAEFGTLKKAAVDYDRSGR 127
Query: 397 PEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLK 453
G A + F+ A + G R + ++ + + E
Sbjct: 128 SLGTADVHFERRADALKAMKQYKGVPLDGRPM---------DIQLVASQIDLEHHHH 175
Score = 47.9 bits (114), Expect = 2e-06
Identities = 20/117 (17%), Positives = 40/117 (34%), Gaps = 23/117 (19%)
Query: 625 KMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-DK--H 681
GE + + ++V NL D V+ D++E ++ G +KK + D+
Sbjct: 79 CGGGEGVETGAKLLVSNL------DFGVS-----DADIQELFAEFGTLKKAAVDYDRSGR 127
Query: 682 PEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLK 738
G A + F+ A + G R + ++ + + E
Sbjct: 128 SLGTADVHFERRADALKAMKQYKGVPLDGRPM---------DIQLVASQIDLEHHHH 175
>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 = 51.2 bits (123), Expect = 3e-08
Identities = 19/93 (20%), Positives = 43/93 (46%), Gaps = 11/93 (11%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
++ K+++ +P +L +++ + ++ G + ++ + D +T KG A T
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKI--------YELTVLKDRFTGMHKGCAFLT 61
Query: 272 YIKKESVDLALSILDGYEIR---GKKIKVERAK 301
Y ++ES A S L + + I+V+ A
Sbjct: 62 YCERESALKAQSALHEQKTLPGMNRPIQVKPAD 94
Score = 50.4 bits (121), Expect = 5e-08
Identities = 20/94 (21%), Positives = 43/94 (45%), Gaps = 11/94 (11%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 555
K + K+++ +P +L +++ + ++ G + ++ + D +T KG A
Sbjct: 9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKI--------YELTVLKDRFTGMHKGCAFL 60
Query: 556 TYIKKESVDLALSILDGYEIR---GKKIKVERAK 586
TY ++ES A S L + + I+V+ A
Sbjct: 61 TYCERESALKAQSALHEQKTLPGMNRPIQVKPAD 94
Score = 31.1 bits (71), Expect = 0.38
Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 13/70 (18%)
Query: 373 YQQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
++DL+ + G + ++ VL D+ +G A + + E E+A + L+ +
Sbjct: 26 DEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQ------- 78
Query: 429 TAETWDGKTR 438
+T G R
Sbjct: 79 --KTLPGMNR 86
Score = 31.1 bits (71), Expect = 0.38
Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 13/70 (18%)
Query: 658 YQQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
++DL+ + G + ++ VL D+ +G A + + E E+A + L+ +
Sbjct: 26 DEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQ------- 78
Query: 714 TAETWDGKTR 723
+T G R
Sbjct: 79 --KTLPGMNR 86
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 51.2 bits (123), Expect = 3e-08
Identities = 16/89 (17%), Positives = 32/89 (35%), Gaps = 14/89 (15%)
Query: 498 QENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 557
T Y+ N+P T+ + + + Q G + + K Y + KG Y
Sbjct: 25 PRVTTAYIGNIPHFATEADLIPLFQNFGFI--------LDFKHYPE------KGCCFIKY 70
Query: 558 IKKESVDLALSILDGYEIRGKKIKVERAK 586
E + + L + +G+ ++ K
Sbjct: 71 DTHEQAAVCIVALANFPFQGRNLRTGWGK 99
Score = 48.8 bits (117), Expect = 2e-07
Identities = 16/87 (18%), Positives = 32/87 (36%), Gaps = 14/87 (16%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
T Y+ N+P T+ + + + Q G ++ K Y + KG Y
Sbjct: 27 VTTAYIGNIPHFATEADLIPLFQNFGFILD--------FKHYPE------KGCCFIKYDT 72
Query: 275 KESVDLALSILDGYEIRGKKIKVERAK 301
E + + L + +G+ ++ K
Sbjct: 73 HEQAAVCIVALANFPFQGRNLRTGWGK 99
Score = 38.8 bits (91), Expect = 7e-04
Identities = 15/92 (16%), Positives = 24/92 (26%), Gaps = 15/92 (16%)
Query: 338 PDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKH 396
D + + + N+ T + DL G + +K
Sbjct: 16 VDHIIRSAPPRVTTAYIGNI------PHFAT-----EADLIPLFQNFGFILDFKHYPEK- 63
Query: 397 PEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
G I + E A C L F R +
Sbjct: 64 --GCCFIKYDTHEQAAVCIVALANFPFQGRNL 93
Score = 38.8 bits (91), Expect = 7e-04
Identities = 15/92 (16%), Positives = 24/92 (26%), Gaps = 15/92 (16%)
Query: 623 PDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKH 681
D + + + N+ T + DL G + +K
Sbjct: 16 VDHIIRSAPPRVTTAYIGNI------PHFAT-----EADLIPLFQNFGFILDFKHYPEK- 63
Query: 682 PEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
G I + E A C L F R +
Sbjct: 64 --GCCFIKYDTHEQAAVCIVALANFPFQGRNL 93
>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 = 51.6 bits (124), Expect = 3e-08
Identities = 23/115 (20%), Positives = 43/115 (37%), Gaps = 20/115 (17%)
Query: 198 GQKRKPEPPKW----FDIG-------EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDV 246
GQ+ +P KW FD G E K+ VSNL ++ + E+ + G +
Sbjct: 7 GQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTL---- 62
Query: 247 DTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
K + D + G A + ++ A+ G + G+ + ++
Sbjct: 63 ----KKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA 112
Score = 46.2 bits (110), Expect = 2e-06
Identities = 14/90 (15%), Positives = 33/90 (36%), Gaps = 9/90 (10%)
Query: 497 AQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 556
+ K+ VSNL ++ + E+ + G + K + D + G A
Sbjct: 32 VETGAKLLVSNLDFGVSDADIQELFAEFGTL--------KKAAVDYDR-SGRSLGTADVH 82
Query: 557 YIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ ++ A+ G + G+ + ++
Sbjct: 83 FERRADALKAMKQYKGVPLDGRPMDIQLVA 112
Score = 43.5 bits (103), Expect = 2e-05
Identities = 25/129 (19%), Positives = 45/129 (34%), Gaps = 25/129 (19%)
Query: 328 KAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHV 387
K Q LFD GE + + ++V NL D V+ D++E ++ G +
Sbjct: 16 KWQHDLFDSGC--GGGEGVETGAKLLVSNL------DFGVS-----DADIQELFAEFGTL 62
Query: 388 KKVVLH-DK--HPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQET 444
KK + D+ G A + F+ A + G R + ++ +
Sbjct: 63 KKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM---------DIQLVAS 113
Query: 445 AEEREARLK 453
+ E
Sbjct: 114 QIDLEHHHH 122
Score = 43.5 bits (103), Expect = 2e-05
Identities = 25/129 (19%), Positives = 45/129 (34%), Gaps = 25/129 (19%)
Query: 613 KAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHV 672
K Q LFD GE + + ++V NL D V+ D++E ++ G +
Sbjct: 16 KWQHDLFDSGC--GGGEGVETGAKLLVSNL------DFGVS-----DADIQELFAEFGTL 62
Query: 673 KKVVLH-DK--HPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQET 729
KK + D+ G A + F+ A + G R + ++ +
Sbjct: 63 KKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM---------DIQLVAS 113
Query: 730 AEEREARLK 738
+ E
Sbjct: 114 QIDLEHHHH 122
>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 = 51.1 bits (123), Expect = 3e-08
Identities = 19/102 (18%), Positives = 38/102 (37%), Gaps = 18/102 (17%)
Query: 500 NTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 559
+YV NL D+T+ +++ + G K+ T+ + + +
Sbjct: 15 PRTLYVGNLSRDVTEVLILQLFSQIGPC--------KSCKMITEHTSN--DPYCFVEFYE 64
Query: 560 KESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPK 601
AL+ ++G +I GK++KV A P +
Sbjct: 65 HRDAAAALAAMNGRKILGKEVKV--------NWATTPSSQKS 98
Score = 50.7 bits (122), Expect = 4e-08
Identities = 19/102 (18%), Positives = 38/102 (37%), Gaps = 18/102 (17%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
+YV NL D+T+ +++ + G K+ T+ + + +
Sbjct: 15 PRTLYVGNLSRDVTEVLILQLFSQIGPC--------KSCKMITEHTSN--DPYCFVEFYE 64
Query: 275 KESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPK 316
AL+ ++G +I GK++KV A P +
Sbjct: 65 HRDAAAALAAMNGRKILGKEVKV--------NWATTPSSQKS 98
Score = 37.6 bits (88), Expect = 0.002
Identities = 17/90 (18%), Positives = 35/90 (38%), Gaps = 14/90 (15%)
Query: 341 MRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKH-PE 398
M + + + + V NL +DVT + + + S+ G K ++ + +
Sbjct: 8 MMEDDGQPRT-LYVGNL------SRDVT-----EVLILQLFSQIGPCKSCKMITEHTSND 55
Query: 399 GVAQIFFKEPEAADACRELLNGRWFGQRQI 428
+ F E A A +NGR +++
Sbjct: 56 PYCFVEFYEHRDAAAALAAMNGRKILGKEV 85
Score = 37.6 bits (88), Expect = 0.002
Identities = 17/90 (18%), Positives = 35/90 (38%), Gaps = 14/90 (15%)
Query: 626 MRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKH-PE 683
M + + + + V NL +DVT + + + S+ G K ++ + +
Sbjct: 8 MMEDDGQPRT-LYVGNL------SRDVT-----EVLILQLFSQIGPCKSCKMITEHTSND 55
Query: 684 GVAQIFFKEPEAADACRELLNGRWFGQRQI 713
+ F E A A +NGR +++
Sbjct: 56 PYCFVEFYEHRDAAAALAAMNGRKILGKEV 85
>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 = 50.3 bits (121), Expect = 4e-08
Identities = 16/88 (18%), Positives = 31/88 (35%), Gaps = 15/88 (17%)
Query: 500 NTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 559
K+Y+ NL +T ++ ++ L + G A Y
Sbjct: 8 MNKLYIGNLSPAVTADDLRQLFGDRKLPL-AGQVLLK-------------SGYAFVDYPD 53
Query: 560 KESVDLALSILDG-YEIRGKKIKVERAK 586
+ A+ L G E+ GK ++V+ +
Sbjct: 54 QNWAIRAIETLSGKVELHGKIMEVDYSV 81
Score = 50.3 bits (121), Expect = 5e-08
Identities = 16/90 (17%), Positives = 31/90 (34%), Gaps = 15/90 (16%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
K+Y+ NL +T ++ ++ L + G A Y
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPL-AGQVLLK-------------SGYAFVDY 51
Query: 273 IKKESVDLALSILDG-YEIRGKKIKVERAK 301
+ A+ L G E+ GK ++V+ +
Sbjct: 52 PDQNWAIRAIETLSGKVELHGKIMEVDYSV 81
>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 = 50.4 bits (121), Expect = 5e-08
Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 14/91 (15%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLV-MKDVDTNQMKIKLYTDPYTKDFKGDALC 270
ES + +SNL T+E EV +K + + + K G A
Sbjct: 12 SGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSK-------------GYAFI 58
Query: 271 TYIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ E AL+ + EI G+ I++E
Sbjct: 59 EFASFEDAKEALNSCNKREIEGRAIRLELQG 89
Score = 48.8 bits (117), Expect = 2e-07
Identities = 20/92 (21%), Positives = 35/92 (38%), Gaps = 14/92 (15%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLV-MKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+ E+ + +SNL T+E EV +K + + + K G A
Sbjct: 11 WSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSK-------------GYAF 57
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ E AL+ + EI G+ I++E
Sbjct: 58 IEFASFEDAKEALNSCNKREIEGRAIRLELQG 89
Score = 31.5 bits (72), Expect = 0.23
Identities = 14/55 (25%), Positives = 19/55 (34%)
Query: 375 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+ L+E K +K + +G A I F E A N R R I
Sbjct: 30 ETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIR 84
Score = 31.5 bits (72), Expect = 0.23
Identities = 14/55 (25%), Positives = 19/55 (34%)
Query: 660 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ L+E K +K + +G A I F E A N R R I
Sbjct: 30 ETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIR 84
>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 = 49.8 bits (120), Expect = 6e-08
Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 9/89 (10%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTD-PYTKDFKGDALCTY 272
+ TKV++ L ++T++ +E+ G + I + + + KG A +
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKM--------IDMPVERMHPHLSKGYAYVEF 54
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
+ + AL +DG +I G++I
Sbjct: 55 ENPDEAEKALKHMDGGQIDGQEITATAVL 83
Score = 47.9 bits (115), Expect = 2e-07
Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 9/89 (10%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTD-PYTKDFKGDALCTY 557
+ TKV++ L ++T++ +E+ G + I + + + KG A +
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKM--------IDMPVERMHPHLSKGYAYVEF 54
Query: 558 IKKESVDLALSILDGYEIRGKKIKVERAK 586
+ + AL +DG +I G++I
Sbjct: 55 ENPDEAEKALKHMDGGQIDGQEITATAVL 83
Score = 32.1 bits (74), Expect = 0.12
Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 374 QQDLREECSKCGHVKKVVL-----HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
+ + E S G +K + + H +G A + F+ P+ A+ + ++G ++I
Sbjct: 18 KDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEI 77
Query: 429 TAE 431
TA
Sbjct: 78 TAT 80
Score = 32.1 bits (74), Expect = 0.12
Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 659 QQDLREECSKCGHVKKVVL-----HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
+ + E S G +K + + H +G A + F+ P+ A+ + ++G ++I
Sbjct: 18 KDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEI 77
Query: 714 TAE 716
TA
Sbjct: 78 TAT 80
>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 = 50.2 bits (120), Expect = 9e-08
Identities = 19/104 (18%), Positives = 36/104 (34%), Gaps = 15/104 (14%)
Query: 488 KKDLEKLKKAQENTKVYVSNLPLDLTQEEFV---EVMQKCGLVMKDVDTNQMKIKLYTDP 544
++ Q+N V+V L L E + E K G + K + +
Sbjct: 4 GSSGASVRVVQKNL-VFVVGLSQRLADPEVLKRPEYFGKFGKIHK--------VVINNST 54
Query: 545 YTKDFKGDALC---TYIKKESVDLALSILDGYEIRGKKIKVERA 585
+G + TYI+ E A+ ++ + G+ +K
Sbjct: 55 SYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLG 98
Score = 46.8 bits (111), Expect = 1e-06
Identities = 17/89 (19%), Positives = 31/89 (34%), Gaps = 14/89 (15%)
Query: 218 VYVSNLPLDLTQEEFV---EVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC---T 271
V+V L L E + E K G + K + + +G + T
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHK--------VVINNSTSYAGSQGPSASAYVT 69
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERA 300
YI+ E A+ ++ + G+ +K
Sbjct: 70 YIRSEDALRAIQCVNNVVVDGRTLKASLG 98
Score = 39.5 bits (92), Expect = 4e-04
Identities = 16/69 (23%), Positives = 25/69 (36%), Gaps = 9/69 (13%)
Query: 378 REECSKCGHVKKVVL-------HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITA 430
E K G + KVV+ + P A + + E A + +N R + A
Sbjct: 36 PEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKA 95
Query: 431 ETWDGKTRY 439
G T+Y
Sbjct: 96 S--LGTTKY 102
Score = 39.5 bits (92), Expect = 4e-04
Identities = 16/69 (23%), Positives = 25/69 (36%), Gaps = 9/69 (13%)
Query: 663 REECSKCGHVKKVVL-------HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITA 715
E K G + KVV+ + P A + + E A + +N R + A
Sbjct: 36 PEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKA 95
Query: 716 ETWDGKTRY 724
G T+Y
Sbjct: 96 S--LGTTKY 102
>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 = 50.3 bits (120), Expect = 1e-07
Identities = 22/113 (19%), Positives = 37/113 (32%), Gaps = 9/113 (7%)
Query: 189 PKAEEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDT 248
P+ ++ V + LP T+EE V+ +V
Sbjct: 16 PRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNG--- 72
Query: 249 NQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
I L DP K G+A + +E + AL I + I+V ++
Sbjct: 73 ----ITLPVDPEGK-ITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKSS 119
Score = 48.7 bits (116), Expect = 3e-07
Identities = 21/91 (23%), Positives = 35/91 (38%), Gaps = 9/91 (9%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 555
+ + V + LP T+EE V+ +V I L DP K G+A
Sbjct: 38 DSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNG-------ITLPVDPEGK-ITGEAFV 89
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ +E + AL I + I+V ++
Sbjct: 90 QFASQELAEKALG-KHKERIGHRYIEVFKSS 119
>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 = 49.2 bits (118), Expect = 2e-07
Identities = 24/108 (22%), Positives = 47/108 (43%), Gaps = 18/108 (16%)
Query: 199 QKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCG-----LVMKDVDTNQMKI 253
+ RK ++ GE + +Y+ NL +T+ + V + + + + T +M+
Sbjct: 9 EIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMR- 67
Query: 254 KLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
G A T+ KE AL +++GY++ GK + +E K
Sbjct: 68 ------------GQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK 103
Score = 45.4 bits (108), Expect = 4e-06
Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 18/99 (18%)
Query: 493 KLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCG-----LVMKDVDTNQMKIKLYTDPYTK 547
+ N +Y+ NL +T+ + V + + + + T +M+
Sbjct: 18 SYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMR---------- 67
Query: 548 DFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
G A T+ KE AL +++GY++ GK + +E K
Sbjct: 68 ---GQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK 103
Score = 37.7 bits (88), Expect = 0.002
Identities = 20/92 (21%), Positives = 32/92 (34%), Gaps = 18/92 (19%)
Query: 342 RGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGV- 400
GE +K + +KNL VT ++DL ++ K + + G
Sbjct: 21 PGEPNKV---LYLKNL------SPRVT-----ERDLVSLFARFQEKKGPPIQFRMMTGRM 66
Query: 401 ---AQIFFKEPEAADACRELLNGRWFGQRQIT 429
A I F E A L+NG + +
Sbjct: 67 RGQAFITFPNKEIAWQALHLVNGYKLYGKILV 98
Score = 37.7 bits (88), Expect = 0.002
Identities = 20/92 (21%), Positives = 32/92 (34%), Gaps = 18/92 (19%)
Query: 627 RGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGV- 685
GE +K + +KNL VT ++DL ++ K + + G
Sbjct: 21 PGEPNKV---LYLKNL------SPRVT-----ERDLVSLFARFQEKKGPPIQFRMMTGRM 66
Query: 686 ---AQIFFKEPEAADACRELLNGRWFGQRQIT 714
A I F E A L+NG + +
Sbjct: 67 RGQAFITFPNKEIAWQALHLVNGYKLYGKILV 98
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 48.8 bits (117), Expect = 2e-07
Identities = 23/127 (18%), Positives = 44/127 (34%), Gaps = 31/127 (24%)
Query: 480 KLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIK 539
L P+ ++ NT+++V PLD+ + E E+ G + ++KI
Sbjct: 13 GLVPRGSHMHHRQE--GELSNTRLFVRPFPLDVQESELNEIFGPFGPM------KEVKIL 64
Query: 540 LYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLK 599
G A + + ES A+ + G + ++V + K
Sbjct: 65 ----------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS-------------K 101
Query: 600 PKKKRKK 606
KR +
Sbjct: 102 LPAKRYR 108
Score = 46.9 bits (112), Expect = 1e-06
Identities = 23/125 (18%), Positives = 43/125 (34%), Gaps = 30/125 (24%)
Query: 198 GQKRKPEPPKWFDIGE-ESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 256
G + GE +T+++V PLD+ + E E+ G + ++KI
Sbjct: 13 GLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPM------KEVKIL-- 64
Query: 257 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPK 316
G A + + ES A+ + G + ++V + K
Sbjct: 65 --------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS-------------KLP 103
Query: 317 KKRKK 321
KR +
Sbjct: 104 AKRYR 108
Score = 37.7 bits (88), Expect = 0.002
Identities = 19/94 (20%), Positives = 36/94 (38%), Gaps = 15/94 (15%)
Query: 338 PDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHP 397
R E + + + V+ DV + +L E G +K+V +
Sbjct: 20 HMHHRQEGELSNTRLFVRPF------PLDVQ-----ESELNEIFGPFGPMKEVKI----L 64
Query: 398 EGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
G A + F+E E+A E ++G+ F + +
Sbjct: 65 NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV 98
Score = 37.7 bits (88), Expect = 0.002
Identities = 19/94 (20%), Positives = 36/94 (38%), Gaps = 15/94 (15%)
Query: 623 PDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHP 682
R E + + + V+ DV + +L E G +K+V +
Sbjct: 20 HMHHRQEGELSNTRLFVRPF------PLDVQ-----ESELNEIFGPFGPMKEVKI----L 64
Query: 683 EGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
G A + F+E E+A E ++G+ F + +
Sbjct: 65 NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV 98
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 48.1 bits (115), Expect = 3e-07
Identities = 17/93 (18%), Positives = 27/93 (29%), Gaps = 10/93 (10%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+ + N+ + + + I+L D T+ +G A
Sbjct: 7 HHMDTIILRNIAPHTVVDSIMTALSPYA------SLAVNNIRLIKDKQTQQNRGFAFVQL 60
Query: 273 IKKESVDLALSILDGYE----IRGKKIKVERAK 301
L IL I GK I V+ AK
Sbjct: 61 SSAMDASQLLQILQSLHPPLKIDGKTIGVDFAK 93
Score = 46.5 bits (111), Expect = 1e-06
Identities = 17/93 (18%), Positives = 27/93 (29%), Gaps = 10/93 (10%)
Query: 498 QENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 557
+ + N+ + + + I+L D T+ +G A
Sbjct: 7 HHMDTIILRNIAPHTVVDSIMTALSPYA------SLAVNNIRLIKDKQTQQNRGFAFVQL 60
Query: 558 IKKESVDLALSILDGYE----IRGKKIKVERAK 586
L IL I GK I V+ AK
Sbjct: 61 SSAMDASQLLQILQSLHPPLKIDGKTIGVDFAK 93
>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 = 48.0 bits (115), Expect = 3e-07
Identities = 20/93 (21%), Positives = 35/93 (37%), Gaps = 15/93 (16%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQKCG-----LVMKDVDTNQMKIKLYTDPYTKDFKGDA 268
S+ +++ NL T+E V K G + K + + + G
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLL----------SMGFG 53
Query: 269 LCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
Y K E AL L G+ + G K++V ++
Sbjct: 54 FVEYKKPEQAQKALKQLQGHTVDGHKLEVRISE 86
Score = 46.9 bits (112), Expect = 8e-07
Identities = 19/93 (20%), Positives = 35/93 (37%), Gaps = 15/93 (16%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCG-----LVMKDVDTNQMKIKLYTDPYTKDFKGDA 553
++ +++ NL T+E V K G + K + + + G
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLL----------SMGFG 53
Query: 554 LCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
Y K E AL L G+ + G K++V ++
Sbjct: 54 FVEYKKPEQAQKALKQLQGHTVDGHKLEVRISE 86
Score = 31.8 bits (73), Expect = 0.19
Identities = 20/91 (21%), Positives = 35/91 (38%), Gaps = 18/91 (19%)
Query: 346 SKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEGVAQ-- 402
S S + +KNL + T ++ L+ SK G +K + K+ GV
Sbjct: 2 SSGSSGLFIKNL------NFSTT-----EETLKGVFSKVGAIKSCTISKKKNKAGVLLSM 50
Query: 403 ----IFFKEPEAADACRELLNGRWFGQRQIT 429
+ +K+PE A + L G ++
Sbjct: 51 GFGFVEYKKPEQAQKALKQLQGHTVDGHKLE 81
Score = 31.8 bits (73), Expect = 0.19
Identities = 20/91 (21%), Positives = 35/91 (38%), Gaps = 18/91 (19%)
Query: 631 SKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEGVAQ-- 687
S S + +KNL + T ++ L+ SK G +K + K+ GV
Sbjct: 2 SSGSSGLFIKNL------NFSTT-----EETLKGVFSKVGAIKSCTISKKKNKAGVLLSM 50
Query: 688 ----IFFKEPEAADACRELLNGRWFGQRQIT 714
+ +K+PE A + L G ++
Sbjct: 51 GFGFVEYKKPEQAQKALKQLQGHTVDGHKLE 81
>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 = 48.5 bits (116), Expect = 3e-07
Identities = 19/105 (18%), Positives = 40/105 (38%), Gaps = 14/105 (13%)
Query: 482 KPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 541
K+ + + + + +N VY + LT + + G + M+I+++
Sbjct: 7 GNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQI--------MEIRVF 58
Query: 542 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ KG + + ES A+ ++G I G +K K
Sbjct: 59 PE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK 97
Score = 45.8 bits (109), Expect = 3e-06
Identities = 20/108 (18%), Positives = 40/108 (37%), Gaps = 18/108 (16%)
Query: 198 GQKRKPEPPKWFDIGEES----TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKI 253
G + ++ D+ +S VY + LT + + G +M+ I
Sbjct: 4 GSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIME--------I 55
Query: 254 KLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
+++ + KG + + ES A+ ++G I G +K K
Sbjct: 56 RVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK 97
Score = 37.7 bits (88), Expect = 0.002
Identities = 15/93 (16%), Positives = 32/93 (34%), Gaps = 15/93 (16%)
Query: 337 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK 395
R + + + S + + +T Q +R+ S G + ++ V +K
Sbjct: 13 RFEDVVNQSSPKNCTVYCGGI------ASGLT-----DQLMRQTFSPFGQIMEIRVFPEK 61
Query: 396 HPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
G + + F E+A +NG +
Sbjct: 62 ---GYSFVRFSTHESAAHAIVSVNGTTIEGHVV 91
Score = 37.7 bits (88), Expect = 0.002
Identities = 15/93 (16%), Positives = 32/93 (34%), Gaps = 15/93 (16%)
Query: 622 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK 680
R + + + S + + +T Q +R+ S G + ++ V +K
Sbjct: 13 RFEDVVNQSSPKNCTVYCGGI------ASGLT-----DQLMRQTFSPFGQIMEIRVFPEK 61
Query: 681 HPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
G + + F E+A +NG +
Sbjct: 62 ---GYSFVRFSTHESAAHAIVSVNGTTIEGHVV 91
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 48.5 bits (116), Expect = 4e-07
Identities = 18/90 (20%), Positives = 40/90 (44%), Gaps = 8/90 (8%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
G E +++ +LP + T + G V+ K++ D T K +
Sbjct: 37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVIS--------AKVFIDKQTSLSKCFGFVS 88
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ +S +A+ ++G+++ K++KV+ K
Sbjct: 89 FDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118
Score = 46.6 bits (111), Expect = 2e-06
Identities = 17/88 (19%), Positives = 39/88 (44%), Gaps = 8/88 (9%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
E +++ +LP + T + G V+ K++ D T K ++
Sbjct: 39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVIS--------AKVFIDKQTSLSKCFGFVSFD 90
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAK 586
+S +A+ ++G+++ K++KV+ K
Sbjct: 91 NPDSAQVAIKAMNGFQVGTKRLKVQLKK 118
Score = 33.1 bits (76), Expect = 0.092
Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 17/82 (20%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEGVAQIF----FK 406
+ + +L ++ T DL G+V V DK +++ F F
Sbjct: 43 LFIYHL------PQEFT-----DTDLASTFLPFGNVISAKVFIDKQ-TSLSKCFGFVSFD 90
Query: 407 EPEAADACRELLNGRWFGQRQI 428
P++A + +NG G +++
Sbjct: 91 NPDSAQVAIKAMNGFQVGTKRL 112
Score = 33.1 bits (76), Expect = 0.092
Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 17/82 (20%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEGVAQIF----FK 691
+ + +L ++ T DL G+V V DK +++ F F
Sbjct: 43 LFIYHL------PQEFT-----DTDLASTFLPFGNVISAKVFIDKQ-TSLSKCFGFVSFD 90
Query: 692 EPEAADACRELLNGRWFGQRQI 713
P++A + +NG G +++
Sbjct: 91 NPDSAQVAIKAMNGFQVGTKRL 112
>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 = 47.2 bits (113), Expect = 5e-07
Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 6/85 (7%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
+Y+ NL T E+ E + G+ D+ ++IK + + KG AL +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVN--DI----LEIKFFENRANGQSKGFALVGVGSEA 56
Query: 277 SVDLALSILDGYEIRGKKIKVERAK 301
S + +L E+ G+ V +
Sbjct: 57 SSKKLMDLLPKRELHGQNPVVTPSN 81
Score = 47.2 bits (113), Expect = 5e-07
Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 6/85 (7%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
+Y+ NL T E+ E + G+ D+ ++IK + + KG AL +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVN--DI----LEIKFFENRANGQSKGFALVGVGSEA 56
Query: 562 SVDLALSILDGYEIRGKKIKVERAK 586
S + +L E+ G+ V +
Sbjct: 57 SSKKLMDLLPKRELHGQNPVVTPSN 81
Score = 31.4 bits (72), Expect = 0.18
Identities = 9/62 (14%), Positives = 21/62 (33%), Gaps = 6/62 (9%)
Query: 374 QQDLREECSKCG--HVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQ 427
+DL E G + ++ ++ +G A + ++ +LL R +
Sbjct: 15 DEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQN 74
Query: 428 IT 429
Sbjct: 75 PV 76
Score = 31.4 bits (72), Expect = 0.18
Identities = 9/62 (14%), Positives = 21/62 (33%), Gaps = 6/62 (9%)
Query: 659 QQDLREECSKCG--HVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQ 712
+DL E G + ++ ++ +G A + ++ +LL R +
Sbjct: 15 DEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQN 74
Query: 713 IT 714
Sbjct: 75 PV 76
>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 = 46.8 bits (112), Expect = 8e-07
Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 16/90 (17%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
G+ STK++V N+ T +E ++ G V + D I KD+ A
Sbjct: 7 GKASTKLHVGNISPTCTNQELRAKFEEYGPV-IECD-----IV-------KDY---AFVH 50
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ E A+ LD E +GK++ V+ +
Sbjct: 51 MERAEDAVEAIRGLDNTEFQGKRMHVQLST 80
Score = 45.7 bits (109), Expect = 2e-06
Identities = 21/91 (23%), Positives = 38/91 (41%), Gaps = 16/91 (17%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 555
+ +TK++V N+ T +E ++ G V + D I KD+ A
Sbjct: 6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPV-IECD-----IV-------KDY---AFV 49
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ E A+ LD E +GK++ V+ +
Sbjct: 50 HMERAEDAVEAIRGLDNTEFQGKRMHVQLST 80
Score = 28.7 bits (65), Expect = 1.7
Identities = 11/65 (16%), Positives = 25/65 (38%), Gaps = 4/65 (6%)
Query: 374 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETW 433
Q+LR + + G V + + + A + + E A L+ F +++ +
Sbjct: 24 NQELRAKFEEYGPVIECDI----VKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS 79
Query: 434 DGKTR 438
+ R
Sbjct: 80 TSRLR 84
Score = 28.7 bits (65), Expect = 1.7
Identities = 11/65 (16%), Positives = 25/65 (38%), Gaps = 4/65 (6%)
Query: 659 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETW 718
Q+LR + + G V + + + A + + E A L+ F +++ +
Sbjct: 24 NQELRAKFEEYGPVIECDI----VKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS 79
Query: 719 DGKTR 723
+ R
Sbjct: 80 TSRLR 84
>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 = 47.0 bits (112), Expect = 8e-07
Identities = 16/90 (17%), Positives = 32/90 (35%), Gaps = 9/90 (10%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
V + LP ++EE V+ +V + L D + G+A
Sbjct: 12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG-------MTLPVDFQGR-STGEAFVQ 63
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ +E + AL I + I++ ++
Sbjct: 64 FASQEIAEKALK-KHKERIGHRYIEIFKSS 92
Score = 46.7 bits (111), Expect = 1e-06
Identities = 16/91 (17%), Positives = 33/91 (36%), Gaps = 9/91 (9%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 555
+ V + LP ++EE V+ +V + L D + G+A
Sbjct: 11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG-------MTLPVDFQGR-STGEAFV 62
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ +E + AL I + I++ ++
Sbjct: 63 QFASQEIAEKALK-KHKERIGHRYIEIFKSS 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 = 47.1 bits (112), Expect = 8e-07
Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 15/85 (17%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
+V VS LP + ++ + M++ G V D + G + +++KE
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVC-YADVYR--------------DGTGVVEFVRKE 61
Query: 277 SVDLALSILDGYEIRGKKIKVERAK 301
+ A+ LD + R + + +
Sbjct: 62 DMTYAVRKLDNTKFRSHEGETAYIR 86
Score = 47.1 bits (112), Expect = 8e-07
Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 15/85 (17%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
+V VS LP + ++ + M++ G V D + G + +++KE
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVC-YADVYR--------------DGTGVVEFVRKE 61
Query: 562 SVDLALSILDGYEIRGKKIKVERAK 586
+ A+ LD + R + + +
Sbjct: 62 DMTYAVRKLDNTKFRSHEGETAYIR 86
>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 = 46.4 bits (111), Expect = 9e-07
Identities = 21/91 (23%), Positives = 40/91 (43%), Gaps = 16/91 (17%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 555
+ K++V N+ T +E + ++ G V + D + KD+ A
Sbjct: 5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRV-IECD-----VV-------KDY---AFV 48
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKVERAK 586
K+ A++ L+G E++GK+I VE +
Sbjct: 49 HMEKEADAKAAIAQLNGKEVKGKRINVELST 79
Score = 46.0 bits (110), Expect = 1e-06
Identities = 21/89 (23%), Positives = 40/89 (44%), Gaps = 16/89 (17%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+ K++V N+ T +E + ++ G V + D + KD+ A
Sbjct: 7 GNTWKIFVGNVSAACTSQELRSLFERRGRV-IECD-----VV-------KDY---AFVHM 50
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
K+ A++ L+G E++GK+I VE +
Sbjct: 51 EKEADAKAAIAQLNGKEVKGKRINVELST 79
Score = 31.8 bits (73), Expect = 0.14
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 374 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
Q+LR + G V + + + A + ++ A A LNG+ ++I E
Sbjct: 23 SQELRSLFERRGRVIECDVV----KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE 76
Score = 31.8 bits (73), Expect = 0.14
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 659 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
Q+LR + G V + + + A + ++ A A LNG+ ++I E
Sbjct: 23 SQELRSLFERRGRVIECDVV----KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE 76
>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 = 47.3 bits (113), Expect = 9e-07
Identities = 19/105 (18%), Positives = 44/105 (41%), Gaps = 9/105 (8%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
G + V+V+NL + ++ EV G+V ++ + D K +G T
Sbjct: 12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVV--------VRADILEDKDGKS-RGIGTVT 62
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPK 316
+ + A+S+ +G + + + V+ + + + P +P+
Sbjct: 63 FEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQ 107
Score = 45.0 bits (107), Expect = 5e-06
Identities = 19/108 (17%), Positives = 46/108 (42%), Gaps = 9/108 (8%)
Query: 494 LKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDA 553
L+ + + V+V+NL + ++ EV G+V ++ + D K +G
Sbjct: 9 LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVV--------VRADILEDKDGKS-RGIG 59
Query: 554 LCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPK 601
T+ + A+S+ +G + + + V+ + + + P +P+
Sbjct: 60 TVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQ 107
Score = 37.7 bits (88), Expect = 0.002
Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 14/81 (17%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK--HPEGVAQIFFKEP 408
+ V NL D V + L+E S G V + +L DK G+ + F++
Sbjct: 18 VFVANL------DYKVG-----WKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQS 66
Query: 409 EAADACRELLNGRWFGQRQIT 429
A + NG+ R +
Sbjct: 67 IEAVQAISMFNGQLLFDRPMH 87
Score = 37.7 bits (88), Expect = 0.002
Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 14/81 (17%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK--HPEGVAQIFFKEP 693
+ V NL D V + L+E S G V + +L DK G+ + F++
Sbjct: 18 VFVANL------DYKVG-----WKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQS 66
Query: 694 EAADACRELLNGRWFGQRQIT 714
A + NG+ R +
Sbjct: 67 IEAVQAISMFNGQLLFDRPMH 87
>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 = 46.9 bits (112), Expect = 1e-06
Identities = 17/89 (19%), Positives = 35/89 (39%), Gaps = 10/89 (11%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+++VSN+P + ++ + G ++ +++ + KG T+
Sbjct: 13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILD--------VEIIFNERGS--KGFGFVTF 62
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
D A L G + G+KI+V A
Sbjct: 63 ENSADADRAREKLHGTVVEGRKIEVNNAT 91
Score = 46.1 bits (110), Expect = 2e-06
Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 10/92 (10%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+ +++VSN+P + ++ + G ++ +++ + KG
Sbjct: 10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILD--------VEIIFNERGS--KGFGF 59
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
T+ D A L G + G+KI+V A
Sbjct: 60 VTFENSADADRAREKLHGTVVEGRKIEVNNAT 91
Score = 35.0 bits (81), Expect = 0.013
Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 374 QQDLREECSKCGHVK--KVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
DLR+ + G + +++ +++ +G + F+ AD RE L+G R+I
Sbjct: 29 DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE 86
Score = 35.0 bits (81), Expect = 0.013
Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 659 QQDLREECSKCGHVK--KVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
DLR+ + G + +++ +++ +G + F+ AD RE L+G R+I
Sbjct: 29 DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE 86
>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 = 47.4 bits (113), Expect = 1e-06
Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 16/103 (15%)
Query: 484 KKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTD 543
+R + + ++ +YV D+T G ++ + +
Sbjct: 23 PFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIID--------LSMDPP 72
Query: 544 PYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ A TY K ES D A++ L+G ++ ++KV A+
Sbjct: 73 ------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR 109
Score = 44.7 bits (106), Expect = 8e-06
Identities = 20/105 (19%), Positives = 39/105 (37%), Gaps = 18/105 (17%)
Query: 197 PGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 256
P ++ P + + +YV D+T G ++ + +
Sbjct: 23 PFRRSDSFPER--RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIID--------LSMD 70
Query: 257 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ A TY K ES D A++ L+G ++ ++KV A+
Sbjct: 71 PP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR 109
Score = 33.2 bits (76), Expect = 0.077
Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 17/86 (19%)
Query: 344 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEGVAQ 402
+ + + V D+T LR S G++ + + + A
Sbjct: 34 RAPRKGNTLYVYGE--------DMT-----PTLLRGAFSPFGNIIDLSMDPPR---NCAF 77
Query: 403 IFFKEPEAADACRELLNGRWFGQRQI 428
+ +++ E+AD LNG Q+
Sbjct: 78 VTYEKMESADQAVAELNGTQVESVQL 103
Score = 33.2 bits (76), Expect = 0.077
Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 17/86 (19%)
Query: 629 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEGVAQ 687
+ + + V D+T LR S G++ + + + A
Sbjct: 34 RAPRKGNTLYVYGE--------DMT-----PTLLRGAFSPFGNIIDLSMDPPR---NCAF 77
Query: 688 IFFKEPEAADACRELLNGRWFGQRQI 713
+ +++ E+AD LNG Q+
Sbjct: 78 VTYEKMESADQAVAELNGTQVESVQL 103
>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 = 47.1 bits (112), Expect = 1e-06
Identities = 19/104 (18%), Positives = 33/104 (31%), Gaps = 13/104 (12%)
Query: 197 PGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 256
GQKR E VY+ LP + + ++ +K +V I +
Sbjct: 11 SGQKRSRSRSP----HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDS-------IYIA 59
Query: 257 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 300
P K G+ + + AL + + I+V
Sbjct: 60 YGPNGK-ATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI 101
Score = 46.8 bits (111), Expect = 2e-06
Identities = 15/103 (14%), Positives = 31/103 (30%), Gaps = 9/103 (8%)
Query: 483 PKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYT 542
+K + VY+ LP + + ++ +K +V I +
Sbjct: 8 KSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDS-------IYIAY 60
Query: 543 DPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 585
P K G+ + + AL + + I+V
Sbjct: 61 GPNGK-ATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI 101
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 46.0 bits (110), Expect = 1e-06
Identities = 17/97 (17%), Positives = 40/97 (41%), Gaps = 16/97 (16%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMK---DVDTNQMKIKLYTDPYTKDFKGDALCT 271
+ +++V NLP D T + + +CG V+ ++ + K G +
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSK-------------GCGVVK 54
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEA 308
+ E + A +++G ++ G++I V + +
Sbjct: 55 FESPEVAERACRMMNGMKLSGREIDVRIDRNASGPSS 91
Score = 45.6 bits (109), Expect = 2e-06
Identities = 17/97 (17%), Positives = 39/97 (40%), Gaps = 16/97 (16%)
Query: 500 NTKVYVSNLPLDLTQEEFVEVMQKCGLVMK---DVDTNQMKIKLYTDPYTKDFKGDALCT 556
+++V NLP D T + + +CG V+ ++ + K G +
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSK-------------GCGVVK 54
Query: 557 YIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEA 593
+ E + A +++G ++ G++I V + +
Sbjct: 55 FESPEVAERACRMMNGMKLSGREIDVRIDRNASGPSS 91
Score = 34.9 bits (81), Expect = 0.011
Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 13/80 (16%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK--KVVLHDKHPEGVAQIFFKEPE 409
I V+NL D T + L+++ ++CGHV + + + +G + F+ PE
Sbjct: 11 IFVRNL------PFDFT-----WKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPE 59
Query: 410 AADACRELLNGRWFGQRQIT 429
A+ ++NG R+I
Sbjct: 60 VAERACRMMNGMKLSGREID 79
Score = 34.9 bits (81), Expect = 0.011
Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 13/80 (16%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK--KVVLHDKHPEGVAQIFFKEPE 694
I V+NL D T + L+++ ++CGHV + + + +G + F+ PE
Sbjct: 11 IFVRNL------PFDFT-----WKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPE 59
Query: 695 AADACRELLNGRWFGQRQIT 714
A+ ++NG R+I
Sbjct: 60 VAERACRMMNGMKLSGREID 79
>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 = 46.5 bits (111), Expect = 1e-06
Identities = 18/90 (20%), Positives = 41/90 (45%), Gaps = 8/90 (8%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
G E +++ +LP + ++ +++ G V+ K++ D T K +
Sbjct: 22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVS--------AKVFIDKQTNLSKCFGFVS 73
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAK 301
Y S A+ ++G++I K++KV+ +
Sbjct: 74 YDNPVSAQAAIQSMNGFQIGMKRLKVQLKR 103
Score = 45.0 bits (107), Expect = 5e-06
Identities = 18/92 (19%), Positives = 42/92 (45%), Gaps = 8/92 (8%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
K+ E +++ +LP + ++ +++ G V+ K++ D T K
Sbjct: 20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVS--------AKVFIDKQTNLSKCFGF 71
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+Y S A+ ++G++I K++KV+ +
Sbjct: 72 VSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR 103
Score = 30.4 bits (69), Expect = 0.78
Identities = 16/83 (19%), Positives = 33/83 (39%), Gaps = 17/83 (20%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEGVAQIF----FK 406
+ + +L ++ QDL + G+V V DK +++ F +
Sbjct: 28 LFIYHL------PQEFG-----DQDLLQMFMPFGNVVSAKVFIDKQ-TNLSKCFGFVSYD 75
Query: 407 EPEAADACRELLNGRWFGQRQIT 429
P +A A + +NG G +++
Sbjct: 76 NPVSAQAAIQSMNGFQIGMKRLK 98
Score = 30.4 bits (69), Expect = 0.78
Identities = 16/83 (19%), Positives = 33/83 (39%), Gaps = 17/83 (20%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEGVAQIF----FK 691
+ + +L ++ QDL + G+V V DK +++ F +
Sbjct: 28 LFIYHL------PQEFG-----DQDLLQMFMPFGNVVSAKVFIDKQ-TNLSKCFGFVSYD 75
Query: 692 EPEAADACRELLNGRWFGQRQIT 714
P +A A + +NG G +++
Sbjct: 76 NPVSAQAAIQSMNGFQIGMKRLK 98
>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 = 46.3 bits (110), Expect = 2e-06
Identities = 15/105 (14%), Positives = 32/105 (30%), Gaps = 16/105 (15%)
Query: 197 PGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 256
G KP P + V V +P + + + + + L
Sbjct: 3 SGSSGKPLPIN-----PDDLYVSVHGMPFSAMENDVRDFFHGLRVD---------AVHLL 48
Query: 257 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
D + G+ L ++ + AL + + + ++V A
Sbjct: 49 KDHVGR-NNGNGLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPAT 91
Score = 43.2 bits (102), Expect = 2e-05
Identities = 12/95 (12%), Positives = 31/95 (32%), Gaps = 11/95 (11%)
Query: 492 EKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKG 551
+ L ++ V V +P + + + + + L D + G
Sbjct: 8 KPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRVD---------AVHLLKDHVGR-NNG 57
Query: 552 DALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ L ++ + AL + + + ++V A
Sbjct: 58 NGLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPAT 91
>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 = 45.7 bits (109), Expect = 2e-06
Identities = 20/92 (21%), Positives = 31/92 (33%), Gaps = 14/92 (15%)
Query: 210 DIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 269
D +YV NL L ++E + KI+ Y A
Sbjct: 10 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPG---AVERVKKIRDY-----------AF 55
Query: 270 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ +E A+ L+G + G I+V AK
Sbjct: 56 VHFSNREDAVEAMKALNGKVLDGSPIEVTLAK 87
Score = 45.0 bits (107), Expect = 5e-06
Identities = 19/90 (21%), Positives = 30/90 (33%), Gaps = 14/90 (15%)
Query: 497 AQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 556
+YV NL L ++E + KI+ Y A
Sbjct: 12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPG---AVERVKKIRDY-----------AFVH 57
Query: 557 YIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ +E A+ L+G + G I+V AK
Sbjct: 58 FSNREDAVEAMKALNGKVLDGSPIEVTLAK 87
Score = 38.0 bits (89), Expect = 0.001
Identities = 13/85 (15%), Positives = 28/85 (32%), Gaps = 13/85 (15%)
Query: 344 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQI 403
+ + ++ V+NL + ++ + +E + + K A +
Sbjct: 10 DTMSSVKILYVRNL------MLSTS-----EEMIEKEFNNIKPGAVERV--KKIRDYAFV 56
Query: 404 FFKEPEAADACRELLNGRWFGQRQI 428
F E A + LNG+ I
Sbjct: 57 HFSNREDAVEAMKALNGKVLDGSPI 81
Score = 38.0 bits (89), Expect = 0.001
Identities = 13/85 (15%), Positives = 28/85 (32%), Gaps = 13/85 (15%)
Query: 629 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQI 688
+ + ++ V+NL + ++ + +E + + K A +
Sbjct: 10 DTMSSVKILYVRNL------MLSTS-----EEMIEKEFNNIKPGAVERV--KKIRDYAFV 56
Query: 689 FFKEPEAADACRELLNGRWFGQRQI 713
F E A + LNG+ I
Sbjct: 57 HFSNREDAVEAMKALNGKVLDGSPI 81
>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 = 46.1 bits (110), Expect = 2e-06
Identities = 19/118 (16%), Positives = 49/118 (41%), Gaps = 29/118 (24%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+ ++V NL +T+E + + G + + +K KD+ A +
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLER------VKKL-------KDY---AFIHF 52
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQ 330
+++ A+ ++G ++ G+ I++ A KP +++K+ + ++A
Sbjct: 53 DERDGAVKAMEEMNGKDLEGENIEIVFA-------------KPPDQKRKERKAQRQAA 97
Score = 45.7 bits (109), Expect = 2e-06
Identities = 19/117 (16%), Positives = 49/117 (41%), Gaps = 29/117 (24%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
+ ++V NL +T+E + + G + + +K KD+ A +
Sbjct: 10 KVKVLFVRNLANTVTEEILEKAFSQFGKLER------VKKL-------KDY---AFIHFD 53
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQ 615
+++ A+ ++G ++ G+ I++ A KP +++K+ + ++A
Sbjct: 54 ERDGAVKAMEEMNGKDLEGENIEIVFA-------------KPPDQKRKERKAQRQAA 97
Score = 36.9 bits (86), Expect = 0.003
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 15/83 (18%)
Query: 346 SKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFF 405
V+ V+NL VT ++ L + S+ G +++V K + A I F
Sbjct: 8 MAKVKVLFVRNL------ANTVT-----EEILEKAFSQFGKLERV----KKLKDYAFIHF 52
Query: 406 KEPEAADACRELLNGRWFGQRQI 428
E + A E +NG+ I
Sbjct: 53 DERDGAVKAMEEMNGKDLEGENI 75
Score = 36.9 bits (86), Expect = 0.003
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 15/83 (18%)
Query: 631 SKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFF 690
V+ V+NL VT ++ L + S+ G +++V K + A I F
Sbjct: 8 MAKVKVLFVRNL------ANTVT-----EEILEKAFSQFGKLERV----KKLKDYAFIHF 52
Query: 691 KEPEAADACRELLNGRWFGQRQI 713
E + A E +NG+ I
Sbjct: 53 DERDGAVKAMEEMNGKDLEGENI 75
>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 = 45.7 bits (109), Expect = 2e-06
Identities = 20/90 (22%), Positives = 34/90 (37%), Gaps = 11/90 (12%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
+ S ++V L D T+E E + ++ TD T KG
Sbjct: 12 SQPSKTLFVKGLSEDTTEETLKESFDGSV-----------RARIVTDRETGSSKGFGFVD 60
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ +E A ++ EI G K+ ++ AK
Sbjct: 61 FNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90
Score = 44.9 bits (107), Expect = 5e-06
Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 11/92 (11%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
++Q + ++V L D T+E E + ++ TD T KG
Sbjct: 10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSV-----------RARIVTDRETGSSKGFGF 58
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ +E A ++ EI G K+ ++ AK
Sbjct: 59 VDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90
Score = 28.0 bits (63), Expect = 3.4
Identities = 10/59 (16%), Positives = 23/59 (38%), Gaps = 5/59 (8%)
Query: 374 QQDLREECSKCGHVKKVVLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
++ L+E + ++ D+ +G + F E A A +E + ++T
Sbjct: 29 EETLKESFDGSVRAR--IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVT 85
Score = 28.0 bits (63), Expect = 3.4
Identities = 10/59 (16%), Positives = 23/59 (38%), Gaps = 5/59 (8%)
Query: 659 QQDLREECSKCGHVKKVVLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
++ L+E + ++ D+ +G + F E A A +E + ++T
Sbjct: 29 EETLKESFDGSVRAR--IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVT 85
>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 = 47.5 bits (114), Expect = 2e-06
Identities = 19/88 (21%), Positives = 40/88 (45%), Gaps = 9/88 (10%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+++ K++V + D+ +EF E + G + + +L D T +G TY
Sbjct: 85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTI--------IDAQLMLDKDTGQSRGFGFVTY 136
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERA 300
++VD + + +KI+++RA
Sbjct: 137 DSADAVDRVCQ-NKFIDFKDRKIEIKRA 163
Score = 47.1 bits (113), Expect = 3e-06
Identities = 19/91 (20%), Positives = 39/91 (42%), Gaps = 9/91 (9%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+ + K++V + D+ +EF E + G + + +L D T +G
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTI--------IDAQLMLDKDTGQSRGFGF 133
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERA 585
TY ++VD + + +KI+++RA
Sbjct: 134 VTYDSADAVDRVCQ-NKFIDFKDRKIEIKRA 163
Score = 44.8 bits (107), Expect = 2e-05
Identities = 43/217 (19%), Positives = 67/217 (30%), Gaps = 69/217 (31%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+ES K+++ L D T++ E K G V D MK DP T +G ++
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTV---TDLKIMK-----DPATGRSRGFGFLSF 52
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEK 332
K SVD + + + GK I +RA P+ + K K
Sbjct: 53 EKPSSVDEVVK--TQHILDGKVIDPKRAI---------PRDEQDKTGK------------ 89
Query: 333 LFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL 392
I V + DV ++ E S+ G + L
Sbjct: 90 -------------------IFVGGI------GPDVR-----PKEFEEFFSQWGTIIDAQL 119
Query: 393 -HDKH---PEGVAQIFFKEPEAADACREL----LNGR 421
DK G + + +A D + R
Sbjct: 120 MLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDR 156
Score = 42.9 bits (102), Expect = 7e-05
Identities = 42/217 (19%), Positives = 67/217 (30%), Gaps = 69/217 (31%)
Query: 498 QENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 557
+E+ K+++ L D T++ E K G V D MK DP T +G ++
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTV---TDLKIMK-----DPATGRSRGFGFLSF 52
Query: 558 IKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEK 617
K SVD + + + GK I +RA P+ + K K
Sbjct: 53 EKPSSVDEVVK--TQHILDGKVIDPKRAI---------PRDEQDKTGK------------ 89
Query: 618 LFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL 677
I V + DV ++ E S+ G + L
Sbjct: 90 -------------------IFVGGI------GPDVR-----PKEFEEFFSQWGTIIDAQL 119
Query: 678 -HDKH---PEGVAQIFFKEPEAADACREL----LNGR 706
DK G + + +A D + R
Sbjct: 120 MLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDR 156
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 45.7 bits (109), Expect = 2e-06
Identities = 24/104 (23%), Positives = 40/104 (38%), Gaps = 16/104 (15%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
KVYV NL + E G + + V I ++ G A +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPL-RTVW-----IA-------RNPPGFAFVEFEDPR 48
Query: 277 SVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRK 320
+ A+ LDG I G +++VE + + +D +P +RK
Sbjct: 49 DAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFD---RPPARRK 89
Score = 45.7 bits (109), Expect = 2e-06
Identities = 24/104 (23%), Positives = 40/104 (38%), Gaps = 16/104 (15%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
KVYV NL + E G + + V I ++ G A +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPL-RTVW-----IA-------RNPPGFAFVEFEDPR 48
Query: 562 SVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRK 605
+ A+ LDG I G +++VE + + +D +P +RK
Sbjct: 49 DAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFD---RPPARRK 89
Score = 36.1 bits (84), Expect = 0.006
Identities = 13/58 (22%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 374 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
+ +L S G ++ V + ++P G A + F++P A+ L+G+ ++ E
Sbjct: 14 KGELERAFSYYGPLRTVWI-ARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVE 70
Score = 36.1 bits (84), Expect = 0.006
Identities = 13/58 (22%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 659 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
+ +L S G ++ V + ++P G A + F++P A+ L+G+ ++ E
Sbjct: 14 KGELERAFSYYGPLRTVWI-ARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVE 70
>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 = 46.4 bits (110), Expect = 2e-06
Identities = 17/116 (14%), Positives = 38/116 (32%), Gaps = 24/116 (20%)
Query: 188 NPKAEEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVD 247
+ G R P S +++ LP+D+T+ E + + G V
Sbjct: 12 SGLVPRGSHMGDSRSAGVP--------SRVIHIRKLPIDVTEGEVISLGLPFGKV----- 58
Query: 248 TNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALS--ILDGYEIRGKKIKVERAK 301
+ + K A +E+ + ++ +RG+ I ++ +
Sbjct: 59 ---TNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN 105
Score = 43.4 bits (102), Expect = 2e-05
Identities = 16/106 (15%), Positives = 39/106 (36%), Gaps = 17/106 (16%)
Query: 484 KKKRKKDLEKLKKAQENTKV-YVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYT 542
R + + A ++V ++ LP+D+T+ E + + G V + +
Sbjct: 14 LVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKV--------TNLLMLK 65
Query: 543 DPYTKDFKGDALCTYIKKESVDLALS--ILDGYEIRGKKIKVERAK 586
K A +E+ + ++ +RG+ I ++ +
Sbjct: 66 G------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN 105
>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 = 48.1 bits (115), Expect = 2e-06
Identities = 30/215 (13%), Positives = 66/215 (30%), Gaps = 66/215 (30%)
Query: 375 QDLREECSKCGHVKKVVL----HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITA 430
+ LR + G + V+ + K G + + E DA
Sbjct: 28 ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---------------- 71
Query: 431 ETWDGKTRYKIQETAEEREARLKKWETFLGKKIKVERAKFTMKGEAYDPKLKPKKKRKKD 490
R ++ G+ ++ +RA ++D
Sbjct: 72 --------------MNARPHKVD------GRVVEPKRAV-----------------SRED 94
Query: 491 LEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFK 550
++ K++V + D + + ++ G + I++ TD + +
Sbjct: 95 SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--------EVIEIMTDRGSGKKR 146
Query: 551 GDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 585
G A T+ +SVD + + + G +V +A
Sbjct: 147 GFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA 180
Score = 46.1 bits (110), Expect = 8e-06
Identities = 17/101 (16%), Positives = 38/101 (37%), Gaps = 12/101 (11%)
Query: 200 KRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDP 259
+ + P K++V + D + + ++ G + I++ TD
Sbjct: 92 REDSQRPGAH---LTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--------EVIEIMTDR 140
Query: 260 YTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 300
+ +G A T+ +SVD + + + G +V +A
Sbjct: 141 GSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA 180
Score = 41.1 bits (97), Expect = 5e-04
Identities = 28/120 (23%), Positives = 51/120 (42%), Gaps = 15/120 (12%)
Query: 483 PKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYT 542
K + K+ E+L+K +++ L + T E ++ G + D M+
Sbjct: 2 SKSESPKEPEQLRK------LFIGGLSFETTDESLRSHFEQWGTL---TDCVVMR----- 47
Query: 543 DPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKK 602
DP TK +G TY E VD A++ +++ G+ ++ +RA + L KK
Sbjct: 48 DPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK 106
Score = 41.1 bits (97), Expect = 5e-04
Identities = 25/105 (23%), Positives = 45/105 (42%), Gaps = 9/105 (8%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
E+ K+++ L + T E ++ G + D M+ DP TK +G TY
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTL---TDCVVMR-----DPNTKRSRGFGFVTY 62
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKK 317
E VD A++ +++ G+ ++ +RA + L KK
Sbjct: 63 ATVEEVDAAMN-ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK 106
>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 = 45.2 bits (108), Expect = 2e-06
Identities = 26/85 (30%), Positives = 38/85 (44%), Gaps = 9/85 (10%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
+YV NL T E+ E+ + G V +KL D TK KG ++E
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKV--------FNVKLIYDRETKKPKGFGFVEM-QEE 53
Query: 277 SVDLALSILDGYEIRGKKIKVERAK 301
SV A++ LD + G+ I+V A
Sbjct: 54 SVSEAIAKLDNTDFMGRTIRVTEAN 78
Score = 45.2 bits (108), Expect = 2e-06
Identities = 26/85 (30%), Positives = 38/85 (44%), Gaps = 9/85 (10%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
+YV NL T E+ E+ + G V +KL D TK KG ++E
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKV--------FNVKLIYDRETKKPKGFGFVEM-QEE 53
Query: 562 SVDLALSILDGYEIRGKKIKVERAK 586
SV A++ LD + G+ I+V A
Sbjct: 54 SVSEAIAKLDNTDFMGRTIRVTEAN 78
Score = 29.8 bits (68), Expect = 0.82
Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 374 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+ ++E S+ G V V +++D+ P+G + +E ++A +L + F R I
Sbjct: 15 SEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKL-DNTDFMGRTIR 73
Score = 29.8 bits (68), Expect = 0.82
Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 659 QQDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ ++E S+ G V V +++D+ P+G + +E ++A +L + F R I
Sbjct: 15 SEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKL-DNTDFMGRTIR 73
>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 = 45.4 bits (108), Expect = 2e-06
Identities = 17/90 (18%), Positives = 34/90 (37%), Gaps = 11/90 (12%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
G V + P ++T++ +E + V I++ + + G
Sbjct: 7 GTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV---------AIRIVRNAHGN-KTGYIFVD 56
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ +E V AL + + G+ I+V R K
Sbjct: 57 FSNEEEVKQALK-CNREYMGGRYIEVFREK 85
Score = 43.8 bits (104), Expect = 9e-06
Identities = 16/91 (17%), Positives = 33/91 (36%), Gaps = 11/91 (12%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 555
V + P ++T++ +E + V I++ + + G
Sbjct: 6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV---------AIRIVRNAHGN-KTGYIFV 55
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ +E V AL + + G+ I+V R K
Sbjct: 56 DFSNEEEVKQALK-CNREYMGGRYIEVFREK 85
>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 = 45.7 bits (109), Expect = 3e-06
Identities = 24/114 (21%), Positives = 44/114 (38%), Gaps = 20/114 (17%)
Query: 198 GQKRKPEPPKW----FDIG-------EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDV 246
G + K P KW FD G E K+ VSNL ++ + E+ + G +
Sbjct: 1 GSRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTL---- 56
Query: 247 DTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 300
K ++ D + G A + +K A+ +G + G+ + ++
Sbjct: 57 ----KKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 105
Score = 43.4 bits (103), Expect = 2e-05
Identities = 19/111 (17%), Positives = 41/111 (36%), Gaps = 13/111 (11%)
Query: 479 PKLKPKKKRKKDLEKLKK----AQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTN 534
PK P K + + + K+ VSNL ++ + E+ + G +
Sbjct: 4 PKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTL------- 56
Query: 535 QMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERA 585
K ++ D + G A + +K A+ +G + G+ + ++
Sbjct: 57 -KKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 105
Score = 41.1 bits (97), Expect = 1e-04
Identities = 28/114 (24%), Positives = 42/114 (36%), Gaps = 20/114 (17%)
Query: 319 RKKDLEKLKKAQEKLFDWRPDKMRGERSKNESV-IIVKNLFDPALFDKDVTLILEYQQDL 377
R K L K Q LFD G ++V NL D V+ D+
Sbjct: 3 RPKQLPD--KWQHDLFD---SGFGGGAGVETGGKLLVSNL------DFGVS-----DADI 46
Query: 378 REECSKCGHVKKVVLH-DK--HPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
+E ++ G +KK +H D+ G A + F+ A + NG R +
Sbjct: 47 QELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 100
Score = 41.1 bits (97), Expect = 1e-04
Identities = 28/114 (24%), Positives = 42/114 (36%), Gaps = 20/114 (17%)
Query: 604 RKKDLEKLKKAQEKLFDWRPDKMRGERSKNESV-IIVKNLFDPALFDKDVTLILEYQQDL 662
R K L K Q LFD G ++V NL D V+ D+
Sbjct: 3 RPKQLPD--KWQHDLFD---SGFGGGAGVETGGKLLVSNL------DFGVS-----DADI 46
Query: 663 REECSKCGHVKKVVLH-DK--HPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
+E ++ G +KK +H D+ G A + F+ A + NG R +
Sbjct: 47 QELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 100
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 45.4 bits (108), Expect = 3e-06
Identities = 17/101 (16%), Positives = 38/101 (37%), Gaps = 10/101 (9%)
Query: 486 KRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPY 545
+ + + +++VSN+P + ++ + G + + +++ +
Sbjct: 15 VPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKI--------LDVEIIFNER 66
Query: 546 TKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
KG T+ D A L G + G+KI+V A
Sbjct: 67 GS--KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 105
Score = 45.0 bits (107), Expect = 5e-06
Identities = 17/89 (19%), Positives = 36/89 (40%), Gaps = 10/89 (11%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+ +++VSN+P + ++ + G ++ +++ + KG T+
Sbjct: 27 SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILD--------VEIIFNERGS--KGFGFVTF 76
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
D A L G + G+KI+V A
Sbjct: 77 ENSADADRAREKLHGTVVEGRKIEVNNAT 105
Score = 35.0 bits (81), Expect = 0.019
Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 13/95 (13%)
Query: 337 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK--KVVLHD 394
R M E + V N+ DLR+ + G + +++ ++
Sbjct: 17 RGSHMNTENKSQPKRLHVSNI------PFRFR-----DPDLRQMFGQFGKILDVEIIFNE 65
Query: 395 KHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+ +G + F+ AD RE L+G R+I
Sbjct: 66 RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE 100
Score = 35.0 bits (81), Expect = 0.019
Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 13/95 (13%)
Query: 622 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK--KVVLHD 679
R M E + V N+ DLR+ + G + +++ ++
Sbjct: 17 RGSHMNTENKSQPKRLHVSNI------PFRFR-----DPDLRQMFGQFGKILDVEIIFNE 65
Query: 680 KHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ +G + F+ AD RE L+G R+I
Sbjct: 66 RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE 100
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 45.6 bits (108), Expect = 3e-06
Identities = 17/118 (14%), Positives = 32/118 (27%), Gaps = 14/118 (11%)
Query: 492 EKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKG 551
+ T + NLP E E + G + P
Sbjct: 2 SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFG-----------SLGRVLLPEGGIT-- 48
Query: 552 DALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLE 609
A+ +++ A L + + +E A + G A K ++ + E
Sbjct: 49 -AIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAE 105
Score = 44.8 bits (106), Expect = 7e-06
Identities = 26/131 (19%), Positives = 44/131 (33%), Gaps = 26/131 (19%)
Query: 625 KMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEG 684
RSK VI+ KNL +++E S+ G + +V+L +
Sbjct: 3 SGSSGRSKT--VILAKNL------PAGTL-----AAEIQETFSRFGSLGRVLLPEGG--I 47
Query: 685 VAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFL 744
A + F EP A L F + E W + ++ +
Sbjct: 48 TAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE-WAPIGVFGAAPQKKDSQ---------- 96
Query: 745 EEEDKKKKEAG 755
E+ +K E+G
Sbjct: 97 HEQPAEKAESG 107
Score = 43.3 bits (102), Expect = 2e-05
Identities = 22/115 (19%), Positives = 37/115 (32%), Gaps = 16/115 (13%)
Query: 340 KMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEG 399
RSK VI+ KNL +++E S+ G + +V+L +
Sbjct: 3 SGSSGRSKT--VILAKNL------PAGTL-----AAEIQETFSRFGSLGRVLLPEGG--I 47
Query: 400 VAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKK 454
A + F EP A L F + E W + ++ +
Sbjct: 48 TAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE-WAPIGVFGAAPQKKDSQHEQPA 101
Score = 42.9 bits (101), Expect = 3e-05
Identities = 17/110 (15%), Positives = 31/110 (28%), Gaps = 14/110 (12%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
T + NLP E E + G + P A+ +++
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFG-----------SLGRVLLPEGGIT---AIVEFLE 55
Query: 275 KESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLE 324
A L + + +E A + G A K ++ + E
Sbjct: 56 PLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAE 105
>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 = 44.9 bits (107), Expect = 4e-06
Identities = 16/99 (16%), Positives = 32/99 (32%), Gaps = 13/99 (13%)
Query: 203 PEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTK 262
P +++ NL + + E + + D T
Sbjct: 8 PVEGSE---STTPFNLFIGNLNPNKSVAELKVAISELFAK---------NDLAVVDVRTG 55
Query: 263 DFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ + E ++ AL L G ++ G +IK+E+ K
Sbjct: 56 TNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK 93
Score = 43.8 bits (104), Expect = 1e-05
Identities = 16/97 (16%), Positives = 35/97 (36%), Gaps = 10/97 (10%)
Query: 490 DLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDF 549
D + ++ +++ NL + + E + + D T
Sbjct: 7 DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAK---------NDLAVVDVRTGTN 57
Query: 550 KGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ + E ++ AL L G ++ G +IK+E+ K
Sbjct: 58 RKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK 93
Score = 36.1 bits (84), Expect = 0.006
Identities = 14/96 (14%), Positives = 29/96 (30%), Gaps = 15/96 (15%)
Query: 337 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDK- 395
D + G S + + NL + + + +L+ S+ + + D
Sbjct: 5 LEDPVEGSESTTPFNLFIGNL------NPNKS-----VAELKVAISELFAKNDLAVVDVR 53
Query: 396 --HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+ F+ E + E L G +I
Sbjct: 54 TGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIK 88
Score = 36.1 bits (84), Expect = 0.006
Identities = 14/96 (14%), Positives = 29/96 (30%), Gaps = 15/96 (15%)
Query: 622 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDK- 680
D + G S + + NL + + + +L+ S+ + + D
Sbjct: 5 LEDPVEGSESTTPFNLFIGNL------NPNKS-----VAELKVAISELFAKNDLAVVDVR 53
Query: 681 --HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ F+ E + E L G +I
Sbjct: 54 TGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIK 88
>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 = 44.9 bits (107), Expect = 4e-06
Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 16/90 (17%)
Query: 497 AQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 556
+ K+++ NLP + T++E + ++ G V + D I K
Sbjct: 5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKV-LECD-----II----------KNYGFVH 48
Query: 557 YIKKESVDLALSILDGYEIRGKKIKVERAK 586
K + + A+ L Y++ G I VE +K
Sbjct: 49 IEDKTAAEDAIRNLHHYKLHGVNINVEASK 78
Score = 44.5 bits (106), Expect = 5e-06
Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 16/88 (18%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
K+++ NLP + T++E + ++ G V + D I K
Sbjct: 7 GMVKLFIGNLPREATEQEIRSLFEQYGKV-LECD-----II----------KNYGFVHIE 50
Query: 274 KKESVDLALSILDGYEIRGKKIKVERAK 301
K + + A+ L Y++ G I VE +K
Sbjct: 51 DKTAAEDAIRNLHHYKLHGVNINVEASK 78
Score = 33.3 bits (77), Expect = 0.041
Identities = 9/58 (15%), Positives = 21/58 (36%), Gaps = 4/58 (6%)
Query: 374 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
+Q++R + G V + + + + ++ AA+ L+ I E
Sbjct: 22 EQEIRSLFEQYGKVLECDI----IKNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVE 75
Score = 33.3 bits (77), Expect = 0.041
Identities = 9/58 (15%), Positives = 21/58 (36%), Gaps = 4/58 (6%)
Query: 659 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
+Q++R + G V + + + + ++ AA+ L+ I E
Sbjct: 22 EQEIRSLFEQYGKVLECDI----IKNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVE 75
>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 = 45.6 bits (108), Expect = 7e-06
Identities = 20/113 (17%), Positives = 34/113 (30%), Gaps = 13/113 (11%)
Query: 189 PKAEEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDT 248
+ V D KVYV NL + + E G +
Sbjct: 47 DATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRS---- 102
Query: 249 NQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ + +P G A + A+ LDG + G +++VE +
Sbjct: 103 ----VWVARNP-----PGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSN 146
Score = 44.9 bits (106), Expect = 1e-05
Identities = 26/152 (17%), Positives = 45/152 (29%), Gaps = 21/152 (13%)
Query: 435 GKTRYKIQETAEEREARLKKWETFLGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKL 494
T TAE+ + G+ + K E + L
Sbjct: 16 TTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPL--- 72
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+ KVYV NL + + E G + + + +P G A
Sbjct: 73 -----DCKVYVGNLGNNGNKTELERAFGYYGPLRS--------VWVARNP-----PGFAF 114
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ A+ LDG + G +++VE +
Sbjct: 115 VEFEDPRDAADAVRELDGRTLCGCRVRVELSN 146
Score = 42.2 bits (99), Expect = 9e-05
Identities = 26/157 (16%), Positives = 53/157 (33%), Gaps = 14/157 (8%)
Query: 284 ILDGYEIRGKKIKVERAKFTMKG--EAYDPKLKPKKKRKKDLEKLKKAQEKLFDWRPDKM 341
IL+G ++G+ T + + Y + D + M
Sbjct: 6 ILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHM 65
Query: 342 RGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVA 401
+ + + V NL + + +L G ++ V + ++P G A
Sbjct: 66 HRDSCPLDCKVYVGNL------GNNGN-----KTELERAFGYYGPLRSVWVA-RNPPGFA 113
Query: 402 QIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTR 438
+ F++P A L+GR ++ E +G+ R
Sbjct: 114 FVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEKR 150
Score = 42.2 bits (99), Expect = 9e-05
Identities = 26/157 (16%), Positives = 53/157 (33%), Gaps = 14/157 (8%)
Query: 569 ILDGYEIRGKKIKVERAKFTMKG--EAYDPKLKPKKKRKKDLEKLKKAQEKLFDWRPDKM 626
IL+G ++G+ T + + Y + D + M
Sbjct: 6 ILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHM 65
Query: 627 RGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVA 686
+ + + V NL + + +L G ++ V + ++P G A
Sbjct: 66 HRDSCPLDCKVYVGNL------GNNGN-----KTELERAFGYYGPLRSVWVA-RNPPGFA 113
Query: 687 QIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTR 723
+ F++P A L+GR ++ E +G+ R
Sbjct: 114 FVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEKR 150
>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 = 44.4 bits (105), Expect = 8e-06
Identities = 14/92 (15%), Positives = 30/92 (32%), Gaps = 16/92 (17%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
S V+V L + + + VE ++K G + + + K AL
Sbjct: 12 VSVSPVVHVRGLCESVVEADLVEALEKFGTI--------CYVMMMPF------KRQALVE 57
Query: 272 YIKKESVDLALSIL--DGYEIRGKKIKVERAK 301
+ +S ++ I G++ +
Sbjct: 58 FENIDSAKECVTFAADVPVYIAGQQAFFNYST 89
Score = 42.9 bits (101), Expect = 3e-05
Identities = 13/86 (15%), Positives = 29/86 (33%), Gaps = 16/86 (18%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
V+V L + + + VE ++K G + + + K AL + +S
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTI--------CYVMMMPF------KRQALVEFENIDS 63
Query: 563 VDLALSIL--DGYEIRGKKIKVERAK 586
++ I G++ +
Sbjct: 64 AKECVTFAADVPVYIAGQQAFFNYST 89
>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 = 44.6 bits (106), Expect = 8e-06
Identities = 22/95 (23%), Positives = 37/95 (38%), Gaps = 19/95 (20%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCG-----LVMKDVDTNQMKIKLYTDPYTKDFKG 266
+ K+++ L + ++ V K G L++KD T +G
Sbjct: 4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD--------------RTSKSRG 49
Query: 267 DALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
A T+ A ++G + GK IKVE+AK
Sbjct: 50 FAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK 84
Score = 44.2 bits (105), Expect = 1e-05
Identities = 23/96 (23%), Positives = 38/96 (39%), Gaps = 19/96 (19%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCG-----LVMKDVDTNQMKIKLYTDPYTKDFK 550
+A K+++ L + ++ V K G L++KD T +
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD--------------RTSKSR 48
Query: 551 GDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
G A T+ A ++G + GK IKVE+AK
Sbjct: 49 GFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK 84
Score = 35.0 bits (81), Expect = 0.017
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 3/58 (5%)
Query: 375 QDLREECSKCGHVKKVVL---HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+ L+ K G + +V+L G A I F+ P A + +NG+ + I
Sbjct: 22 KMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIK 79
Score = 35.0 bits (81), Expect = 0.017
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 3/58 (5%)
Query: 660 QDLREECSKCGHVKKVVL---HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ L+ K G + +V+L G A I F+ P A + +NG+ + I
Sbjct: 22 KMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIK 79
>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 = 44.2 bits (105), Expect = 9e-06
Identities = 22/96 (22%), Positives = 39/96 (40%), Gaps = 10/96 (10%)
Query: 493 KLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPY-TKDFKG 551
++ K Q +K+ V N+P Q E E+ G + K V +L T +G
Sbjct: 8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGEL-KTV-------RLPKKMTGTGAHRG 59
Query: 552 DALCTYIKKESVDLALSIL-DGYEIRGKKIKVERAK 586
+I K+ A + L + G+++ +E A
Sbjct: 60 FGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWAD 95
Score = 42.7 bits (101), Expect = 3e-05
Identities = 20/91 (21%), Positives = 37/91 (40%), Gaps = 10/91 (10%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPY-TKDFKGDALCT 271
+ ++K+ V N+P Q E E+ G + K V +L T +G
Sbjct: 13 QTTSKILVRNIPFQANQREIRELFSTFGEL-KTV-------RLPKKMTGTGAHRGFGFVD 64
Query: 272 YIKKESVDLALSIL-DGYEIRGKKIKVERAK 301
+I K+ A + L + G+++ +E A
Sbjct: 65 FITKQDAKKAFNALCHSTHLYGRRLVLEWAD 95
Score = 33.4 bits (77), Expect = 0.056
Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 17/91 (18%)
Query: 344 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL-HDKHPEGVAQ 402
+ + S I+V+N+ Q+++RE S G +K V L G +
Sbjct: 10 PKKQTTSKILVRNI------PFQAN-----QREIRELFSTFGELKTVRLPKKMTGTGAHR 58
Query: 403 IF----FKEPEAAD-ACRELLNGRWFGQRQI 428
F F + A A L + R++
Sbjct: 59 GFGFVDFITKQDAKKAFNALCHSTHLYGRRL 89
Score = 33.4 bits (77), Expect = 0.056
Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 17/91 (18%)
Query: 629 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL-HDKHPEGVAQ 687
+ + S I+V+N+ Q+++RE S G +K V L G +
Sbjct: 10 PKKQTTSKILVRNI------PFQAN-----QREIRELFSTFGELKTVRLPKKMTGTGAHR 58
Query: 688 IF----FKEPEAAD-ACRELLNGRWFGQRQI 713
F F + A A L + R++
Sbjct: 59 GFGFVDFITKQDAKKAFNALCHSTHLYGRRL 89
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif,
U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein;
2.50A {Homo sapiens}
Length = 143
Score = 45.2 bits (107), Expect = 1e-05
Identities = 21/130 (16%), Positives = 50/130 (38%), Gaps = 4/130 (3%)
Query: 458 FLGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEK-LKKAQENTKVYVSNLPLDLTQEE 516
LG ++ + E ++ ++ + + + + N ++YV NL + +++
Sbjct: 2 PLGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKD 61
Query: 517 FVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIR 576
+ + + I+L KG A +++ AL +GY +
Sbjct: 62 LKYIFGRYVDFSSETQRIMFDIRLMK---EGRMKGQAFIGLPNEKAAAKALKEANGYVLF 118
Query: 577 GKKIKVERAK 586
GK + V+ A+
Sbjct: 119 GKPMVVQFAR 128
Score = 44.8 bits (106), Expect = 1e-05
Identities = 19/109 (17%), Positives = 44/109 (40%), Gaps = 3/109 (2%)
Query: 193 EKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMK 252
++ + + ++ GE + ++YV NL + +++ + + +
Sbjct: 23 GRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFD 82
Query: 253 IKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
I+L KG A +++ AL +GY + GK + V+ A+
Sbjct: 83 IRLMK---EGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFAR 128
Score = 32.1 bits (73), Expect = 0.26
Identities = 20/126 (15%), Positives = 44/126 (34%), Gaps = 21/126 (16%)
Query: 312 KLKPKKKRKKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLIL 371
++ + +++LEK + + + E + I VKNL K V
Sbjct: 9 EMPSECISRRELEK-GRISREEMETLSVFRSYEPGEPNCRIYVKNL------AKHVQ--- 58
Query: 372 EYQQDLREECSKCGHV----KKVVLHDKHPE-----GVAQIFFKEPEAADACRELLNGRW 422
++DL+ + ++++ + + G A I +AA + NG
Sbjct: 59 --EKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYV 116
Query: 423 FGQRQI 428
+ +
Sbjct: 117 LFGKPM 122
Score = 32.1 bits (73), Expect = 0.26
Identities = 20/126 (15%), Positives = 44/126 (34%), Gaps = 21/126 (16%)
Query: 597 KLKPKKKRKKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLIL 656
++ + +++LEK + + + E + I VKNL K V
Sbjct: 9 EMPSECISRRELEK-GRISREEMETLSVFRSYEPGEPNCRIYVKNL------AKHVQ--- 58
Query: 657 EYQQDLREECSKCGHV----KKVVLHDKHPE-----GVAQIFFKEPEAADACRELLNGRW 707
++DL+ + ++++ + + G A I +AA + NG
Sbjct: 59 --EKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYV 116
Query: 708 FGQRQI 713
+ +
Sbjct: 117 LFGKPM 122
>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 = 44.4 bits (105), Expect = 1e-05
Identities = 20/106 (18%), Positives = 39/106 (36%), Gaps = 21/106 (19%)
Query: 197 PGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 256
P + P + +V VS LP + ++ + M++ G V Y
Sbjct: 4 PRGRYGPPSRR------SENRVVVSGLPPSGSWQDLKDHMREAGDV------------CY 45
Query: 257 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKF 302
D Y G + +++KE + A+ LD + R + + +
Sbjct: 46 ADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV 88
Score = 44.0 bits (104), Expect = 1e-05
Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 15/86 (17%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
+V VS LP + ++ + M++ G V Y D Y G + +++KE
Sbjct: 18 RVVVSGLPPSGSWQDLKDHMREAGDV------------CYADVYRD---GTGVVEFVRKE 62
Query: 562 SVDLALSILDGYEIRGKKIKVERAKF 587
+ A+ LD + R + + +
Sbjct: 63 DMTYAVRKLDNTKFRSHEGETAYIRV 88
>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 = 43.5 bits (103), Expect = 1e-05
Identities = 17/88 (19%), Positives = 36/88 (40%), Gaps = 17/88 (19%)
Query: 500 NTKVYVSNLPL-DLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
+++++ NLPL ++++E+ + G +M Q+ IK +
Sbjct: 22 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIM------QINIK----------NAFGFIQFD 65
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAK 586
+SV A+ GKK+ +E +
Sbjct: 66 NPQSVRDAIEXESQEMNFGKKLILEVSS 93
Score = 43.1 bits (102), Expect = 2e-05
Identities = 17/88 (19%), Positives = 36/88 (40%), Gaps = 17/88 (19%)
Query: 215 STKVYVSNLPL-DLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
+++++ NLPL ++++E+ + G +M Q+ IK +
Sbjct: 22 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIM------QINIK----------NAFGFIQFD 65
Query: 274 KKESVDLALSILDGYEIRGKKIKVERAK 301
+SV A+ GKK+ +E +
Sbjct: 66 NPQSVRDAIEXESQEMNFGKKLILEVSS 93
Score = 37.7 bits (88), Expect = 0.001
Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 4/58 (6%)
Query: 374 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
++DL S GH+ ++ + I F P++ E + +++ E
Sbjct: 37 KEDLFRIFSPYGHIMQINIK----NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE 90
Score = 37.7 bits (88), Expect = 0.001
Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 4/58 (6%)
Query: 659 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
++DL S GH+ ++ + I F P++ E + +++ E
Sbjct: 37 KEDLFRIFSPYGHIMQINIK----NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE 90
>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 = 44.4 bits (105), Expect = 2e-05
Identities = 17/117 (14%), Positives = 36/117 (30%), Gaps = 12/117 (10%)
Query: 197 PGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 256
R ++ V++ LP T+ + V ++ +
Sbjct: 28 QQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV---------RVHIE 78
Query: 257 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFT-MKGEAYDPK 312
P + G+A + E A+S D ++ + I++ T AY +
Sbjct: 79 IGPDGR-VTGEADVEFATHEEAVAAMS-KDRANMQHRYIELFLNSTTGASNGAYSSQ 133
Score = 41.8 bits (98), Expect = 1e-04
Identities = 18/117 (15%), Positives = 39/117 (33%), Gaps = 12/117 (10%)
Query: 482 KPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 541
+ + D E ++ V++ LP T+ + V ++ +
Sbjct: 28 QQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV---------RVHIE 78
Query: 542 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFT-MKGEAYDPK 597
P + G+A + E A+S D ++ + I++ T AY +
Sbjct: 79 IGPDGR-VTGEADVEFATHEEAVAAMS-KDRANMQHRYIELFLNSTTGASNGAYSSQ 133
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 43.1 bits (102), Expect = 2e-05
Identities = 14/90 (15%), Positives = 28/90 (31%), Gaps = 14/90 (15%)
Query: 497 AQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 556
+ V+VS P + + E G V + D F A+
Sbjct: 5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPV----------ASVVMDKDKGVF---AIVE 51
Query: 557 YIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ + LS + + G +++V +
Sbjct: 52 MGDVGAREAVLS-QSQHSLGGHRLRVRPRE 80
Score = 42.7 bits (101), Expect = 2e-05
Identities = 14/85 (16%), Positives = 27/85 (31%), Gaps = 14/85 (16%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
V+VS P + + E G V + D F A+
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPV----------ASVVMDKDKGVF---AIVEMGDVG 56
Query: 277 SVDLALSILDGYEIRGKKIKVERAK 301
+ + LS + + G +++V +
Sbjct: 57 AREAVLS-QSQHSLGGHRLRVRPRE 80
Score = 31.5 bits (72), Expect = 0.18
Identities = 13/51 (25%), Positives = 17/51 (33%), Gaps = 5/51 (9%)
Query: 375 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACREL----LNGR 421
L E G V VV+ DK A + + A +A L G
Sbjct: 23 AQLSEYFLAFGPVASVVM-DKDKGVFAIVEMGDVGAREAVLSQSQHSLGGH 72
Score = 31.5 bits (72), Expect = 0.18
Identities = 13/51 (25%), Positives = 17/51 (33%), Gaps = 5/51 (9%)
Query: 660 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACREL----LNGR 706
L E G V VV+ DK A + + A +A L G
Sbjct: 23 AQLSEYFLAFGPVASVVM-DKDKGVFAIVEMGDVGAREAVLSQSQHSLGGH 72
>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 = 43.1 bits (102), Expect = 2e-05
Identities = 16/88 (18%), Positives = 31/88 (35%), Gaps = 17/88 (19%)
Query: 500 NTKVYVSNLPLDL-TQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
N++V++ NL L + + + K G V + KG A Y
Sbjct: 27 NSRVFIGNLNTALVKKSDVETIFSKYGRVA------GCSVH----------KGYAFVQYS 70
Query: 559 KKESVDLALSILDGYEIRGKKIKVERAK 586
+ A+ +G + G+ + + A
Sbjct: 71 NERHARAAVLGENGRVLAGQTLDINMAG 98
Score = 42.8 bits (101), Expect = 4e-05
Identities = 15/88 (17%), Positives = 31/88 (35%), Gaps = 17/88 (19%)
Query: 215 STKVYVSNLPLDL-TQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
+++V++ NL L + + + K G V + KG A Y
Sbjct: 27 NSRVFIGNLNTALVKKSDVETIFSKYGRVA------GCSVH----------KGYAFVQYS 70
Query: 274 KKESVDLALSILDGYEIRGKKIKVERAK 301
+ A+ +G + G+ + + A
Sbjct: 71 NERHARAAVLGENGRVLAGQTLDINMAG 98
Score = 35.8 bits (83), Expect = 0.010
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 4/58 (6%)
Query: 374 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
+ D+ SK G V +H +G A + + A A NGR + +
Sbjct: 42 KSDVETIFSKYGRVAGCSVH----KGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN 95
Score = 35.8 bits (83), Expect = 0.010
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 4/58 (6%)
Query: 659 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
+ D+ SK G V +H +G A + + A A NGR + +
Sbjct: 42 KSDVETIFSKYGRVAGCSVH----KGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN 95
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 42.9 bits (101), Expect = 3e-05
Identities = 15/92 (16%), Positives = 35/92 (38%), Gaps = 16/92 (17%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
G S +++ LP+D+T+ E + + G V + + K A
Sbjct: 13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKV--------TNLLMLKG------KNQAFIE 58
Query: 272 YIKKESVDLALS--ILDGYEIRGKKIKVERAK 301
+E+ + ++ +RG+ I ++ +
Sbjct: 59 MNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN 90
Score = 41.0 bits (96), Expect = 1e-04
Identities = 14/95 (14%), Positives = 36/95 (37%), Gaps = 17/95 (17%)
Query: 495 KKAQENTKV-YVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDA 553
+ ++V ++ LP+D+T+ E + + G V + + K A
Sbjct: 10 HGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKV--------TNLLMLKG------KNQA 55
Query: 554 LCTYIKKESVDLALS--ILDGYEIRGKKIKVERAK 586
+E+ + ++ +RG+ I ++ +
Sbjct: 56 FIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN 90
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 42.4 bits (100), Expect = 3e-05
Identities = 14/102 (13%), Positives = 32/102 (31%), Gaps = 16/102 (15%)
Query: 484 KKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTD 543
++ + K + V++ L + + + VE +Q+ G + + +
Sbjct: 5 HHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPI--------SYVVVMPK 56
Query: 544 PYTKDFKGDALCTYIKKESVDLALSIL--DGYEIRGKKIKVE 583
K AL + A++ + I G V
Sbjct: 57 ------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN 92
Score = 40.5 bits (95), Expect = 2e-04
Identities = 16/105 (15%), Positives = 31/105 (29%), Gaps = 18/105 (17%)
Query: 198 GQKRKPEPPKWFD--IGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKL 255
G + D S V++ L + + + VE +Q+ G + + +
Sbjct: 2 GHHHHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPI--------SYVVV 53
Query: 256 YTDPYTKDFKGDALCTYIKKESVDLALSIL--DGYEIRGKKIKVE 298
K AL + A++ + I G V
Sbjct: 54 MPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN 92
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 43.0 bits (101), Expect = 3e-05
Identities = 19/89 (21%), Positives = 31/89 (34%), Gaps = 6/89 (6%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
E V + LP T EE V + + + I T P + GDA +
Sbjct: 21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKE----GILFVTYPDGR-PTGDAFVLF 75
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
+E AL + + I++ R+
Sbjct: 76 ACEEYAQNALR-KHKDLLGKRYIELFRST 103
Score = 42.6 bits (100), Expect = 5e-05
Identities = 18/98 (18%), Positives = 34/98 (34%), Gaps = 6/98 (6%)
Query: 489 KDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKD 548
++ + + V + LP T EE V + + + I T P +
Sbjct: 12 NEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKE----GILFVTYPDGR- 66
Query: 549 FKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
GDA + +E AL + + I++ R+
Sbjct: 67 PTGDAFVLFACEEYAQNALR-KHKDLLGKRYIELFRST 103
>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 = 41.5 bits (98), Expect = 5e-05
Identities = 11/89 (12%), Positives = 32/89 (35%), Gaps = 15/89 (16%)
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
T +YV L +T+ + + G + I + + A +
Sbjct: 11 TITTLYVGGLGDTITETDLRNHFYQFGEI--------RTITVVQR------QQCAFIQFA 56
Query: 559 KKESVDLAL-SILDGYEIRGKKIKVERAK 586
+++ ++A + + G+++ V+ +
Sbjct: 57 TRQAAEVAAEKSFNKLIVNGRRLNVKWGR 85
Score = 39.2 bits (92), Expect = 3e-04
Identities = 11/87 (12%), Positives = 32/87 (36%), Gaps = 15/87 (17%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 275
T +YV L +T+ + + G + I + + A + +
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEI--------RTITVVQR------QQCAFIQFATR 58
Query: 276 ESVDLAL-SILDGYEIRGKKIKVERAK 301
++ ++A + + G+++ V+ +
Sbjct: 59 QAAEVAAEKSFNKLIVNGRRLNVKWGR 85
>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 = 42.3 bits (100), Expect = 5e-05
Identities = 16/89 (17%), Positives = 33/89 (37%), Gaps = 8/89 (8%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
V+V +L ++T E+ G + ++ D T KG ++
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISD--------ARVVKDMATGKSKGYGFVSF 64
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
K + A+ + G + G++I+ A
Sbjct: 65 FNKWDAENAIQQMGGQWLGGRQIRTNWAT 93
Score = 42.3 bits (100), Expect = 5e-05
Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 8/92 (8%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
K + V+V +L ++T E+ G + ++ D T KG
Sbjct: 10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISD--------ARVVKDMATGKSKGYGF 61
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
++ K + A+ + G + G++I+ A
Sbjct: 62 VSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT 93
Score = 31.6 bits (72), Expect = 0.28
Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 375 QDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+D++ + G + V+ D +G + F A+ + + G+W G RQI
Sbjct: 30 EDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR 88
Score = 31.6 bits (72), Expect = 0.28
Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 660 QDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+D++ + G + V+ D +G + F A+ + + G+W G RQI
Sbjct: 30 EDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR 88
>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 = 42.6 bits (100), Expect = 5e-05
Identities = 20/107 (18%), Positives = 35/107 (32%), Gaps = 14/107 (13%)
Query: 197 PGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLY 256
G PE G E V + LP + E+ + C + +
Sbjct: 6 SGMMLGPE-------GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAG-----VHFI 53
Query: 257 TDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFT 303
+ G+A ++ V LAL D + + I+V ++ T
Sbjct: 54 YTREGR-QSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSHRT 98
Score = 41.8 bits (98), Expect = 9e-05
Identities = 16/94 (17%), Positives = 32/94 (34%), Gaps = 7/94 (7%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+ E V + LP + E+ + C + + + G+A
Sbjct: 12 PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAG-----VHFIYTREGR-QSGEAF 65
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAKFT 588
++ V LAL D + + I+V ++ T
Sbjct: 66 VELESEDDVKLALK-KDRESMGHRYIEVFKSHRT 98
>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 = 41.3 bits (98), Expect = 5e-05
Identities = 10/87 (11%), Positives = 33/87 (37%), Gaps = 8/87 (9%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
+ ++V +L +++ E + + + D T +G ++
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLS--------GHVMWDMQTGSSRGYGFVSFTS 52
Query: 275 KESVDLALSILDGYEIRGKKIKVERAK 301
++ A+ + G ++ G+ +++ A
Sbjct: 53 QDDAQNAMDSMQGQDLNGRPLRINWAA 79
Score = 39.4 bits (93), Expect = 3e-04
Identities = 10/86 (11%), Positives = 32/86 (37%), Gaps = 8/86 (9%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
++V +L +++ E + + + D T +G ++ +
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLS--------GHVMWDMQTGSSRGYGFVSFTSQ 53
Query: 561 ESVDLALSILDGYEIRGKKIKVERAK 586
+ A+ + G ++ G+ +++ A
Sbjct: 54 DDAQNAMDSMQGQDLNGRPLRINWAA 79
Score = 30.5 bits (70), Expect = 0.33
Identities = 9/59 (15%), Positives = 17/59 (28%), Gaps = 4/59 (6%)
Query: 375 QDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+ LR V+ D G + F + A + + G+ R +
Sbjct: 16 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR 74
Score = 30.5 bits (70), Expect = 0.33
Identities = 9/59 (15%), Positives = 17/59 (28%), Gaps = 4/59 (6%)
Query: 660 QDLREECSKCGHVKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ LR V+ D G + F + A + + G+ R +
Sbjct: 16 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR 74
>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 = 41.3 bits (97), Expect = 7e-05
Identities = 14/106 (13%), Positives = 33/106 (31%), Gaps = 24/106 (22%)
Query: 198 GQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYT 257
+ P S +++ LP ++T+ E + + G V I +
Sbjct: 6 SGDKMDGAP--------SRVLHIRKLPGEVTETEVIALGLPFGKV--------TNILMLK 49
Query: 258 DPYTKDFKGDALCTYIKKESVDLALS--ILDGYEIRGKKIKVERAK 301
K A +E+ ++ +R + I ++ +
Sbjct: 50 G------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN 89
Score = 39.8 bits (93), Expect = 3e-04
Identities = 12/86 (13%), Positives = 30/86 (34%), Gaps = 16/86 (18%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
+++ LP ++T+ E + + G V I + K A +E+
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKV--------TNILMLKG------KNQAFLELATEEA 63
Query: 563 VDLALS--ILDGYEIRGKKIKVERAK 586
++ +R + I ++ +
Sbjct: 64 AITMVNYYSAVTPHLRNQPIYIQYSN 89
>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 = 40.6 bits (96), Expect = 1e-04
Identities = 24/90 (26%), Positives = 48/90 (53%), Gaps = 9/90 (10%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
G +S K++V +P + + E E +K G+V + + D + +G T
Sbjct: 7 GSKSNKIFVGGIPHNCGETELREYFKKFGVV---TEVVMI-----YDAEKQRPRGFGFIT 58
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ ++SVD A++ + ++I GKK++V+RA+
Sbjct: 59 FEDEQSVDQAVN-MHFHDIMGKKVEVKRAE 87
Score = 39.5 bits (93), Expect = 3e-04
Identities = 22/92 (23%), Positives = 47/92 (51%), Gaps = 9/92 (9%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
++ K++V +P + + E E +K G+V + + D + +G
Sbjct: 5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVV---TEVVMI-----YDAEKQRPRGFGF 56
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
T+ ++SVD A++ + ++I GKK++V+RA+
Sbjct: 57 ITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAE 87
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 40.5 bits (95), Expect = 2e-04
Identities = 23/114 (20%), Positives = 43/114 (37%), Gaps = 15/114 (13%)
Query: 492 EKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKG 551
LK +N VY+ P D T ++ E ++ G V + I++ K FKG
Sbjct: 3 WILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQV--------LNIQMRRTL-HKAFKG 53
Query: 552 DALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRK 605
+ ES + G + + + + K + + K + +K+ K
Sbjct: 54 SIFVVFDSIESAKKFVE-TPGQKYKETDLLIL-----FKDDYFAKKNEERKQNK 101
Score = 37.8 bits (88), Expect = 0.002
Identities = 20/107 (18%), Positives = 41/107 (38%), Gaps = 15/107 (14%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
++ VY+ P D T ++ E ++ G V + I++ K FKG +
Sbjct: 10 KNRSVYIKGFPTDATLDDIKEWLEDKGQV--------LNIQMRRTL-HKAFKGSIFVVFD 60
Query: 274 KKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRK 320
ES + G + + + + K + + K + +K+ K
Sbjct: 61 SIESAKKFVE-TPGQKYKETDLLIL-----FKDDYFAKKNEERKQNK 101
Score = 32.8 bits (75), Expect = 0.084
Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 12/94 (12%)
Query: 363 FDKDVTLILEYQQDLREECSKCGHVKKVVL---HDKHPEGVAQIFFKEPEAADACRELLN 419
F D T D++E G V + + K +G + F E+A E
Sbjct: 19 FPTDAT-----LDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG 73
Query: 420 GRWFGQRQITAETWDGKTRYKIQETAEEREARLK 453
++ + K Y ++ E ++ +++
Sbjct: 74 QKYKETDLLIL----FKDDYFAKKNEERKQNKVE 103
Score = 32.8 bits (75), Expect = 0.084
Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 12/94 (12%)
Query: 648 FDKDVTLILEYQQDLREECSKCGHVKKVVL---HDKHPEGVAQIFFKEPEAADACRELLN 704
F D T D++E G V + + K +G + F E+A E
Sbjct: 19 FPTDAT-----LDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG 73
Query: 705 GRWFGQRQITAETWDGKTRYKIQETAEEREARLK 738
++ + K Y ++ E ++ +++
Sbjct: 74 QKYKETDLLIL----FKDDYFAKKNEERKQNKVE 103
>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 = 44.3 bits (104), Expect = 2e-04
Identities = 61/321 (19%), Positives = 102/321 (31%), Gaps = 122/321 (38%)
Query: 237 QKCGLVMKDVDTNQMKIKLYT------------DPYTKDFKGDALCTYIKKESVDLALSI 284
Q+ G M + LY D + KD G ++ + V+L I
Sbjct: 1627 QEQG----------MGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLT--I 1674
Query: 285 LDGYEIRGKKIKVERAKFT-MKGEAY-DPKLKPKKKRKKDLEKLKKAQEKLFDWRPDKMR 342
G E +GK+I R ++ M E D KLK +K K+ E + +R +K
Sbjct: 1675 HFGGE-KGKRI---RENYSAMIFETIVDGKLKTEKIFKEINEHSTS-----YTFRSEK-- 1723
Query: 343 GERSKNESVIIVKNLFD-----PALFDKDVTLILEYQ--QDLREECSKCGHVKKVVLHDK 395
G L PAL ++E +DL+ + G + D
Sbjct: 1724 GL------------LSATQFTQPALT------LMEKAAFEDLKSK----GLIPA----DA 1757
Query: 396 ----HPEG-------VAQIF-FKEPEAADACRELLNGRWFGQRQITAETWD--GKTRYKI 441
H G +A + ++ R G A D G++ Y +
Sbjct: 1758 TFAGHSLGEYAALASLADVMSI-----ESLVE-VVFYR--GMTMQVAVPRDELGRSNYGM 1809
Query: 442 -------------QETAEEREARLKKWETFLGKKIKVERAKF-----------TMKG-EA 476
QE + R+ K +L VE + ++ +
Sbjct: 1810 IAINPGRVAASFSQEALQYVVERVGKRTGWL-----VEIVNYNVENQQYVAAGDLRALDT 1864
Query: 477 YDPKLKPKKKRKKDLEKLKKA 497
L K +K D+ +L+K+
Sbjct: 1865 VTNVLNFIKLQKIDIIELQKS 1885
Score = 41.6 bits (97), Expect = 0.001
Identities = 42/337 (12%), Positives = 76/337 (22%), Gaps = 167/337 (49%)
Query: 99 IQRQDMSKGSYGYEGDTHTYTDSTDGTVYIWDKEKNAWFPKVDDDFLARYQMSYGF-IEQ 157
Q Q M Y ++ +W++ A D+ + +YGF I
Sbjct: 1626 SQEQGMGMDLY----------KTSKAAQDVWNR---A------DNHF---KDTYGFSI-- 1661
Query: 158 PNTVDEKKPSADLVQSKVEEKSVDATAPMENPKAEEKVVPGQK----------------- 200
D+V NP G+K
Sbjct: 1662 ----------LDIVI--------------NNPVNLTIHFGGEKGKRIRENYSAMIFETIV 1697
Query: 201 -RKPEPPKWFDIGEESTKVYVSNLP---LDLTQEEF------------VEVMQKCG---- 240
K + K F E + Y L TQ F E ++ G
Sbjct: 1698 DGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQ--FTQPALTLMEKAAFEDLKSKGLIPA 1755
Query: 241 -----------------------------LV----------------------MKDVDTN 249
+V M ++
Sbjct: 1756 DATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPG 1815
Query: 250 QMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSI----LDG--YEIRGKKIKVERAKFT 303
++ + + + K + L + I ++ Y G ++
Sbjct: 1816 RVAASFSQE------ALQYVVERVGKRTGWL-VEIVNYNVENQQYVAAGDLRALDTV--- 1865
Query: 304 MKGEAYDPKLKPKKKRKKDLEKLK------KAQEKLF 334
L K +K D+ +L+ + + LF
Sbjct: 1866 --TNV----LNFIKLQKIDIIELQKSLSLEEVEGHLF 1896
Score = 39.3 bits (91), Expect = 0.006
Identities = 41/274 (14%), Positives = 79/274 (28%), Gaps = 106/274 (38%)
Query: 72 LVTSDKAADSSDEEEYDEN-------------NAQKTAP-----PIQRQDMSKGSYGYEG 113
LVT+ A++ E + + + P P +D + + EG
Sbjct: 277 LVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENN---EG 333
Query: 114 DTHTY----TDSTDGTV--YIWDKEKNAWFPKVDDDFLARY----QM-------S-YGFI 155
+ ++ T V Y+ + N+ P ++ + S YG
Sbjct: 334 -VPSPMLSISNLTQEQVQDYV--NKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLN 390
Query: 156 EQPNTVDEKKPSADLVQSKVEEKSVDATAPMENPKAEEKVVPGQKRKPEPPKWFDIGEES 215
T+ + K + L QS++ P +RK + F
Sbjct: 391 ---LTLRKAKAPSGLDQSRI---------------------PFSERKLKFSNRF------ 420
Query: 216 TKVYVSNLP---------LDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYT-KDFK 265
LP L + + + K + + ++I +Y D + D +
Sbjct: 421 -------LPVASPFHSHLLVPASDLINKDLVKNNV---SFNAKDIQIPVY-DTFDGSDLR 469
Query: 266 G------DALCTYIKKESVD-------LALSILD 286
+ + I + V A ILD
Sbjct: 470 VLSGSISERIVDCIIRLPVKWETTTQFKATHILD 503
Score = 37.7 bits (87), Expect = 0.017
Identities = 58/340 (17%), Positives = 107/340 (31%), Gaps = 117/340 (34%)
Query: 321 KDL-EKLKKAQEKLFDWRPDKMRGERSKNESVI-IVKNLFDPALFDKDVTLILEYQ--QD 376
DL + K AQ+ +++ R D + + S++ IV N +P ++T+ + +
Sbjct: 1633 MDLYKTSKAAQD-VWN-RADNHFKD-TYGFSILDIVIN--NP----VNLTIHFGGEKGKR 1683
Query: 377 LRE-------ECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+RE E G +K + + E F+ + LL+ F Q +T
Sbjct: 1684 IRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEK------GLLSATQFTQPALT 1737
Query: 430 AETWDGKTRYKIQETAEEREARLKKWETFLGKKIKVERAKF-----TMKGE--AYDPKLK 482
E LK G + A F GE A
Sbjct: 1738 L------MEKAAFE-------DLKSK----G--LIPADATFAGHSL---GEYAA------ 1769
Query: 483 PKKKRKKDLEKLKKAQENTKVYVSN-LPLDLTQEEFVEVMQKCG-LVMKDVDTNQMKIKL 540
L +++ + + E VEV+ G + V +++
Sbjct: 1770 -----------L--------ASLADVMSI----ESLVEVVFYRGMTMQVAVPRDELGRSN 1806
Query: 541 YT----DPYT--KDFKGDAL---CTYIKKESVDLALSI----LDG--YEIRGKKIKVERA 585
Y +P F +AL + K + L + I ++ Y G ++
Sbjct: 1807 YGMIAINPGRVAASFSQEALQYVVERVGKRTGWL-VEIVNYNVENQQYVAAGDLRALDTV 1865
Query: 586 KFTMKGEAYDPKLKPKKKRKKDLEKLK------KAQEKLF 619
L K +K D+ +L+ + + LF
Sbjct: 1866 -----TNV----LNFIKLQKIDIIELQKSLSLEEVEGHLF 1896
>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 = 40.6 bits (95), Expect = 2e-04
Identities = 15/92 (16%), Positives = 31/92 (33%), Gaps = 7/92 (7%)
Query: 210 DIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 269
+ ++ + LP T E+ + C + + I + K +GDAL
Sbjct: 6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENG-----IHFLLNRDGK-RRGDAL 59
Query: 270 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
++ V AL + + ++V
Sbjct: 60 IEMESEQDVQKALE-KHRMYMGQRYVEVYEIN 90
Score = 39.1 bits (91), Expect = 6e-04
Identities = 15/92 (16%), Positives = 31/92 (33%), Gaps = 7/92 (7%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
++ + + LP T E+ + C + + I + K +GDAL
Sbjct: 6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENG-----IHFLLNRDGK-RRGDAL 59
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
++ V AL + + ++V
Sbjct: 60 IEMESEQDVQKALE-KHRMYMGQRYVEVYEIN 90
>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 = 42.9 bits (100), Expect = 2e-04
Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 8/78 (10%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEGVAQIFFKEPEA 410
I + NL ++ + E ++ L S+ G + + V G A + FKE +
Sbjct: 12 IYINNL------NEKIK-KDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 411 ADACRELLNGRWFGQRQI 428
A + G F + +
Sbjct: 65 ATNALRSMQGFPFYDKPM 82
Score = 42.9 bits (100), Expect = 2e-04
Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 8/78 (10%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEGVAQIFFKEPEA 695
I + NL ++ + E ++ L S+ G + + V G A + FKE +
Sbjct: 12 IYINNL------NEKIK-KDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 696 ADACRELLNGRWFGQRQI 713
A + G F + +
Sbjct: 65 ATNALRSMQGFPFYDKPM 82
Score = 38.3 bits (88), Expect = 0.006
Identities = 21/136 (15%), Positives = 47/136 (34%), Gaps = 15/136 (11%)
Query: 500 NTKVYVSNLPLDLTQEE----FVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 555
N +Y++NL + ++E + + G + +D + + +G A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQI---LDILVSR--------SLKMRGQAFV 57
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQ 615
+ + S AL + G+ K ++++ AK A ++ RK++ K K +
Sbjct: 58 IFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQE 117
Query: 616 EKLFDWRPDKMRGERS 631
Sbjct: 118 TPATKKAVQGGGATPV 133
Score = 36.8 bits (84), Expect = 0.019
Identities = 20/136 (14%), Positives = 47/136 (34%), Gaps = 15/136 (11%)
Query: 215 STKVYVSNLPLDLTQEE----FVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 270
+ +Y++NL + ++E + + G + +D + + +G A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQI---LDILVSR--------SLKMRGQAFV 57
Query: 271 TYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQ 330
+ + S AL + G+ K ++++ AK A ++ RK++ K K +
Sbjct: 58 IFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQE 117
Query: 331 EKLFDWRPDKMRGERS 346
Sbjct: 118 TPATKKAVQGGGATPV 133
Score = 36.8 bits (84), Expect = 0.021
Identities = 12/54 (22%), Positives = 19/54 (35%), Gaps = 1/54 (1%)
Query: 374 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQ 427
+ L ++ K+V L +A + F A A R+ L G Q
Sbjct: 221 ELMLSMLFNQFPGFKEVRLVPGRH-DIAFVEFDNEVQAGAARDALQGFKITQNN 273
Score = 36.8 bits (84), Expect = 0.021
Identities = 12/54 (22%), Positives = 19/54 (35%), Gaps = 1/54 (1%)
Query: 659 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQ 712
+ L ++ K+V L +A + F A A R+ L G Q
Sbjct: 221 ELMLSMLFNQFPGFKEVRLVPGRH-DIAFVEFDNEVQAGAARDALQGFKITQNN 273
>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 = 39.9 bits (94), Expect = 3e-04
Identities = 15/94 (15%), Positives = 33/94 (35%), Gaps = 18/94 (19%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMK-DVDTNQMKIKLYTDPYTKDFKGDAL 554
KA T+++V L + + + G + D A
Sbjct: 13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG---------------DSFAY 57
Query: 555 CTYIKKESVDLALSILDGYEIRG--KKIKVERAK 586
Y ++ A + + G+ + G ++++V+ AK
Sbjct: 58 IQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK 91
Score = 38.4 bits (90), Expect = 8e-04
Identities = 13/90 (14%), Positives = 32/90 (35%), Gaps = 18/90 (20%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMK-DVDTNQMKIKLYTDPYTKDFKGDALCTYI 273
+T+++V L + + + G + D A Y
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG---------------DSFAYIQYE 61
Query: 274 KKESVDLALSILDGYEIRG--KKIKVERAK 301
++ A + + G+ + G ++++V+ AK
Sbjct: 62 SLDAAQAACAKMRGFPLGGPDRRLRVDFAK 91
Score = 34.1 bits (79), Expect = 0.026
Identities = 12/81 (14%), Positives = 27/81 (33%), Gaps = 15/81 (18%)
Query: 345 RSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEGVAQI 403
++ + + V L + + L E + G ++ + + A I
Sbjct: 13 KANPTTRLWVGGL------GPNTS-----LAALAREFDRFGSIRTIDHVKGD---SFAYI 58
Query: 404 FFKEPEAADACRELLNGRWFG 424
++ +AA A + G G
Sbjct: 59 QYESLDAAQAACAKMRGFPLG 79
Score = 34.1 bits (79), Expect = 0.026
Identities = 12/81 (14%), Positives = 27/81 (33%), Gaps = 15/81 (18%)
Query: 630 RSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDKHPEGVAQI 688
++ + + V L + + L E + G ++ + + A I
Sbjct: 13 KANPTTRLWVGGL------GPNTS-----LAALAREFDRFGSIRTIDHVKGD---SFAYI 58
Query: 689 FFKEPEAADACRELLNGRWFG 709
++ +AA A + G G
Sbjct: 59 QYESLDAAQAACAKMRGFPLG 79
>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 = 39.6 bits (93), Expect = 3e-04
Identities = 18/92 (19%), Positives = 36/92 (39%), Gaps = 16/92 (17%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+ ++ +YV D+T G ++ + + + A
Sbjct: 10 RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIID--------LSMDPP------RNCAF 53
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
TY K ES D A++ L+G ++ ++KV A+
Sbjct: 54 VTYEKMESADQAVAELNGTQVESVQLKVNIAR 85
Score = 37.7 bits (88), Expect = 0.002
Identities = 18/89 (20%), Positives = 34/89 (38%), Gaps = 16/89 (17%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+ +YV D+T G ++ + + + A TY
Sbjct: 13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIID--------LSMDPP------RNCAFVTY 56
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
K ES D A++ L+G ++ ++KV A+
Sbjct: 57 EKMESADQAVAELNGTQVESVQLKVNIAR 85
Score = 30.7 bits (70), Expect = 0.40
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 375 QDLREECSKCGHVKKV-VLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
LR S G++ + + + A + +++ E+AD LNG Q+
Sbjct: 28 TLLRGAFSPFGNIIDLSMDPPR---NCAFVTYEKMESADQAVAELNGTQVESVQL 79
Score = 30.7 bits (70), Expect = 0.40
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 660 QDLREECSKCGHVKKV-VLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
LR S G++ + + + A + +++ E+AD LNG Q+
Sbjct: 28 TLLRGAFSPFGNIIDLSMDPPR---NCAFVTYEKMESADQAVAELNGTQVESVQL 79
>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 = 39.9 bits (94), Expect = 3e-04
Identities = 24/100 (24%), Positives = 40/100 (40%), Gaps = 9/100 (9%)
Query: 202 KPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYT 261
P+ +G K+++ L TQE E + G V + M+ DP T
Sbjct: 12 SGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEV---KECLVMR-----DPLT 63
Query: 262 KDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
K +G T++ + VD L+ +E+ K I + A
Sbjct: 64 KRSRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTIDPKVAF 102
Score = 37.6 bits (88), Expect = 0.002
Identities = 22/92 (23%), Positives = 36/92 (39%), Gaps = 9/92 (9%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
K+++ L TQE E + G V + M+ DP TK +G
Sbjct: 20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEV---KECLVMR-----DPLTKRSRGFGF 71
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
T++ + VD L+ +E+ K I + A
Sbjct: 72 VTFMDQAGVDKVLAQ-SRHELDSKTIDPKVAF 102
>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 = 39.1 bits (92), Expect = 3e-04
Identities = 18/89 (20%), Positives = 31/89 (34%), Gaps = 15/89 (16%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+KV+V D+T EE + + G V VD K F+ A T+
Sbjct: 9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEV---VDVFIP----------KPFRAFAFVTF 55
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
+ + I+G + + A+
Sbjct: 56 ADDKVAQSLCG--EDLIIKGISVHISNAE 82
Score = 38.7 bits (91), Expect = 5e-04
Identities = 18/92 (19%), Positives = 31/92 (33%), Gaps = 15/92 (16%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+KV+V D+T EE + + G V VD K F+ A
Sbjct: 6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEV---VDVFIP----------KPFRAFAF 52
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
T+ + + I+G + + A+
Sbjct: 53 VTFADDKVAQSLCG--EDLIIKGISVHISNAE 82
>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 = 39.5 bits (93), Expect = 4e-04
Identities = 19/102 (18%), Positives = 35/102 (34%), Gaps = 11/102 (10%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
V+V + + + + E + G V ++K+ TD T KG ++
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSV--------KEVKIITDR-TGVSKGYGFVSFYN 59
Query: 275 KESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPK 316
V + GKK+K+ A Y + +P
Sbjct: 60 DVDVQKI--VESQINFHGKKLKLGPAIRKQNLSTYHVQPRPL 99
Score = 38.8 bits (91), Expect = 7e-04
Identities = 19/101 (18%), Positives = 35/101 (34%), Gaps = 11/101 (10%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKK 560
V+V + + + + E + G V ++K+ TD T KG ++
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSV--------KEVKIITDR-TGVSKGYGFVSFYND 60
Query: 561 ESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPK 601
V + GKK+K+ A Y + +P
Sbjct: 61 VDVQKI--VESQINFHGKKLKLGPAIRKQNLSTYHVQPRPL 99
>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 = 39.5 bits (93), Expect = 4e-04
Identities = 18/108 (16%), Positives = 38/108 (35%), Gaps = 21/108 (19%)
Query: 486 KRKKDLEKLKKAQE--NTKVYVSNLPLDLTQEEFVEVMQKCGL-----VMKDVDTNQMKI 538
K ++ K QE T +Y+SNLPL + ++E +++ G +++D +
Sbjct: 9 KASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTS-- 65
Query: 539 KLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+G E + + +G I+ +
Sbjct: 66 -----------RGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 102
Score = 38.0 bits (89), Expect = 0.002
Identities = 16/103 (15%), Positives = 30/103 (29%), Gaps = 17/103 (16%)
Query: 330 QEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKK 389
+ + K + + N + + NL + +Q+L G V
Sbjct: 9 KASGVQAQMAKQQEQDPTN---LYISNL------PLSMD-----EQELENMLKPFGQVIS 54
Query: 390 V-VLHDK--HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+L D GV + E +A NG++
Sbjct: 55 TRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGV 97
Score = 38.0 bits (89), Expect = 0.002
Identities = 16/103 (15%), Positives = 30/103 (29%), Gaps = 17/103 (16%)
Query: 615 QEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKK 674
+ + K + + N + + NL + +Q+L G V
Sbjct: 9 KASGVQAQMAKQQEQDPTN---LYISNL------PLSMD-----EQELENMLKPFGQVIS 54
Query: 675 V-VLHDK--HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+L D GV + E +A NG++
Sbjct: 55 TRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGV 97
Score = 37.6 bits (88), Expect = 0.002
Identities = 14/94 (14%), Positives = 34/94 (36%), Gaps = 19/94 (20%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGL-----VMKDVDTNQMKIKLYTDPYTKDFKGD 267
++ T +Y+SNLPL + ++E +++ G +++D + +G
Sbjct: 23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTS-------------RGV 68
Query: 268 ALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
E + + +G I+ +
Sbjct: 69 GFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 102
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 38.7 bits (91), Expect = 6e-04
Identities = 15/89 (16%), Positives = 32/89 (35%), Gaps = 17/89 (19%)
Query: 499 ENTKVYVSNLPLDLTQEEFVE-VMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 557
+++++ NLPL +E + + G + ++ IK +
Sbjct: 9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHI-MQIN-----IK----------NAFGFIQF 52
Query: 558 IKKESVDLALSILDGYEIRGKKIKVERAK 586
+SV A+ GKK+ +E +
Sbjct: 53 DNPQSVRDAIECESQEMNFGKKLILEVSS 81
Score = 37.6 bits (88), Expect = 0.002
Identities = 15/89 (16%), Positives = 32/89 (35%), Gaps = 17/89 (19%)
Query: 214 ESTKVYVSNLPLDLTQEEFVE-VMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
+++++ NLPL +E + + G + ++ IK +
Sbjct: 9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHI-MQIN-----IK----------NAFGFIQF 52
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
+SV A+ GKK+ +E +
Sbjct: 53 DNPQSVRDAIECESQEMNFGKKLILEVSS 81
Score = 33.3 bits (77), Expect = 0.044
Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 4/58 (6%)
Query: 374 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
++DL S GH+ ++ + I F P++ E + +++ E
Sbjct: 25 KEDLFRIFSPYGHIMQINIK----NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE 78
Score = 33.3 bits (77), Expect = 0.044
Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 4/58 (6%)
Query: 659 QQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
++DL S GH+ ++ + I F P++ E + +++ E
Sbjct: 25 KEDLFRIFSPYGHIMQINIK----NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE 78
>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 = 38.3 bits (90), Expect = 8e-04
Identities = 17/87 (19%), Positives = 40/87 (45%), Gaps = 7/87 (8%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
S+ +++ NL ++ ++ + G++++ K+ DP T + KG A +
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQT-------PKIMRDPDTGNSKGYAFINFAS 57
Query: 275 KESVDLALSILDGYEIRGKKIKVERAK 301
++ D A+ ++G + + I V A
Sbjct: 58 FDASDAAIEAMNGQYLCNRPITVSYAF 84
Score = 37.9 bits (89), Expect = 0.001
Identities = 16/87 (18%), Positives = 40/87 (45%), Gaps = 7/87 (8%)
Query: 500 NTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 559
++ +++ NL ++ ++ + G++++ K+ DP T + KG A +
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQT-------PKIMRDPDTGNSKGYAFINFAS 57
Query: 560 KESVDLALSILDGYEIRGKKIKVERAK 586
++ D A+ ++G + + I V A
Sbjct: 58 FDASDAAIEAMNGQYLCNRPITVSYAF 84
Score = 33.7 bits (78), Expect = 0.039
Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 16/83 (19%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHV---KKVVLHDK--HPEGVAQIFFK 406
I + NL D ++ ++ L + S G + K++ + +G A I F
Sbjct: 8 IFIGNL------DPEID-----EKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFA 56
Query: 407 EPEAADACRELLNGRWFGQRQIT 429
+A+DA E +NG++ R IT
Sbjct: 57 SFDASDAAIEAMNGQYLCNRPIT 79
Score = 33.7 bits (78), Expect = 0.039
Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 16/83 (19%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHV---KKVVLHDK--HPEGVAQIFFK 691
I + NL D ++ ++ L + S G + K++ + +G A I F
Sbjct: 8 IFIGNL------DPEID-----EKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFA 56
Query: 692 EPEAADACRELLNGRWFGQRQIT 714
+A+DA E +NG++ R IT
Sbjct: 57 SFDASDAAIEAMNGQYLCNRPIT 79
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 38.4 bits (90), Expect = 8e-04
Identities = 16/100 (16%), Positives = 34/100 (34%), Gaps = 22/100 (22%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGL-----VMKDVDTNQMKIKLYTDPYTKDF 549
+ + K++V L ++E+ + + Q G+ V++ D +
Sbjct: 10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSS-------------- 55
Query: 550 KGDALCTYIKKESVDLALSILDGYEI---RGKKIKVERAK 586
KG A + A+ L G + + V+ A
Sbjct: 56 KGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFAD 95
Score = 38.0 bits (89), Expect = 0.001
Identities = 17/98 (17%), Positives = 33/98 (33%), Gaps = 22/98 (22%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGL-----VMKDVDTNQMKIKLYTDPYTKDFKG 266
G K++V L ++E+ + + Q G+ V++ D + KG
Sbjct: 12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSS--------------KG 57
Query: 267 DALCTYIKKESVDLALSILDGYEI---RGKKIKVERAK 301
A + A+ L G + + V+ A
Sbjct: 58 CAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFAD 95
Score = 36.5 bits (85), Expect = 0.004
Identities = 15/81 (18%), Positives = 27/81 (33%), Gaps = 14/81 (17%)
Query: 344 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK--HPEGV 400
R + + V L +K + ++D+ G + + VL +G
Sbjct: 10 SRGGRDRKLFVGML------NKQQS-----EEDVLRLFQPFGVIDECTVLRGPDGSSKGC 58
Query: 401 AQIFFKEPEAADACRELLNGR 421
A + F A A L+G
Sbjct: 59 AFVKFSSHTEAQAAIHALHGS 79
Score = 36.5 bits (85), Expect = 0.004
Identities = 15/81 (18%), Positives = 27/81 (33%), Gaps = 14/81 (17%)
Query: 629 ERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKV-VLHDK--HPEGV 685
R + + V L +K + ++D+ G + + VL +G
Sbjct: 10 SRGGRDRKLFVGML------NKQQS-----EEDVLRLFQPFGVIDECTVLRGPDGSSKGC 58
Query: 686 AQIFFKEPEAADACRELLNGR 706
A + F A A L+G
Sbjct: 59 AFVKFSSHTEAQAAIHALHGS 79
>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 = 38.0 bits (89), Expect = 9e-04
Identities = 17/89 (19%), Positives = 32/89 (35%), Gaps = 15/89 (16%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
S+ V+V D+T++E E + G V +D K F+ A T+
Sbjct: 3 SGSSGVFVGRCTGDMTEDELREFFSQYGDV---MDVFIP----------KPFRAFAFVTF 49
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
+ + I+G + + A+
Sbjct: 50 ADDQIAQSLCG--EDLIIKGISVHISNAE 76
Score = 36.4 bits (85), Expect = 0.003
Identities = 16/89 (17%), Positives = 32/89 (35%), Gaps = 15/89 (16%)
Query: 498 QENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 557
++ V+V D+T++E E + G V +D K F+ A T+
Sbjct: 3 SGSSGVFVGRCTGDMTEDELREFFSQYGDV---MDVFIP----------KPFRAFAFVTF 49
Query: 558 IKKESVDLALSILDGYEIRGKKIKVERAK 586
+ + I+G + + A+
Sbjct: 50 ADDQIAQSLCG--EDLIIKGISVHISNAE 76
>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 = 38.4 bits (90), Expect = 0.001
Identities = 16/90 (17%), Positives = 32/90 (35%), Gaps = 10/90 (11%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
++++ + V LP T+++ E G V + K D T KG
Sbjct: 12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEV---LMVQVKK-----DLKTGHSKGFGFVR 63
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ + E+ +S + I G+ +
Sbjct: 64 FTEYETQVKVMS--QRHMIDGRWCDCKLPN 91
>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 = 37.9 bits (89), Expect = 0.001
Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 9/88 (10%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
E++ K++V L D ++++ + K G V VD DP T +G +
Sbjct: 9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEV---VDCTIKM-----DPNTGRSRGFGFILF 60
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERA 300
SV+ L + + G+ I ++A
Sbjct: 61 KDAASVEKVLDQKEH-RLDGRVIDPKKA 87
Score = 37.5 bits (88), Expect = 0.001
Identities = 20/91 (21%), Positives = 37/91 (40%), Gaps = 9/91 (9%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
K ++ K++V L D ++++ + K G V VD DP T +G
Sbjct: 6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEV---VDCTIKM-----DPNTGRSRGFGF 57
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERA 585
+ SV+ L + + G+ I ++A
Sbjct: 58 ILFKDAASVEKVLDQKEH-RLDGRVIDPKKA 87
>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 = 38.1 bits (89), Expect = 0.001
Identities = 10/88 (11%), Positives = 29/88 (32%), Gaps = 11/88 (12%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
V++ LP T+ + + ++ + P + G+A +
Sbjct: 13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM---------RVHIEIGPDGR-VTGEADVEF 62
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERA 300
E A++ D ++ + +++
Sbjct: 63 ATHEDAVAAMA-KDKANMQHRYVELFLN 89
Score = 37.8 bits (88), Expect = 0.002
Identities = 10/90 (11%), Positives = 31/90 (34%), Gaps = 11/90 (12%)
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 555
++ V++ LP T+ + + ++ + P + G+A
Sbjct: 11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM---------RVHIEIGPDGR-VTGEADV 60
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKVERA 585
+ E A++ D ++ + +++
Sbjct: 61 EFATHEDAVAAMA-KDKANMQHRYVELFLN 89
>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 = 38.4 bits (90), Expect = 0.001
Identities = 20/108 (18%), Positives = 35/108 (32%), Gaps = 18/108 (16%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
TK++V LP T + + G + + + TD T +G T
Sbjct: 15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDI---EEAVVI-----TDRQTGKSRGYGFVTM 66
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRK 320
+ + + A + I G+K V A KP+ +
Sbjct: 67 ADRAAAERACKDPNP-IIDGRKANVNLAY---------LGAKPRSLQT 104
Score = 36.5 bits (85), Expect = 0.005
Identities = 21/111 (18%), Positives = 37/111 (33%), Gaps = 18/111 (16%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+K TK++V LP T + + G + + + TD T +G
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDI---EEAVVI-----TDRQTGKSRGYGF 63
Query: 555 CTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRK 605
T + + + A + I G+K V A KP+ +
Sbjct: 64 VTMADRAAAERACKDPNP-IIDGRKANVNLAY---------LGAKPRSLQT 104
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 37.4 bits (87), Expect = 0.001
Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 11/82 (13%)
Query: 349 ESVIIVKNL--FDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH--DKHPEGVAQIF 404
+SVI+V N+ P +K + + + SK G + D +G +
Sbjct: 1 DSVIVVDNVPQVGPDRLEKL-------KNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLE 53
Query: 405 FKEPEAADACRELLNGRWFGQR 426
+ P A + +G ++
Sbjct: 54 YASPAHAVDAVKNADGYKLDKQ 75
Score = 37.4 bits (87), Expect = 0.001
Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 11/82 (13%)
Query: 634 ESVIIVKNL--FDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH--DKHPEGVAQIF 689
+SVI+V N+ P +K + + + SK G + D +G +
Sbjct: 1 DSVIVVDNVPQVGPDRLEKL-------KNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLE 53
Query: 690 FKEPEAADACRELLNGRWFGQR 711
+ P A + +G ++
Sbjct: 54 YASPAHAVDAVKNADGYKLDKQ 75
Score = 31.2 bits (71), Expect = 0.18
Identities = 13/87 (14%), Positives = 27/87 (31%), Gaps = 16/87 (18%)
Query: 500 NTKVYVSNLP------LDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDA 553
++ + V N+P L+ + ++ K G + + KG
Sbjct: 1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKI----------TNDFYPEEDGKTKGYI 50
Query: 554 LCTYIKKESVDLALSILDGYEIRGKKI 580
Y A+ DGY++ +
Sbjct: 51 FLEYASPAHAVDAVKNADGYKLDKQHT 77
Score = 30.4 bits (69), Expect = 0.39
Identities = 13/86 (15%), Positives = 26/86 (30%), Gaps = 16/86 (18%)
Query: 216 TKVYVSNLP------LDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 269
+ + V N+P L+ + ++ K G + + KG
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKI----------TNDFYPEEDGKTKGYIF 51
Query: 270 CTYIKKESVDLALSILDGYEIRGKKI 295
Y A+ DGY++ +
Sbjct: 52 LEYASPAHAVDAVKNADGYKLDKQHT 77
>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 = 38.9 bits (90), Expect = 0.002
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 14/88 (15%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
+ V NL +T + ++ K G V+K + +TK+ + AL Y S
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKII------------TFTKNNQFQALLQYADPVS 96
Query: 278 VDLALSILDGYEI--RGKKIKVERAKFT 303
A LDG I ++++ +K T
Sbjct: 97 AQHAKLSLDGQNIYNACCTLRIDFSKLT 124
Score = 38.9 bits (90), Expect = 0.002
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 14/88 (15%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
+ V NL +T + ++ K G V+K + +TK+ + AL Y S
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKII------------TFTKNNQFQALLQYADPVS 96
Query: 563 VDLALSILDGYEI--RGKKIKVERAKFT 588
A LDG I ++++ +K T
Sbjct: 97 AQHAKLSLDGQNIYNACCTLRIDFSKLT 124
Score = 34.3 bits (78), Expect = 0.067
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 11/70 (15%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAA 411
IIV+NLF P D L + SK G V K++ K+ + A + + +P +A
Sbjct: 49 IIVENLFYPVTLD-----------VLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSA 97
Query: 412 DACRELLNGR 421
+ L+G+
Sbjct: 98 QHAKLSLDGQ 107
Score = 34.3 bits (78), Expect = 0.067
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 11/70 (15%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAA 696
IIV+NLF P D L + SK G V K++ K+ + A + + +P +A
Sbjct: 49 IIVENLFYPVTLD-----------VLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSA 97
Query: 697 DACRELLNGR 706
+ L+G+
Sbjct: 98 QHAKLSLDGQ 107
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 38.0 bits (88), Expect = 0.002
Identities = 17/94 (18%), Positives = 31/94 (32%), Gaps = 12/94 (12%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTY 272
S KV+V LP D+ ++E ++ G ++ D KG A +
Sbjct: 6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAE------SKSYFPPKGYAFLLF 59
Query: 273 IKKESVDLALSILD------GYEIRGKKIKVERA 300
++ SV + + IK +
Sbjct: 60 QEESSVQALIDACLEEDGKLYLCVSSPTIKDKPV 93
Score = 36.9 bits (85), Expect = 0.005
Identities = 16/97 (16%), Positives = 32/97 (32%), Gaps = 12/97 (12%)
Query: 495 KKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDAL 554
+ + KV+V LP D+ ++E ++ G ++ D KG A
Sbjct: 3 SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAE------SKSYFPPKGYAF 56
Query: 555 CTYIKKESVDLALSILD------GYEIRGKKIKVERA 585
+ ++ SV + + IK +
Sbjct: 57 LLFQEESSVQALIDACLEEDGKLYLCVSSPTIKDKPV 93
>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 = 40.6 bits (94), Expect = 0.002
Identities = 32/198 (16%), Positives = 65/198 (32%), Gaps = 25/198 (12%)
Query: 439 YKIQETAEEREARLKKWETFLGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQ 498
ET EER R ++ +KI+ + + + + +DP P +
Sbjct: 57 PTRAETREERMERKRR------EKIERRQQEVETELKMWDPHNDPNAQ---------GDA 101
Query: 499 ENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYI 558
T ++V+ + D T+ + + G + + I + + +G A Y
Sbjct: 102 FKT-LFVARVNYDTTESKLRREFEVYGPIKR--------IHMVYSKRSGKPRGYAFIEYE 152
Query: 559 KKESVDLALSILDGYEIRGKKIKVERA-KFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEK 617
+ + A DG +I G+++ V+ T+KG ++ +
Sbjct: 153 HERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSG 212
Query: 618 LFDWRPDKMRGERSKNES 635
D R S
Sbjct: 213 RDDTSRYDERPGPSPLPH 230
Score = 32.9 bits (74), Expect = 0.37
Identities = 20/134 (14%), Positives = 43/134 (32%), Gaps = 9/134 (6%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
++V+ + D T+ + + G + + I + + +G A Y +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKR--------IHMVYSKRSGKPRGYAFIEYEHERD 156
Query: 278 VDLALSILDGYEIRGKKIKVERA-KFTMKGEAYDPKLKPKKKRKKDLEKLKKAQEKLFDW 336
+ A DG +I G+++ V+ T+KG ++ + D
Sbjct: 157 MHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDT 216
Query: 337 RPDKMRGERSKNES 350
R S
Sbjct: 217 SRYDERPGPSPLPH 230
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 36.7 bits (86), Expect = 0.002
Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 9/84 (10%)
Query: 217 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 276
K+++ L TQE E + G V + M+ DP TK +G T++ +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEV---KECLVMR-----DPLTKRSRGFGFVTFMDQA 53
Query: 277 SVDLALSILDGYEIRGKKIKVERA 300
VD L+ +E+ K I + A
Sbjct: 54 GVDKVLAQ-SRHELDSKTIDPKVA 76
Score = 36.7 bits (86), Expect = 0.002
Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 9/84 (10%)
Query: 502 KVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKE 561
K+++ L TQE E + G V + M+ DP TK +G T++ +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEV---KECLVMR-----DPLTKRSRGFGFVTFMDQA 53
Query: 562 SVDLALSILDGYEIRGKKIKVERA 585
VD L+ +E+ K I + A
Sbjct: 54 GVDKVLAQ-SRHELDSKTIDPKVA 76
>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 = 36.8 bits (86), Expect = 0.002
Identities = 15/87 (17%), Positives = 31/87 (35%), Gaps = 8/87 (9%)
Query: 215 STKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 274
V+V +L ++T G + ++ D T KG ++
Sbjct: 6 HFHVFVGDLSPEITTAAIAAAFAPFGRISD--------ARVVKDMATGKSKGYGFVSFFN 57
Query: 275 KESVDLALSILDGYEIRGKKIKVERAK 301
K + A+ + G + G++I+ A
Sbjct: 58 KWDAENAIQQMGGQWLGGRQIRTNWAT 84
Score = 36.8 bits (86), Expect = 0.002
Identities = 15/87 (17%), Positives = 32/87 (36%), Gaps = 8/87 (9%)
Query: 500 NTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIK 559
+ V+V +L ++T G + ++ D T KG ++
Sbjct: 6 HFHVFVGDLSPEITTAAIAAAFAPFGRISD--------ARVVKDMATGKSKGYGFVSFFN 57
Query: 560 KESVDLALSILDGYEIRGKKIKVERAK 586
K + A+ + G + G++I+ A
Sbjct: 58 KWDAENAIQQMGGQWLGGRQIRTNWAT 84
Score = 31.0 bits (71), Expect = 0.29
Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 4/59 (6%)
Query: 375 QDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+ + G + V+ D +G + F A+ + + G+W G RQI
Sbjct: 21 AAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR 79
Score = 31.0 bits (71), Expect = 0.29
Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 4/59 (6%)
Query: 660 QDLREECSKCGHVKKV-VLHDK---HPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+ + G + V+ D +G + F A+ + + G+W G RQI
Sbjct: 21 AAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR 79
>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 35.3 bits (82), Expect = 0.010
Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 16/95 (16%)
Query: 337 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK--KVVLHD 394
D++ + N + VKNL D + + LR+ S G + KV++
Sbjct: 6 SGDRITRYQVVN---LYVKNL------DDGID-----DERLRKAFSPFGTITSAKVMMEG 51
Query: 395 KHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 429
+G + F PE A +NGR + +
Sbjct: 52 GRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLY 86
Score = 35.3 bits (82), Expect = 0.010
Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 16/95 (16%)
Query: 622 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVK--KVVLHD 679
D++ + N + VKNL D + + LR+ S G + KV++
Sbjct: 6 SGDRITRYQVVN---LYVKNL------DDGID-----DERLRKAFSPFGTITSAKVMMEG 51
Query: 680 KHPEGVAQIFFKEPEAADACRELLNGRWFGQRQIT 714
+G + F PE A +NGR + +
Sbjct: 52 GRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLY 86
Score = 32.6 bits (75), Expect = 0.099
Identities = 17/100 (17%), Positives = 33/100 (33%), Gaps = 21/100 (21%)
Query: 492 EKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGL-----VMKDVDTNQMKIKLYTDPYT 546
+++ + Q +YV NL + E + G VM +
Sbjct: 8 DRITRYQ-VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME---------------G 51
Query: 547 KDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
KG + E A++ ++G + K + V A+
Sbjct: 52 GRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ 91
Score = 32.6 bits (75), Expect = 0.11
Identities = 16/94 (17%), Positives = 29/94 (30%), Gaps = 20/94 (21%)
Query: 213 EESTKVYVSNLPLDLTQEEFVEVMQKCGL-----VMKDVDTNQMKIKLYTDPYTKDFKGD 267
+ +YV NL + E + G VM + KG
Sbjct: 13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME---------------GGRSKGF 57
Query: 268 ALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ E A++ ++G + K + V A+
Sbjct: 58 GFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ 91
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 36.0 bits (83), Expect = 0.011
Identities = 16/116 (13%), Positives = 37/116 (31%), Gaps = 15/116 (12%)
Query: 190 KAEEKVVPGQKRKPEPPKWFDIGEESTKVYVSNLPLDLTQEEFVEVM----QKCGLVMKD 245
A K P+ E S V ++N+ ++ +E+ ++ G ++
Sbjct: 4 TAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD- 62
Query: 246 VDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
I + A + +ES + GY +G + + ++
Sbjct: 63 -------IVVDLSDDNSGK---AYIVFATQESAQAFVEAFQGYPFQGNPLVITFSE 108
Score = 35.6 bits (82), Expect = 0.013
Identities = 20/102 (19%), Positives = 36/102 (35%), Gaps = 8/102 (7%)
Query: 328 KAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHV 387
K + + D ++ V+++ N+ + +V + Q L S G +
Sbjct: 8 KFERQHMDSPDLGSTPPHTEPSQVVLITNI------NPEVP-KEKLQALLYALASSQGDI 60
Query: 388 KKVVLH-DKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 428
+V+ G A I F E+A A E G F +
Sbjct: 61 LDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL 102
Score = 35.6 bits (82), Expect = 0.013
Identities = 20/102 (19%), Positives = 36/102 (35%), Gaps = 8/102 (7%)
Query: 613 KAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHV 672
K + + D ++ V+++ N+ + +V + Q L S G +
Sbjct: 8 KFERQHMDSPDLGSTPPHTEPSQVVLITNI------NPEVP-KEKLQALLYALASSQGDI 60
Query: 673 KKVVLH-DKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQI 713
+V+ G A I F E+A A E G F +
Sbjct: 61 LDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL 102
Score = 34.5 bits (79), Expect = 0.030
Identities = 12/112 (10%), Positives = 37/112 (33%), Gaps = 18/112 (16%)
Query: 482 KPKKKRKKDLEKLKKAQE---NTKVYVSNLPLDLTQEEFVEVM----QKCGLVMKDVDTN 534
K +++ + + V ++N+ ++ +E+ ++ G ++
Sbjct: 8 KFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD----- 62
Query: 535 QMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
I + A + +ES + GY +G + + ++
Sbjct: 63 ---IVVDLSDDNSGK---AYIVFATQESAQAFVEAFQGYPFQGNPLVITFSE 108
>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 = 35.3 bits (82), Expect = 0.011
Identities = 16/91 (17%), Positives = 37/91 (40%), Gaps = 15/91 (16%)
Query: 500 NTKVYVSNLPLDLTQEEFVEVMQ----KCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 555
N +Y++NL + ++E + + + G ++ I + +G A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILD--------ILVSRSL---KMRGQAFV 56
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKVERAK 586
+ + S AL + G+ K ++++ AK
Sbjct: 57 IFKEVSSATNALRSMQGFPFYDKPMRIQYAK 87
Score = 34.9 bits (81), Expect = 0.014
Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 8/80 (10%)
Query: 350 SVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-DKHPEGVAQIFFKEP 408
I + NL ++ + E ++ L S+ G + +++ G A + FKE
Sbjct: 9 HTIYINNL------NEKIK-KDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 409 EAADACRELLNGRWFGQRQI 428
+A + G F + +
Sbjct: 62 SSATNALRSMQGFPFYDKPM 81
Score = 34.9 bits (81), Expect = 0.014
Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 8/80 (10%)
Query: 635 SVIIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLH-DKHPEGVAQIFFKEP 693
I + NL ++ + E ++ L S+ G + +++ G A + FKE
Sbjct: 9 HTIYINNL------NEKIK-KDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 694 EAADACRELLNGRWFGQRQI 713
+A + G F + +
Sbjct: 62 SSATNALRSMQGFPFYDKPM 81
Score = 34.5 bits (80), Expect = 0.020
Identities = 15/94 (15%), Positives = 37/94 (39%), Gaps = 15/94 (15%)
Query: 212 GEESTKVYVSNLPLDLTQEEFVEVMQ----KCGLVMKDVDTNQMKIKLYTDPYTKDFKGD 267
+ +Y++NL + ++E + + + G ++ I + +G
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILD--------ILVSRSL---KMRGQ 53
Query: 268 ALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
A + + S AL + G+ K ++++ AK
Sbjct: 54 AFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK 87
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 34.7 bits (80), Expect = 0.018
Identities = 11/86 (12%), Positives = 22/86 (25%), Gaps = 13/86 (15%)
Query: 349 ESVIIVKNL--FDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL----HDKHPEGVAQ 402
+ I+V A ++ L SK G V + +G
Sbjct: 6 DQYIVVNGAPVIPSAKVPVL-------KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLF 58
Query: 403 IFFKEPEAADACRELLNGRWFGQRQI 428
+ A + +G+ +
Sbjct: 59 VECGSMNDAKKIIKSFHGKRLDLKHR 84
Score = 34.7 bits (80), Expect = 0.018
Identities = 11/86 (12%), Positives = 22/86 (25%), Gaps = 13/86 (15%)
Query: 634 ESVIIVKNL--FDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL----HDKHPEGVAQ 687
+ I+V A ++ L SK G V + +G
Sbjct: 6 DQYIVVNGAPVIPSAKVPVL-------KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLF 58
Query: 688 IFFKEPEAADACRELLNGRWFGQRQI 713
+ A + +G+ +
Sbjct: 59 VECGSMNDAKKIIKSFHGKRLDLKHR 84
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 34.7 bits (80), Expect = 0.018
Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 11/82 (13%)
Query: 349 ESVIIVKNL--FDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL--HDKHPEGVAQIF 404
+SVI+V N+ P +K + + SK G + D +G +
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKN-------VIHKIFSKFGKITNDFYPEEDGKTKGYIFLE 67
Query: 405 FKEPEAADACRELLNGRWFGQR 426
+ P A + +G ++
Sbjct: 68 YASPAHAVDAVKNADGYKLDKQ 89
Score = 34.7 bits (80), Expect = 0.018
Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 11/82 (13%)
Query: 634 ESVIIVKNL--FDPALFDKDVTLILEYQQDLREECSKCGHVKKVVL--HDKHPEGVAQIF 689
+SVI+V N+ P +K + + SK G + D +G +
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKN-------VIHKIFSKFGKITNDFYPEEDGKTKGYIFLE 67
Query: 690 FKEPEAADACRELLNGRWFGQR 711
+ P A + +G ++
Sbjct: 68 YASPAHAVDAVKNADGYKLDKQ 89
Score = 34.3 bits (79), Expect = 0.024
Identities = 13/85 (15%), Positives = 26/85 (30%), Gaps = 16/85 (18%)
Query: 215 STKVYVSNLP------LDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDA 268
+ + V N+P L+ + ++ K G + + KG
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKI----------TNDFYPEEDGKTKGYI 64
Query: 269 LCTYIKKESVDLALSILDGYEIRGK 293
Y A+ DGY++ +
Sbjct: 65 FLEYASPAHAVDAVKNADGYKLDKQ 89
Score = 33.9 bits (78), Expect = 0.030
Identities = 13/85 (15%), Positives = 27/85 (31%), Gaps = 16/85 (18%)
Query: 500 NTKVYVSNLP------LDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDA 553
++ + V N+P L+ + ++ K G + + KG
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKI----------TNDFYPEEDGKTKGYI 64
Query: 554 LCTYIKKESVDLALSILDGYEIRGK 578
Y A+ DGY++ +
Sbjct: 65 FLEYASPAHAVDAVKNADGYKLDKQ 89
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 35.0 bits (80), Expect = 0.025
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 14/88 (15%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
+ V NL +T + ++ K G V+K + +TK+ + AL Y S
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKII------------TFTKNNQFQALLQYADPVS 78
Query: 278 VDLALSILDGYEI--RGKKIKVERAKFT 303
A LDG I ++++ +K T
Sbjct: 79 AQHAKLSLDGQNIYNACCTLRIDFSKLT 106
Score = 35.0 bits (80), Expect = 0.025
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 14/88 (15%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
+ V NL +T + ++ K G V+K + +TK+ + AL Y S
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKII------------TFTKNNQFQALLQYADPVS 78
Query: 563 VDLALSILDGYEI--RGKKIKVERAKFT 588
A LDG I ++++ +K T
Sbjct: 79 AQHAKLSLDGQNIYNACCTLRIDFSKLT 106
Score = 31.9 bits (72), Expect = 0.29
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 11/70 (15%)
Query: 352 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAA 411
IIV+NLF P VTL L + SK G V K++ K+ + A + + +P +A
Sbjct: 31 IIVENLFYP------VTL-----DVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSA 79
Query: 412 DACRELLNGR 421
+ L+G+
Sbjct: 80 QHAKLSLDGQ 89
Score = 31.9 bits (72), Expect = 0.29
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 11/70 (15%)
Query: 637 IIVKNLFDPALFDKDVTLILEYQQDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAA 696
IIV+NLF P VTL L + SK G V K++ K+ + A + + +P +A
Sbjct: 31 IIVENLFYP------VTL-----DVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSA 79
Query: 697 DACRELLNGR 706
+ L+G+
Sbjct: 80 QHAKLSLDGQ 89
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment
2, heavy meromyosin, essential light chain, motor
protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1
PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 36.7 bits (85), Expect = 0.037
Identities = 37/182 (20%), Positives = 68/182 (37%), Gaps = 16/182 (8%)
Query: 436 KTRYKIQETAEEREARLKKWETFLGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLK 495
+ ++ AEE RL + L + + A+ + E KKK ++ + L+
Sbjct: 902 QAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLE 961
Query: 496 KAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALC 555
+ E + L Q E V K + + I + D K K L
Sbjct: 962 EQLEEEEAARQKL-----QLEKVTADGK-------IKKMEDDILIMEDQNNKLTKERKL- 1008
Query: 556 TYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQ 615
+E V + L E + K + + K + +LK ++K +++LEK+K+
Sbjct: 1009 ---LEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKL 1065
Query: 616 EK 617
E
Sbjct: 1066 EG 1067
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 34.6 bits (79), Expect = 0.070
Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 11/65 (16%)
Query: 337 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQ-DLREECSKCGHV--KKVVLH 393
DK G R N ++++ P ++ + + D+ C+ CG V K+V
Sbjct: 6 SIDKRAGRRGPNLNIVLTC----PECKVYPPKIVERFSEGDVV--CALCGLVLSDKLV-- 57
Query: 394 DKHPE 398
D E
Sbjct: 58 DTRSE 62
Score = 34.6 bits (79), Expect = 0.070
Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 11/65 (16%)
Query: 622 RPDKMRGERSKNESVIIVKNLFDPALFDKDVTLILEYQQ-DLREECSKCGHV--KKVVLH 678
DK G R N ++++ P ++ + + D+ C+ CG V K+V
Sbjct: 6 SIDKRAGRRGPNLNIVLTC----PECKVYPPKIVERFSEGDVV--CALCGLVLSDKLV-- 57
Query: 679 DKHPE 683
D E
Sbjct: 58 DTRSE 62
Score = 29.2 bits (65), Expect = 4.0
Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 8/60 (13%)
Query: 195 VVPGQKRKPEPPKWFDIGEEST----KVYVSNLPLDLTQEEFVEVMQKCGLVMKD--VDT 248
+ K + ++ T KVY + ++ + V CGLV+ D VDT
Sbjct: 2 MTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVV--CALCGLVLSDKLVDT 59
>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 = 33.0 bits (75), Expect = 0.072
Identities = 21/93 (22%), Positives = 34/93 (36%), Gaps = 15/93 (16%)
Query: 213 EESTKVYVSNLPLDLT----QEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDA 268
V VSN+ L+ Q+ E + G V ++L D++ A
Sbjct: 7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKS--------VELSPH---TDYQLKA 55
Query: 269 LCTYIKKESVDLALSILDGYEIRGKKIKVERAK 301
+ + A++ L Y+I KKI V A
Sbjct: 56 VVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT 88
Score = 32.3 bits (73), Expect = 0.12
Identities = 21/94 (22%), Positives = 35/94 (37%), Gaps = 15/94 (15%)
Query: 497 AQENTKVYVSNLPLDLT----QEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGD 552
+ V VSN+ L+ Q+ E + G V ++L D++
Sbjct: 6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKS--------VELSPH---TDYQLK 54
Query: 553 ALCTYIKKESVDLALSILDGYEIRGKKIKVERAK 586
A+ + A++ L Y+I KKI V A
Sbjct: 55 AVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT 88
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 34.0 bits (77), Expect = 0.091
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 8/44 (18%)
Query: 725 KIQETAEEREARLKKWETFLEEEDKKKKEAGKGSIDEKESKELQ 768
I++ EE+ RL++ L+ K ++ EK K+L+
Sbjct: 86 SIRKWREEQRKRLQE----LDAASKVMEQE----WREKAKKDLE 121
Score = 33.2 bits (75), Expect = 0.19
Identities = 16/78 (20%), Positives = 35/78 (44%), Gaps = 9/78 (11%)
Query: 692 EPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLEEEDKKK 751
EPE+ R+ W +++ + D ++ QE E+ + L++W E+ +K
Sbjct: 83 EPESI---RK-----WREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKN 134
Query: 752 KEAGKGSIDEKESKELQA 769
K + + D+ ++ A
Sbjct: 135 KINNRIA-DKAFYQQPDA 151
Score = 31.7 bits (71), Expect = 0.51
Identities = 10/80 (12%), Positives = 27/80 (33%), Gaps = 18/80 (22%)
Query: 440 KIQETAEEREARLKKWETFLGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLKKAQE 499
I++ EE+ RL++ + + + +A + +++ + +EK K
Sbjct: 86 SIRKWREEQRKRLQE------LDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNR 139
Query: 500 NTKVYVSNLPLDLTQEEFVE 519
+ F +
Sbjct: 140 I------------ADKAFYQ 147
Score = 29.0 bits (64), Expect = 4.1
Identities = 13/70 (18%), Positives = 30/70 (42%), Gaps = 10/70 (14%)
Query: 407 EPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLGKKIKVE 466
EPE+ R+ W +++ + D ++ QE E+ + L++W +++ E
Sbjct: 83 EPESI---RK-----WREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQV--E 132
Query: 467 RAKFTMKGEA 476
+ K +
Sbjct: 133 KNKINNRIAD 142
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 99
Score = 31.5 bits (72), Expect = 0.21
Identities = 12/67 (17%), Positives = 23/67 (34%), Gaps = 8/67 (11%)
Query: 371 LEYQ---QDLREECSKCGH-VKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRW 422
LE + + G V V ++ ++ P G + F + A+ C +NG+
Sbjct: 17 LEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKP 76
Query: 423 FGQRQIT 429
Sbjct: 77 LPGATPA 83
Score = 31.5 bits (72), Expect = 0.21
Identities = 12/67 (17%), Positives = 23/67 (34%), Gaps = 8/67 (11%)
Query: 656 LEYQ---QDLREECSKCGH-VKKV-VLHDKH---PEGVAQIFFKEPEAADACRELLNGRW 707
LE + + G V V ++ ++ P G + F + A+ C +NG+
Sbjct: 17 LEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKP 76
Query: 708 FGQRQIT 714
Sbjct: 77 LPGATPA 83
>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 = 31.8 bits (72), Expect = 0.24
Identities = 10/49 (20%), Positives = 19/49 (38%), Gaps = 4/49 (8%)
Query: 374 QQDLREECSKCGHVKKV-VLHDKHPEGVAQIFFKEPEAADACRELLNGR 421
+ L KCG V + + +K + ++ E + LNG+
Sbjct: 41 RNQLLPVLEKCGLVDALLMPPNK---PYSFARYRTTEESKRAYVTLNGK 86
Score = 31.8 bits (72), Expect = 0.24
Identities = 10/49 (20%), Positives = 19/49 (38%), Gaps = 4/49 (8%)
Query: 659 QQDLREECSKCGHVKKV-VLHDKHPEGVAQIFFKEPEAADACRELLNGR 706
+ L KCG V + + +K + ++ E + LNG+
Sbjct: 41 RNQLLPVLEKCGLVDALLMPPNK---PYSFARYRTTEESKRAYVTLNGK 86
>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase;
1.70A {Bacillus subtilis} PDB: 3moj_B
Length = 76
Score = 30.2 bits (69), Expect = 0.37
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 273 IKKESVDLALSILDGYEIRGKKIKVERAK 301
I L ++ ++GK++KV +A
Sbjct: 47 ILNGKGPHVLKVMKNTTVKGKQLKVNKAN 75
Score = 30.2 bits (69), Expect = 0.37
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 558 IKKESVDLALSILDGYEIRGKKIKVERAK 586
I L ++ ++GK++KV +A
Sbjct: 47 ILNGKGPHVLKVMKNTTVKGKQLKVNKAN 75
>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 = 32.1 bits (72), Expect = 0.42
Identities = 18/102 (17%), Positives = 36/102 (35%), Gaps = 12/102 (11%)
Query: 208 WFDIGEESTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGD 267
+ ++ VY+ P D T ++ E ++ G V ++++ K FKG
Sbjct: 102 EYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQV------LNIQMRRTLH---KAFKGS 152
Query: 268 ALCTYIKKESVDLALSILDGYEIRGKKIKVERAK--FTMKGE 307
+ ES + G + + + + F K E
Sbjct: 153 IFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDDYFAKKNE 193
Score = 31.7 bits (71), Expect = 0.59
Identities = 22/125 (17%), Positives = 44/125 (35%), Gaps = 12/125 (9%)
Query: 470 FTMKGEAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMK 529
+ + + P K + ++ K +N VY+ P D T ++ E ++ G V
Sbjct: 79 MEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQV-- 136
Query: 530 DVDTNQMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAK--F 587
++++ K FKG + ES + G + + + + F
Sbjct: 137 ----LNIQMRRTLH---KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDDYF 188
Query: 588 TMKGE 592
K E
Sbjct: 189 AKKNE 193
Score = 29.4 bits (65), Expect = 3.1
Identities = 10/55 (18%), Positives = 19/55 (34%), Gaps = 3/55 (5%)
Query: 374 QQDLREECSKCGHVKKVVL---HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQ 425
D++E G V + + K +G + F E+A E ++
Sbjct: 123 LDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKET 177
Score = 29.4 bits (65), Expect = 3.1
Identities = 10/55 (18%), Positives = 19/55 (34%), Gaps = 3/55 (5%)
Query: 659 QQDLREECSKCGHVKKVVL---HDKHPEGVAQIFFKEPEAADACRELLNGRWFGQ 710
D++E G V + + K +G + F E+A E ++
Sbjct: 123 LDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKET 177
>2xyi_A Probable histone-binding protein CAF1; transcription, repressor,
phosphoprotein, WD-repeat; HET: PG4; 1.75A {Drosophila
melanogaster} PDB: 3c99_A 3c9c_A 2yb8_B 2yba_A 2xu7_A*
3gfc_A 3cfs_B 3cfv_B
Length = 430
Score = 32.4 bits (74), Expect = 0.61
Identities = 10/78 (12%), Positives = 26/78 (33%), Gaps = 7/78 (8%)
Query: 69 SVPLVTSDKAADSSDEEEYDENNAQKTAPPIQRQ-------DMSKGSYGYEGDTHTYTDS 121
+P + D E+ + I+ + ++++ Y + T +
Sbjct: 89 QLPSEDAQFDGSHYDNEKGEFGGFGSVCGKIEIEIKINHEGEVNRARYMPQNACVIATKT 148
Query: 122 TDGTVYIWDKEKNAWFPK 139
V ++D K+ P+
Sbjct: 149 PSSDVLVFDYTKHPSKPE 166
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 29.6 bits (66), Expect = 0.83
Identities = 13/57 (22%), Positives = 20/57 (35%), Gaps = 2/57 (3%)
Query: 375 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 431
LR C + G + + G+A + E A+ + LN I AE
Sbjct: 22 PTLRTLCMQHGPLVSFHPYLNQ--GIALCKYTTREEANKAQMALNNCVLANTTIFAE 76
Score = 29.6 bits (66), Expect = 0.83
Identities = 13/57 (22%), Positives = 20/57 (35%), Gaps = 2/57 (3%)
Query: 660 QDLREECSKCGHVKKVVLHDKHPEGVAQIFFKEPEAADACRELLNGRWFGQRQITAE 716
LR C + G + + G+A + E A+ + LN I AE
Sbjct: 22 PTLRTLCMQHGPLVSFHPYLNQ--GIALCKYTTREEANKAQMALNNCVLANTTIFAE 76
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 30.7 bits (68), Expect = 1.1
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 6/30 (20%)
Query: 492 EK--LKKAQENTKVYVSN----LPLDLTQE 515
EK LKK Q + K+Y + L + T E
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKATME 47
Score = 28.4 bits (62), Expect = 4.9
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 21/43 (48%)
Query: 320 KKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPAL 362
K+ L+KL +A KL+ D S PAL
Sbjct: 19 KQALKKL-QASLKLYA--DD----------SA--------PAL 40
Score = 28.4 bits (62), Expect = 4.9
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 21/43 (48%)
Query: 605 KKDLEKLKKAQEKLFDWRPDKMRGERSKNESVIIVKNLFDPAL 647
K+ L+KL +A KL+ D S PAL
Sbjct: 19 KQALKKL-QASLKLYA--DD----------SA--------PAL 40
>1mx3_A CTBP1, C-terminal binding protein 1; nuclear protein,
phosphorylation, transcriptional corepresso
transcription repressor; HET: NAD; 1.95A {Homo sapiens}
SCOP: c.2.1.4 c.23.12.1 PDB: 1hku_A* 1hl3_A* 2hu2_A*
3ga0_A 2ome_A*
Length = 347
Score = 31.5 bits (72), Expect = 1.1
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 12/57 (21%)
Query: 287 GYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKKKRKKDLEKLKKAQE 331
IRG+ + + RAK F YDP L +R L+++ Q+
Sbjct: 163 AARIRGETLGIIGLGRVGQAVALRAKAFGFNVLFYDPYLSDGVERALGLQRVSTLQD 219
Score = 31.5 bits (72), Expect = 1.1
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 12/57 (21%)
Query: 572 GYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKKKRKKDLEKLKKAQE 616
IRG+ + + RAK F YDP L +R L+++ Q+
Sbjct: 163 AARIRGETLGIIGLGRVGQAVALRAKAFGFNVLFYDPYLSDGVERALGLQRVSTLQD 219
>2x24_A Acetyl-COA carboxylase; fatty acid biosynthesis, ligase, lipid
synthesis; HET: X24; 2.40A {Bos taurus} PDB: 3ff6_A*
3tdc_A*
Length = 793
Score = 31.3 bits (71), Expect = 1.4
Identities = 16/85 (18%), Positives = 29/85 (34%), Gaps = 5/85 (5%)
Query: 682 PEGVAQIFFKEPEAADACRELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKW- 740
PEG +I +++ + R L Q+ R +++ + RE L
Sbjct: 566 PEGTVEIKYQKKDLVKTIRRLDPISKKLVEQLGVSELSDTDRKELEGQLKAREDLLLPMY 625
Query: 741 ----ETFLEEEDKKKKEAGKGSIDE 761
F + D + KG I +
Sbjct: 626 HQVALHFADLHDTAGRMLEKGVIYD 650
>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 = 29.2 bits (65), Expect = 1.9
Identities = 21/109 (19%), Positives = 32/109 (29%), Gaps = 14/109 (12%)
Query: 213 EESTKVYVSNLPLDL-TQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCT 271
S+ + D+ ++ E + T Q Y K FK
Sbjct: 3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQ---------YFKSFK-RVRIN 52
Query: 272 YIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKLKPKKKRK 320
+ S A L E GK++K+ A+ G L P K
Sbjct: 53 FSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHIG---SSHLAPPNPDK 98
>1wwk_A Phosphoglycerate dehydrogenase; riken structural
genomics/proteomics initiative, RSGI, structural
genomics, oxidoreductase; HET: NAD; 1.90A {Pyrococcus
horikoshii}
Length = 307
Score = 30.6 bits (70), Expect = 2.0
Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 12/52 (23%)
Query: 287 GYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKKKRKKDLEKL 326
G E+ GK I + + A M YDP ++ ++ + + +
Sbjct: 137 GIELEGKTIGIIGFGRIGYQVAKIANALGMNILLYDPYPNEERAKEVNGKFV 188
Score = 30.6 bits (70), Expect = 2.0
Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 12/52 (23%)
Query: 572 GYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKKKRKKDLEKL 611
G E+ GK I + + A M YDP ++ ++ + + +
Sbjct: 137 GIELEGKTIGIIGFGRIGYQVAKIANALGMNILLYDPYPNEERAKEVNGKFV 188
>1ygy_A PGDH, D-3-phosphoglycerate dehydrogenase; oxidoreductase, serine
biosy structural genomics, PSI, protein structure
initiative; HET: TAR; 2.30A {Mycobacterium tuberculosis}
SCOP: c.2.1.4 c.23.12.1 d.58.18.1 d.81.2.2 PDB: 3dc2_A*
3ddn_A*
Length = 529
Score = 30.7 bits (70), Expect = 2.2
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 12/52 (23%)
Query: 287 GYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKKKRKKDLEKL 326
G EI GK + V +R F AYDP + P + + +E L
Sbjct: 137 GTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELL 188
Score = 30.7 bits (70), Expect = 2.2
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 12/52 (23%)
Query: 572 GYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKKKRKKDLEKL 611
G EI GK + V +R F AYDP + P + + +E L
Sbjct: 137 GTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELL 188
>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 = 28.8 bits (64), Expect = 2.4
Identities = 19/109 (17%), Positives = 42/109 (38%), Gaps = 18/109 (16%)
Query: 197 PGQKRKPEPPKWFDIGEESTKV-YVSNLPLD-LTQEEFVEVMQKCGLVMKDVDTNQMKIK 254
G+K + +P + FD +E +V ++SNLP + +++ + G +
Sbjct: 6 SGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKI--------KNYI 57
Query: 255 LYTDPYTKDFKGDALCTYIKKESVDLALS--ILDGYEIRGKKIKVERAK 301
L K A +E + + +G+ +KV+ ++
Sbjct: 58 LMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSE 100
>3gvx_A Glycerate dehydrogenase related protein; NYSGXRC, PSI-II, 11143J,
structural genomics, protein structure initiative; 2.20A
{Thermoplasma acidophilum}
Length = 290
Score = 29.9 bits (68), Expect = 3.0
Identities = 9/54 (16%), Positives = 15/54 (27%), Gaps = 14/54 (25%)
Query: 287 GYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKK--KRKKDLEKL 326
+ GK + + AK F M+ AY + + L
Sbjct: 117 TTLLYGKALGILGYGGIGRRVAHLAKAFGMRVIAYTRSSVDQNVDVISESPADL 170
Score = 29.9 bits (68), Expect = 3.0
Identities = 9/54 (16%), Positives = 15/54 (27%), Gaps = 14/54 (25%)
Query: 572 GYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKK--KRKKDLEKL 611
+ GK + + AK F M+ AY + + L
Sbjct: 117 TTLLYGKALGILGYGGIGRRVAHLAKAFGMRVIAYTRSSVDQNVDVISESPADL 170
>2ekl_A D-3-phosphoglycerate dehydrogenase; structural genomics, NPPSFA,
national project on protein structural and functional
analyses; HET: NAD; 1.77A {Sulfolobus tokodaii}
Length = 313
Score = 29.8 bits (68), Expect = 3.3
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 12/52 (23%)
Query: 287 GYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKKKRKKDLEKL 326
G E+ GK I + A MK AYD +K K + + +
Sbjct: 137 GLELAGKTIGIVGFGRIGTKVGIIANAMGMKVLAYDILDIREKAEKINAKAV 188
Score = 29.8 bits (68), Expect = 3.3
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 12/52 (23%)
Query: 572 GYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKKKRKKDLEKL 611
G E+ GK I + A MK AYD +K K + + +
Sbjct: 137 GLELAGKTIGIVGFGRIGTKVGIIANAMGMKVLAYDILDIREKAEKINAKAV 188
>2j6i_A Formate dehydrogenase; oxidoreductase, D-specific-2- hydroxy acid
dehydrogenase, cofactor regenerator, yeast, CBFDH; HET:
PG4; 1.55A {Candida boidinii} PDB: 2fss_A
Length = 364
Score = 29.6 bits (67), Expect = 3.6
Identities = 12/50 (24%), Positives = 16/50 (32%), Gaps = 12/50 (24%)
Query: 286 DGYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKKKRKKDL 323
D Y+I GK I ER F K Y K ++ +
Sbjct: 158 DAYDIEGKTIATIGAGRIGYRVLERLVPFNPKELLYYDYQALPKDAEEKV 207
Score = 29.6 bits (67), Expect = 3.6
Identities = 12/50 (24%), Positives = 16/50 (32%), Gaps = 12/50 (24%)
Query: 571 DGYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKKKRKKDL 608
D Y+I GK I ER F K Y K ++ +
Sbjct: 158 DAYDIEGKTIATIGAGRIGYRVLERLVPFNPKELLYYDYQALPKDAEEKV 207
>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N
domain, MIF4G domain; 1.95A {Homo sapiens} SCOP:
d.58.7.4
Length = 91
Score = 27.8 bits (62), Expect = 3.7
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 216 TKVYVSNLPLDLTQEEFVEVMQ 237
+KV + LP LT+E+ E +Q
Sbjct: 2 SKVVIRRLPPTLTKEQLQEHLQ 23
Score = 27.8 bits (62), Expect = 3.7
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 501 TKVYVSNLPLDLTQEEFVEVMQ 522
+KV + LP LT+E+ E +Q
Sbjct: 2 SKVVIRRLPPTLTKEQLQEHLQ 23
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 28.5 bits (63), Expect = 3.7
Identities = 15/86 (17%), Positives = 28/86 (32%), Gaps = 15/86 (17%)
Query: 218 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 277
+ + N +T + V G V + V K A+ +
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIV-------------IFKRNGIQAMVEFESVLC 74
Query: 278 VDLALSILDGYEIRGK--KIKVERAK 301
A + L+G +I +K+E A+
Sbjct: 75 AQKAKAALNGADIYAGCCTLKIEYAR 100
Score = 28.5 bits (63), Expect = 3.7
Identities = 15/86 (17%), Positives = 28/86 (32%), Gaps = 15/86 (17%)
Query: 503 VYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKGDALCTYIKKES 562
+ + N +T + V G V + V K A+ +
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIV-------------IFKRNGIQAMVEFESVLC 74
Query: 563 VDLALSILDGYEIRGK--KIKVERAK 586
A + L+G +I +K+E A+
Sbjct: 75 AQKAKAALNGADIYAGCCTLKIEYAR 100
>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator,
structural genomics, PSI-2, protei structure initiative;
NMR {Homo sapiens}
Length = 97
Score = 27.8 bits (62), Expect = 4.1
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 498 QENTKVYVSNLPLDLTQEEFVEVMQ 522
+ V + LP LT+E+ E ++
Sbjct: 7 HHSHMVVIRRLPPGLTKEQLEEQLR 31
Score = 27.8 bits (62), Expect = 4.8
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 214 ESTKVYVSNLPLDLTQEEFVEVMQ 237
S V + LP LT+E+ E ++
Sbjct: 8 HSHMVVIRRLPPGLTKEQLEEQLR 31
>2g76_A 3-PGDH, D-3-phosphoglycerate dehydrogenase; oxidoreductase,
phosphoglycerate dehydrogenase deficiency, S metabolism,
2-hydroxyacid dehydrogenases; HET: NAD; 1.70A {Homo
sapiens}
Length = 335
Score = 29.5 bits (67), Expect = 4.2
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 12/52 (23%)
Query: 287 GYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKKKRKKDLEKL 326
G E+ GK + + R + F MK YDP + P+ +++L
Sbjct: 160 GTELNGKTLGILGLGRIGREVATRMQSFGMKTIGYDPIISPEVSASFGVQQL 211
Score = 29.5 bits (67), Expect = 4.2
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 12/52 (23%)
Query: 572 GYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKKKRKKDLEKL 611
G E+ GK + + R + F MK YDP + P+ +++L
Sbjct: 160 GTELNGKTLGILGLGRIGREVATRMQSFGMKTIGYDPIISPEVSASFGVQQL 211
>3pdf_A Cathepsin C, dipeptidyl peptidase 1; two domains, cystein protease,
hydrolase-hydrolase inhibitor; HET: LXV NAG; 1.85A {Homo
sapiens} PDB: 1jqp_A* 2djf_B* 1k3b_B* 2djg_B* 2djf_A*
1k3b_A* 2djg_A* 2djf_C* 1k3b_C* 2djg_C*
Length = 441
Score = 29.8 bits (67), Expect = 4.4
Identities = 10/75 (13%), Positives = 20/75 (26%), Gaps = 7/75 (9%)
Query: 453 KKWETFLGKKIKVERAKFTMKGEAYDPKLKPKKKRKKDLEKLK------KAQENTKVYVS 506
+ W F GKK+ + A+ + K + Q++
Sbjct: 108 RNWACFTGKKVGTASENVYVN-TAHLKNSQEKYSNRLYKYDHNFVKAINAIQKSWTATTY 166
Query: 507 NLPLDLTQEEFVEVM 521
LT + +
Sbjct: 167 MEYETLTLGDMIRRS 181
>2fic_A Bridging integrator 1; BAR domain, homodimer, coiled-coils,
endocytosis/exocytosis, protein complex,
endocytosis-exocytosis; 1.99A {Homo sapiens} PDB: 2rmy_A
2rnd_A
Length = 251
Score = 29.0 bits (64), Expect = 5.1
Identities = 28/188 (14%), Positives = 66/188 (35%), Gaps = 15/188 (7%)
Query: 440 KIQETAEEREARLKKWETFLGKKIKVERAKFTMK------GEAYDPKLKPKKKRKKDLEK 493
+ AE + + + K+ RA+ + E D + + +
Sbjct: 7 RGSHMAEMGSKGVTAGKIASNVQKKLTRAQEKVLQKLGKADETKDEQFEQCVQNFNKQLT 66
Query: 494 -LKKAQENTKVYVSNLP-LDLTQEEFVEVMQKCGLVMKDVDTNQMKIKLYTDPYTKDFKG 551
+ Q++ + Y++++ + ++ E +Q+ KI D D+
Sbjct: 67 EGTRLQKDLRTYLASVKAMHEASKKLNECLQEVYEPDWPGRDEANKIAENNDLLWMDYHQ 126
Query: 552 DALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAYDPKL-KPKKKRKKDLEK 610
+ + ++D L + R K R + + ++ + +KKD K
Sbjct: 127 KLVDQAL--LTMDTYLGQFPDIKSRIAK----RGRKLVDYDSARHHYESLQTAKKKDEAK 180
Query: 611 LKKAQEKL 618
+ KA+E+L
Sbjct: 181 IAKAEEEL 188
>2nac_A NAD-dependent formate dehydrogenase;
oxidoreductase(aldehyde(D),NAD+(A)); 1.80A {Pseudomonas
SP} SCOP: c.2.1.4 c.23.12.1 PDB: 2nad_A* 2go1_A 2gug_A*
2gsd_A* 3fn4_A
Length = 393
Score = 29.2 bits (66), Expect = 5.3
Identities = 7/61 (11%), Positives = 14/61 (22%), Gaps = 19/61 (31%)
Query: 285 LDGYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKKKRKK-------DLEK 325
Y++ + R F + D P+ K+ E
Sbjct: 184 SHAYDLEAMHVGTVAAGRIGLAVLRRLAPFDVHLHYTDRHRLPESVEKELNLTWHATRED 243
Query: 326 L 326
+
Sbjct: 244 M 244
Score = 29.2 bits (66), Expect = 5.3
Identities = 7/61 (11%), Positives = 14/61 (22%), Gaps = 19/61 (31%)
Query: 570 LDGYEIRGKKIKV-----------ERAK-FTMKGEAYDPKLKPKKKRKK-------DLEK 610
Y++ + R F + D P+ K+ E
Sbjct: 184 SHAYDLEAMHVGTVAAGRIGLAVLRRLAPFDVHLHYTDRHRLPESVEKELNLTWHATRED 243
Query: 611 L 611
+
Sbjct: 244 M 244
>1k8k_C P40, ARP2/3 complex 41 kDa subunit, P41-ARC; beta-propeller,
structural protein; 2.00A {Bos taurus} SCOP: b.69.4.1
PDB: 1tyq_C* 1u2v_C* 2p9i_C* 2p9k_C* 2p9l_C 2p9n_C*
2p9p_C* 2p9s_C* 2p9u_C* 3rse_C 3dxm_C* 3dxk_C
Length = 372
Score = 29.1 bits (66), Expect = 5.4
Identities = 6/18 (33%), Positives = 8/18 (44%)
Query: 121 STDGTVYIWDKEKNAWFP 138
TD Y+W + W P
Sbjct: 71 GTDRNAYVWTLKGRTWKP 88
>2bib_A CBPE, teichoic acid phosphorylcholine esterase/ choline protein;
choline-binding protein, PCE, phosphorylcholine estera
hydrolase; HET: PC BTB; 1.92A {Streptococcus pneumoniae}
SCOP: b.109.1.1 d.157.1.8 PDB: 1wra_A*
Length = 547
Score = 29.3 bits (65), Expect = 6.1
Identities = 20/138 (14%), Positives = 39/138 (28%), Gaps = 2/138 (1%)
Query: 5 YVHYEGDVAVYTDPQSRQQYTWDNEKNEWKLRQIDYEFDGSNYFYKDKTGTKYKWDTASN 64
Y+ + T+ ++ +D + K WD SN
Sbjct: 126 LYGYDKVLQTATETGVSVIQNITQGDAHFQFGDMDIQLYNYENETDSSGELKKIWDDNSN 185
Query: 65 SWVPSVPLVTSDKAADSSDEEEYDENNAQKTAPPIQRQDMSKGSYGYEGDTHTYTDSTDG 124
S + V V K D + K P I + D+ K ++ ++ + D
Sbjct: 186 SLISVV-KVNGKKIYLGGDLDNVHGAED-KYGPLIGKVDLMKFNHHHDTNKSNTKDFIKN 243
Query: 125 TVYIWDKEKNAWFPKVDD 142
+ + P +
Sbjct: 244 LSPSLIVQTSDSLPWKNG 261
>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM,
protein engineering, structural protein; HET: ADP; 2.80A
{Dictyostelium discoideum} SCOP: k.1.1.1
Length = 1010
Score = 28.9 bits (65), Expect = 7.6
Identities = 22/203 (10%), Positives = 53/203 (26%), Gaps = 5/203 (2%)
Query: 415 RELLNGRWFGQRQITAETWDGKTRYKIQETAEEREARLKKWETFLGKKIKVERAKFTMKG 474
++ + ++ E A +
Sbjct: 812 KKTEKPPKGQEVSELEAIYNSLQTKLRLIKREPFVAPAGLTPNEIDSTWSALEKAEQEHA 871
Query: 475 EAYDPKLKPKKKRKKDLEKLKKAQENTKVYVSNLPLDLTQEEFVEVMQKCGLVMKDVDTN 534
EA +LK +KK L+K + + + + + + L E + + +K+++
Sbjct: 872 EALRIELKRQKKIAVLLQKYNRILKKLENWATTKSVYLGSNETGDSITAVQAKLKNLEAF 931
Query: 535 QMKIKLYTDPYTKDFKGDALCTYIKKESVDLALSILDGYEIRGKKIKVERAKFTMKGEAY 594
+ + D + L+ E + + E Y
Sbjct: 932 DGECQSLEGQSNSDLLSILAQLTELNYNGVPELT-----ERKDTFFAQQWTGVKSSAETY 986
Query: 595 DPKLKPKKKRKKDLEKLKKAQEK 617
L + +R + +E L
Sbjct: 987 KNTLLAELERLQKIEDLHHHHHH 1009
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
0.313 0.132 0.385
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 12,065,682
Number of extensions: 756706
Number of successful extensions: 3672
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3198
Number of HSP's successfully gapped: 720
Length of query: 773
Length of database: 6,701,793
Length adjustment: 101
Effective length of query: 672
Effective length of database: 3,881,772
Effective search space: 2608550784
Effective search space used: 2608550784
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: 61 (28.0 bits)