RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3345
(787 letters)
>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 = 134 bits (338), Expect = 5e-36
Identities = 38/192 (19%), Positives = 77/192 (40%), Gaps = 9/192 (4%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
LY+ N+ F TE+++ F + +T A + + F++F + +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKS------SNVAKQTGSKILVRNIPF 695
QA+ ++++R + + S V + K+ + +P
Sbjct: 66 QAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 696 QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLY 755
+V+EL +FG LK L K +GL +G+ F E++ N +A+ L L
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDS-ATGLSKGYAFCEYVDINVTDQAIAGL-NGMQLG 182
Query: 756 GRRLVLEWAEEA 767
++L+++ A
Sbjct: 183 DKKLLVQRASVG 194
Score = 105 bits (264), Expect = 4e-26
Identities = 40/199 (20%), Positives = 73/199 (36%), Gaps = 17/199 (8%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP-----IDKETDKTKGFALVTFLMP 388
A + R++V N+ + +TE+ + F L + + + ++ K FA + F
Sbjct: 2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61
Query: 389 EHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKR 448
+ TQA DG +F G+ L + + + S + VV + +
Sbjct: 62 DETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENP----SVYVPGVVSTVVPDSAHK 116
Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNS 502
+ + LP +K L FG L + TGL E++ N A
Sbjct: 117 LF-IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 503 LAYTKFKEVPLYLEWAPEG 521
L + + L ++ A G
Sbjct: 176 LNGMQLGDKKLLVQRASVG 194
Score = 96.3 bits (240), Expect = 7e-23
Identities = 33/196 (16%), Positives = 69/196 (35%), Gaps = 28/196 (14%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKP-LPLASVRTTFL------------GMAYIGFKDEKNCN 272
+ V N+P G+ ++ + +F + L + A++ F+
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 273 KALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAED 332
+A+ + ++G+ L I + D M + + V
Sbjct: 66 QAMAFDGIIFQGQSLKIRR-----------PHDYQPLPGMSENPSVY----VPGVVSTVV 110
Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
+ ++F+ L + +D + +L +GPL L D T +KG+A ++
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170
Query: 393 QAYQHLDGTVFLGRML 408
QA L+G + L
Sbjct: 171 QAIAGLNGMQLGDKKL 186
Score = 83.9 bits (208), Expect = 1e-18
Identities = 38/231 (16%), Positives = 74/231 (32%), Gaps = 51/231 (22%)
Query: 444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT-----------GLVEFLQ 492
A ++R+ V N+P+ + F LG + P +EF
Sbjct: 2 AMARRL-YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60
Query: 493 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKEN 552
++ A + F+ L + + +
Sbjct: 61 VDETTQAM-AFDGIIFQGQSLKIRRP---------------------------HDYQPLP 92
Query: 553 TAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 612
E+ VP V V P+ L+I L +D ++ GP+ + +
Sbjct: 93 GMSENPSVYVPGVVSTVV------PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNL 146
Query: 613 ARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSN 663
KD + G S GY F ++ +QA+ L L + ++ ++R++
Sbjct: 147 V--KDSAT-GL--SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 192
Score = 47.3 bits (113), Expect = 4e-06
Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 1/67 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
+ +Q+K G + L + G + +AF Y + A+ N + +
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185
Query: 88 IKVEKCS 94
+ V++ S
Sbjct: 186 LLVQRAS 192
Score = 37.3 bits (87), Expect = 0.007
Identities = 14/105 (13%), Positives = 35/105 (33%), Gaps = 11/105 (10%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE------GKFRRFAFIGYHREDQAQAALDYFNN 80
+ IT+E + F + + + + + FAF+ + D+ A+ F+
Sbjct: 14 FGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDG 72
Query: 81 TYVFSSRIKVEKCSN----LGDTTKPKSWSKYAPDSSAYQKLHNI 121
+K+ + + G + P + + H +
Sbjct: 73 IIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKL 117
Score = 29.6 bits (67), Expect = 3.2
Identities = 14/88 (15%), Positives = 27/88 (30%), Gaps = 8/88 (9%)
Query: 198 KTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVR-- 254
+ + P + V H + + LP + +K PL +
Sbjct: 88 YQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLV 147
Query: 255 ---TTFL--GMAYIGFKDEKNCNKALNK 277
T L G A+ + D ++A+
Sbjct: 148 KDSATGLSKGYAFCEYVDINVTDQAIAG 175
>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 = 129 bits (327), Expect = 9e-36
Identities = 51/95 (53%), Positives = 63/95 (66%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
+ SGR+FVRNLSYT +E+DL KLF YGPL+E+ PID T K KGFA VTF+ PEH
Sbjct: 3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62
Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGK 425
A +AY +DG VF GRMLH++P K+
Sbjct: 63 AVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPS 97
Score = 74.6 bits (184), Expect = 2e-16
Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 2/81 (2%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
++ VRN+ + + + ++E+LF A+G L + P + + +GF FV F+ A +A
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL-TKKPKGFAFVTFMFPEHAVKAY 67
Query: 746 KALCQSTHLYGRRLVLEWAEE 766
+ GR L + +
Sbjct: 68 AEV-DGQVFQGRMLHVLPSTI 87
Score = 61.8 bits (151), Expect = 4e-12
Identities = 15/80 (18%), Positives = 32/80 (40%), Gaps = 5/80 (6%)
Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
L+++NL++ S+E+ + + F GP++ + D + + G+ FV
Sbjct: 2 SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYP--IDSLT-KK--PKGFAFVT 56
Query: 634 FYTRESLNQALKVLQNSSLD 653
F E +A +
Sbjct: 57 FMFPEHAVKAYAEVDGQVFQ 76
Score = 47.2 bits (113), Expect = 6e-07
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
+ V+NL Y + DL+ LF +G L + P +T V F+ A A+ +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Score = 44.9 bits (107), Expect = 4e-06
Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 1/67 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y ++E L+ F G ++++ + K + FAF+ + + A A +
Sbjct: 18 YTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG 77
Query: 86 SRIKVEK 92
+ V
Sbjct: 78 RMLHVLP 84
Score = 29.1 bits (66), Expect = 1.8
Identities = 20/90 (22%), Positives = 38/90 (42%), Gaps = 13/90 (14%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASV-----RTT--FLGMAYIGFKDEKNCNKALNK 277
+ V+NL ++DL+ F PL+ + T G A++ F ++ KA +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 278 -NKSFWKGKQLNI----YKYSKDNSAKYSG 302
+ ++G+ L++ K S SG
Sbjct: 70 VDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99
>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 = 128 bits (324), Expect = 2e-35
Identities = 66/98 (67%), Positives = 73/98 (74%)
Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 733
KQT SKILVRNIPFQA Q E+ ELF FGELK VRLPKKM G+G HRGFGFV
Sbjct: 4 GSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFV 63
Query: 734 EFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVE 771
+FITK +AK+A ALC STHLYGRRLVLEWA+ V+
Sbjct: 64 DFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101
Score = 83.1 bits (206), Expect = 2e-19
Identities = 24/91 (26%), Positives = 39/91 (42%), Gaps = 2/91 (2%)
Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKE-TDKTKGFALVTFLMP 388
+ +I VRN+ + + ++ +LF +G L V LP T +GF V F+
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68
Query: 389 EHATQAYQHL-DGTVFLGRMLHLIPGKPKEN 418
+ A +A+ L T GR L L +
Sbjct: 69 QDAKKAFNALCHSTHLYGRRLVLEWADSEVT 99
Score = 68.9 bits (169), Expect = 2e-14
Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 4/79 (5%)
Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
+ + + + + ++N+ F + + IR F G + +V + +K G G+GFV
Sbjct: 8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMT--GTGA--HRGFGFV 63
Query: 633 QFYTRESLNQALKVLQNSS 651
F T++ +A L +S+
Sbjct: 64 DFITKQDAKKAFNALCHST 82
Score = 50.8 bits (122), Expect = 4e-08
Identities = 33/99 (33%), Positives = 50/99 (50%), Gaps = 8/99 (8%)
Query: 440 QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGL------VEFLQ 492
QV + ++ ILV+N+P++ +++ LF FG+L V +P TG V+F+
Sbjct: 8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67
Query: 493 KNQAKAAFNSLA-YTKFKEVPLYLEWAPEGVFAEAKEKS 530
K AK AFN+L T L LEWA V ++ S
Sbjct: 68 KQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106
Score = 48.1 bits (115), Expect = 4e-07
Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL--KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF 84
++ Q +++ F G + V+L K T G R F F+ + + A+ A + ++
Sbjct: 25 FQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHL 84
Query: 85 SSR-IKVEK 92
R + +E
Sbjct: 85 YGRRLVLEW 93
Score = 34.2 bits (79), Expect = 0.029
Identities = 19/101 (18%), Positives = 43/101 (42%), Gaps = 12/101 (11%)
Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF--------LGMAYIGF 265
S K+ I+V+N+P +++++ F L +VR G ++ F
Sbjct: 6 SGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDF 65
Query: 266 KDEKNCNKALN--KNKSFWKGKQLNIYKYSKDNSAKYSGAA 304
+++ KA N + + G++L + +++ SG +
Sbjct: 66 ITKQDAKKAFNALCHSTHLYGRRLVL-EWADSEVTVQSGPS 105
>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 = 126 bits (320), Expect = 7e-34
Identities = 37/195 (18%), Positives = 82/195 (42%), Gaps = 26/195 (13%)
Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
E E L+I NLN N + ++ + + V + + +G+
Sbjct: 5 VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGT------NRKFGY 58
Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVR 691
V F + E L +AL+ L + ++I+L++ + + + +L +
Sbjct: 59 VDFESAEDLEKALE-LTGLKVFGNEIKLEKP------------KGRDSKKVRAARTLLAK 105
Query: 692 NIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQS 751
N+ F + E++E+F+ E++ V G +G ++EF ++ +A++ ++ Q
Sbjct: 106 NLSFNITEDELKEVFEDALEIRLVS------QDGKSKGIAYIEFKSEADAEKNLEEK-QG 158
Query: 752 THLYGRRLVLEWAEE 766
+ GR + L + E
Sbjct: 159 AEIDGRSVSLYYTGE 173
Score = 95.4 bits (238), Expect = 7e-23
Identities = 33/192 (17%), Positives = 67/192 (34%), Gaps = 30/192 (15%)
Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
+ +F+ NL+ + +L + ++ + +D T + F V F E
Sbjct: 7 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAE 65
Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRI 449
+A + L G G + L K ++++ + R+ R
Sbjct: 66 DLEKALE-LTGLKVFGNEIKLEKPKGRDSK-----------------------KVRAART 101
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQAKAAFNSLAYT 506
+L KNL + +LK +FE ++ LV G + +EF + A+
Sbjct: 102 LLAKNLSFNITEDELKEVFEDALEI--RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGA 159
Query: 507 KFKEVPLYLEWA 518
+ + L +
Sbjct: 160 EIDGRSVSLYYT 171
Score = 85.3 bits (212), Expect = 2e-19
Identities = 36/203 (17%), Positives = 63/203 (31%), Gaps = 45/203 (22%)
Query: 221 KRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRT------TFLGMAYIGFKDEKNCNK 273
+ + NL +LK L + T Y+ F+ ++ K
Sbjct: 10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69
Query: 274 ALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDI 333
AL G ++ + K +S K A
Sbjct: 70 ALELTGLKVFGNEIKLEKPKGRDSKKVRAAR----------------------------- 100
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
+ +NLS+ +TED+L ++FE + + + K+KG A + F A +
Sbjct: 101 ----TLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEK 151
Query: 394 AYQHLDGTVFLGRMLHLIPGKPK 416
+ G GR + L K
Sbjct: 152 NLEEKQGAEIDGRSVSLYYTGEK 174
Score = 77.3 bits (191), Expect = 2e-16
Identities = 36/228 (15%), Positives = 64/228 (28%), Gaps = 69/228 (30%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 496
E+ + + + NL +LK + V TG V+F
Sbjct: 9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDL 67
Query: 497 KAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEE 556
+ A L K + LE
Sbjct: 68 EKALE-LTGLKVFGNEIKLEKP-------------------------------------- 88
Query: 557 DNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 616
+ + ++ TL KNL+FN TED ++ F+ I V+ K
Sbjct: 89 -------------KGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGK- 134
Query: 617 DPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
S G +++F + + L+ Q + +D + L +
Sbjct: 135 ---------SKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173
Score = 47.6 bits (114), Expect = 2e-06
Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 1/66 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ +LK E D+ + G R+F ++ + + + AL+ VF +
Sbjct: 23 PNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGN 81
Query: 87 RIKVEK 92
IK+EK
Sbjct: 82 EIKLEK 87
Score = 45.7 bits (109), Expect = 1e-05
Identities = 14/64 (21%), Positives = 30/64 (46%), Gaps = 4/64 (6%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ IT+++LK FE+ + V + +GK + A+I + E A+ L+ +
Sbjct: 109 FNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGR 164
Query: 87 RIKV 90
+ +
Sbjct: 165 SVSL 168
Score = 35.3 bits (82), Expect = 0.031
Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 4/80 (5%)
Query: 212 PPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTT--FLGMAYIGFKDE 268
P + R T++ KNL + + +LK F+ + V G+AYI FK E
Sbjct: 87 KPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSE 146
Query: 269 KNCNKALNK-NKSFWKGKQL 287
+ K L + + G+ +
Sbjct: 147 ADAEKNLEEKQGAEIDGRSV 166
>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 = 127 bits (322), Expect = 8e-33
Identities = 35/192 (18%), Positives = 82/192 (42%), Gaps = 17/192 (8%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPGQFLSMGYGFVQF 634
+ TL++ N + T+ +IR + +A S+ + + S + ++
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTS------RRFAYIDV 166
Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIP 694
++E ++ L ++ + + K SN K K ++ A G +I++RN+
Sbjct: 167 TSKEDARYCVEKLNGLKIEGYTLVTKVSNPL-------EKSKRTDSATLEGREIMIRNLS 219
Query: 695 FQA-KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTH 753
+ ++ + E F+ FG ++ + +P + F+ F K+ A+RA++ +
Sbjct: 220 TELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQM--NRSL 277
Query: 754 LYGRRLVLEWAE 765
L R + + A+
Sbjct: 278 LGNREISVSLAD 289
Score = 126 bits (318), Expect = 2e-32
Identities = 38/220 (17%), Positives = 81/220 (36%), Gaps = 34/220 (15%)
Query: 547 EEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGP 606
+ +E + + E R E TT+ +KNL + ++ + ++FK CGP
Sbjct: 9 RPDSKRPLDEGSPAAAGLTSKKANEALTRNRE-LTTVLVKNLPKSYNQNKVYKYFKHCGP 67
Query: 607 IASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNL 666
I V VA + + ++F + A+ + + +++I
Sbjct: 68 IIHVDVADSLKK-------NFRFARIEFARYDGALAAITKT-HKVVGQNEII-------- 111
Query: 667 ESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSG 725
V+ T + + N P Q + +L + + +RLP +
Sbjct: 112 -------------VSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNT- 157
Query: 726 LHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE 765
R F +++ +K +A+ ++ L + G LV + +
Sbjct: 158 -SRRFAYIDVTSKEDARYCVEKL-NGLKIEGYTLVTKVSN 195
Score = 120 bits (302), Expect = 3e-30
Identities = 49/369 (13%), Positives = 109/369 (29%), Gaps = 93/369 (25%)
Query: 303 AADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGP 362
A D+ E A + + + + E + V+NL + ++ + K F+ GP
Sbjct: 8 ARPDSKRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGP 67
Query: 363 LAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNV 422
+ V + K FA + F + A A V
Sbjct: 68 IIHVDVA--DSLKKNFRFARIEFARYDGALAAITKTHKVVG---------QNEI------ 110
Query: 423 DGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY 482
+V ++ + + N P +++ L + + + P
Sbjct: 111 ------------------IVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPS 152
Query: 483 GITGL------VEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKE 536
++ K A+ L K + L + + + ++ +
Sbjct: 153 LRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS-----------NPLEKSK 201
Query: 537 KNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNST-ED 595
+ + EG + I+NL+ E+
Sbjct: 202 RTDSATLEG-----------------------------------REIMIRNLSTELLDEN 226
Query: 596 SIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEH 655
+R F+ G I + + + S + F+ F ++S +AL+ + S L
Sbjct: 227 LLRESFEGFGSIEKINIPAGQKEHSF----NNCCAFMVFENKDSAERALQ-MNRSLLGNR 281
Query: 656 QIELKRSNR 664
+I + +++
Sbjct: 282 EISVSLADK 290
Score = 105 bits (263), Expect = 5e-25
Identities = 51/318 (16%), Positives = 96/318 (30%), Gaps = 75/318 (23%)
Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF-----LGMAYIGFKDE 268
++A R+ T++VKNLP + + YFK P+ V A I F
Sbjct: 32 NEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARY 91
Query: 269 KNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQ 328
A+ K ++ + ++
Sbjct: 92 DGALAAITKTHKVVGQNEIIVSHLTECT-------------------------------- 119
Query: 329 FAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMP 388
+++ N + T+ ++ L + +A I + ++ FA +
Sbjct: 120 ----------LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSK 169
Query: 389 EHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKR 448
E A + L+G G L P E D A + E
Sbjct: 170 EDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDS------------ATLEGRE----- 212
Query: 449 IILVKNLPYRTLP-TDLKALFEPFGDLGRVLVPPYGIT-------GLVEFLQKNQAKAAF 500
I+++NL L L+ FE FG + ++ +P + F K+ A+ A
Sbjct: 213 -IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 271
Query: 501 NSLAYTKFKEVPLYLEWA 518
+ + + + A
Sbjct: 272 Q-MNRSLLGNREISVSLA 288
Score = 50.0 bits (120), Expect = 1e-06
Identities = 11/67 (16%), Positives = 26/67 (38%), Gaps = 1/67 (1%)
Query: 27 YKITQEQLKAKFEEKGTVT-DVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
TQ ++ ++ V ++L RRFA+I ++ A+ ++ N +
Sbjct: 127 PSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG 186
Query: 86 SRIKVEK 92
+ +
Sbjct: 187 YTLVTKV 193
Score = 42.7 bits (101), Expect = 3e-04
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 2/69 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
Q ++ F+ G + V + + K RFA I + R D A AA+ + V +
Sbjct: 51 KSYNQNKVYKYFKHCGPIIHVDVA-DSLKKNFRFARIEFARYDGALAAITKTHK-VVGQN 108
Query: 87 RIKVEKCSN 95
I V +
Sbjct: 109 EIIVSHLTE 117
Score = 38.4 bits (90), Expect = 0.006
Identities = 14/68 (20%), Positives = 28/68 (41%), Gaps = 4/68 (5%)
Query: 27 YKITQEQ-LKAKFEEKGTVTDVQL--KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
++ E L+ FE G++ + + AF+ + +D A+ AL N + +
Sbjct: 220 TELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLL 278
Query: 84 FSSRIKVE 91
+ I V
Sbjct: 279 GNREISVS 286
>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 = 124 bits (314), Expect = 8e-32
Identities = 56/348 (16%), Positives = 89/348 (25%), Gaps = 101/348 (29%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
+I +R L VT ++ L Y DK KG A VT L E
Sbjct: 17 RQFRNRRKILIRGLPGDVTNQEVHDLLSDYELK-------YCFVDKYKGTAFVTLLNGEQ 69
Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRII 450
A A + R L V + ++
Sbjct: 70 AEAAINAFHQSRLREREL-------------------------------SVQLQPTDALL 98
Query: 451 LVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSLA 504
V NLP + L PFG L R + TG E+++K+ A A + L
Sbjct: 99 CVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLL 158
Query: 505 YTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPE 564
LY+ W G A S+
Sbjct: 159 GKPLGPRTLYVHWTDAGQLTPALLHSR--------------------------------- 185
Query: 565 VEENVEEDEEREPEPDTTLYIKNLNFNSTE-DSIRRHFKKCGPIASVTVARKKDPKSPGQ 623
L + L + D++ R +A +D +
Sbjct: 186 -----------------CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQ---- 224
Query: 624 FLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEAT 671
G+ +++ T E +A + SL + + +
Sbjct: 225 --LKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSM 270
Score = 120 bits (303), Expect = 2e-30
Identities = 42/212 (19%), Positives = 69/212 (32%), Gaps = 34/212 (16%)
Query: 571 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYG 630
E ER+ + I+ L + T + + V + K G
Sbjct: 13 EHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYK-----------GTA 60
Query: 631 FVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILV 690
FV E A+ S L E ++ ++ T + + V
Sbjct: 61 FVTLLNGEQAEAAINAFHQSRLRERELSVQLQ--------------------PTDALLCV 100
Query: 691 RNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ 750
N+P Q + EEL + FG L+ L +G +G+GF E++ K+ A RA L
Sbjct: 101 ANLPPSLTQQQFEELVRPFGSLERCFLVYSER-TGQSKGYGFAEYMKKDSAARAKSDL-L 158
Query: 751 STHLYGRRLVLEWAEEADNVEDIRKRTNRYFG 782
L R L + W + +
Sbjct: 159 GKPLGPRTLYVHWTDAGQLTPALLHSRCLCVD 190
Score = 118 bits (298), Expect = 9e-30
Identities = 34/196 (17%), Positives = 65/196 (33%), Gaps = 20/196 (10%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
+ D L + NL + T+ + G + + ++ GQ S GYGF ++
Sbjct: 90 QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVY--SERT-GQ--SKGYGFAEY 144
Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIP 694
++S +A L L + + ++ + A S + V +P
Sbjct: 145 MKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPA---LLHSRC--------LCVDRLP 193
Query: 695 FQAKQSE-VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTH 753
+ + A F +L G +GF +E+ T A+ A +
Sbjct: 194 PGFNDVDALCRALSAVHSPTFCQLACGQ--DGQLKGFAVLEYETAEMAEEAQQQA-DGLS 250
Query: 754 LYGRRLVLEWAEEADN 769
L G L + +
Sbjct: 251 LGGSHLRVSFCAPGPP 266
Score = 105 bits (263), Expect = 4e-25
Identities = 41/304 (13%), Positives = 83/304 (27%), Gaps = 77/304 (25%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASVRTTF-LGMAYIGFKDEKNCNKALNK-NKSFWK 283
I+++ LP V +++ L G A++ + + A+N ++S +
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLR 83
Query: 284 GKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRN 343
++L SVQ + V N
Sbjct: 84 EREL--------------------------------------SVQLQP---TDALLCVAN 102
Query: 344 LSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVF 403
L ++T+ +L +G L L + T ++KG+ ++ + A +A L G
Sbjct: 103 LPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL 162
Query: 404 LGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTD 463
R L++ + R + V LP D
Sbjct: 163 GPRTLYVHWTDAGQLTP----------------------ALLHSRCLCVDRLPPGFNDVD 200
Query: 464 -LKALFEPFGDLGRVLVPP--------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY 514
L + + + +E+ A+ A L
Sbjct: 201 ALCRALSAVHSPTFCQLACGQDGQLKGFAV---LEYETAEMAEEAQQQADGLSLGGSHLR 257
Query: 515 LEWA 518
+ +
Sbjct: 258 VSFC 261
Score = 75.8 bits (187), Expect = 4e-15
Identities = 28/207 (13%), Positives = 58/207 (28%), Gaps = 43/207 (20%)
Query: 222 RQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF-------LGMAYIGFKDEKNCNK 273
+ V NLP + ++ + +P L + G + + + + +
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152
Query: 274 ALNK-NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAED 332
A + + L ++ D + + ++
Sbjct: 153 AKSDLLGKPLGPRTLYVHWT-------------DAGQLTPALLHSR-------------- 185
Query: 333 IAESGRIFVRNLSYTVTEDD-LTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
+ V L + D L + L + + KGFA++ + E A
Sbjct: 186 -----CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAVLEYETAEMA 239
Query: 392 TQAYQHLDGTVFLGRMLHLIPGKPKEN 418
+A Q DG G L + P
Sbjct: 240 EEAQQQADGLSLGGSHLRVSFCAPGPP 266
Score = 48.4 bits (116), Expect = 3e-06
Identities = 20/113 (17%), Positives = 41/113 (36%), Gaps = 18/113 (15%)
Query: 409 HLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALF 468
H++ + + + + R++R IL++ LP ++ L
Sbjct: 1 HMLDPEEIRKR----------LEHTE-------RQFRNRRKILIRGLPGDVTNQEVHDLL 43
Query: 469 EPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG 521
+ + G T V L QA+AA N+ ++ +E L ++ P
Sbjct: 44 SDYELKYCFVDKYKG-TAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD 95
Score = 48.4 bits (116), Expect = 4e-06
Identities = 12/60 (20%), Positives = 24/60 (40%)
Query: 31 QEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV 90
+ L + T QL +G+ + FA + Y + A+ A + + S ++V
Sbjct: 199 VDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258
Score = 48.1 bits (115), Expect = 5e-06
Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 1/66 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+TQ+Q + G++ L Y+ G+ + + F Y ++D A A +
Sbjct: 105 PSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP 164
Query: 86 SRIKVE 91
+ V
Sbjct: 165 RTLYVH 170
Score = 40.7 bits (96), Expect = 0.001
Identities = 13/66 (19%), Positives = 30/66 (45%), Gaps = 6/66 (9%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+T +++ + LKY K++ AF+ +QA+AA++ F+ + +
Sbjct: 32 GDVTNQEVHDLLSDYE------LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRER 85
Query: 87 RIKVEK 92
+ V+
Sbjct: 86 ELSVQL 91
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 121 bits (305), Expect = 2e-31
Identities = 39/192 (20%), Positives = 90/192 (46%), Gaps = 10/192 (5%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
+ +Y+ ++ + ED+IR+ F GPI S+ ++ D + G+ FV++
Sbjct: 23 GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSW--DSVTMK---HKGFAFVEY 77
Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIP 694
E+ AL+ + + L I++ R + +++ + + ++I V ++
Sbjct: 78 EVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEA---RAFNRIYVASVH 134
Query: 695 FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL 754
+++ +F+AFG++K L + +G H+G+GF+E+ ++ A+ ++ L
Sbjct: 135 QDLSDDDIKSVFEAFGKIKSATLARDP-TTGKHKGYGFIEYEKAQSSQDAVSSM-NLFDL 192
Query: 755 YGRRLVLEWAEE 766
G+ L + A
Sbjct: 193 GGQYLRVGKAVT 204
Score = 97.4 bits (243), Expect = 4e-23
Identities = 43/215 (20%), Positives = 86/215 (40%), Gaps = 20/215 (9%)
Query: 310 ASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP 369
+ M ++ + + Q +A R++V ++ Y + ED + + F +GP+ + +
Sbjct: 2 SHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMS 61
Query: 370 IDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCC 429
D T K KGFA V + +PE A A + ++ + GR + +
Sbjct: 62 WDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI------------- 108
Query: 430 ISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL-- 487
+ + EAR+ I V ++ D+K++FE FG + + TG
Sbjct: 109 -GQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHK 167
Query: 488 ----VEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 518
+E+ + ++ A +S+ L + A
Sbjct: 168 GYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
Score = 90.8 bits (226), Expect = 6e-21
Identities = 36/221 (16%), Positives = 76/221 (34%), Gaps = 37/221 (16%)
Query: 205 APSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVR-------TT 256
+ + R Y V ++ + + ++ F P P+ S+
Sbjct: 13 MGRGSAAQRQGALAIMSRVY----VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMK 68
Query: 257 FLGMAYIGFKDEKNCNKALNK-NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENI 315
G A++ ++ + AL + N G+ + + + S A
Sbjct: 69 HKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQA----------------- 111
Query: 316 KAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETD 375
Q Q AE+ RI+V ++ +++DD+ +FE +G + L D T
Sbjct: 112 -------QPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTG 164
Query: 376 KTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPK 416
K KG+ + + + + A ++ G+ L +
Sbjct: 165 KHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205
Score = 81.6 bits (202), Expect = 1e-17
Identities = 34/219 (15%), Positives = 74/219 (33%), Gaps = 53/219 (24%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSLAY 505
V ++ Y ++ F PFG + + + +T VE+ A+ A +
Sbjct: 33 VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS 92
Query: 506 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEV 565
+ + S + + ++ E
Sbjct: 93 VMLGGRNIKVGRP-----------SNIGQAQPIIDQLAE--------------------- 120
Query: 566 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
E +Y+ +++ + ++D I+ F+ G I S T+AR DP + G+
Sbjct: 121 ----------EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLAR--DPTT-GK-- 165
Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
GYGF+++ +S A+ + L + + ++
Sbjct: 166 HKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVT 204
Score = 47.3 bits (113), Expect = 5e-06
Identities = 14/63 (22%), Positives = 28/63 (44%), Gaps = 1/63 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
++ + +K+ FE G + L GK + + FI Y + +Q A+ N +
Sbjct: 137 LSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQY 196
Query: 88 IKV 90
++V
Sbjct: 197 LRV 199
Score = 43.1 bits (102), Expect = 1e-04
Identities = 21/93 (22%), Positives = 46/93 (49%), Gaps = 3/93 (3%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKY-TTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y++ ++ ++ F G + + + + + K + FAF+ Y + AQ AL+ N+ +
Sbjct: 38 YELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGG 97
Query: 86 SRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKL 118
IKV + SN+G + A ++ A+ ++
Sbjct: 98 RNIKVGRPSNIGQ--AQPIIDQLAEEARAFNRI 128
>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 = 117 bits (294), Expect = 2e-31
Identities = 50/109 (45%), Positives = 66/109 (60%)
Query: 439 NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKA 498
+ RSK +IL KNLP TL +++ F FG LGRVL+P GIT +VEFL+ +A+
Sbjct: 2 SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARK 61
Query: 499 AFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEE 547
AF LAY+KF VPLYLEWAP GVF A +K + ++ E+
Sbjct: 62 AFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGPSS 110
Score = 76.8 bits (189), Expect = 4e-17
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
I +NL ++ + F ++G L V+LP + A+V FL P A +A++HL
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHL 66
Query: 399 DGTVFLGRMLHL 410
+ F L+L
Sbjct: 67 AYSKFHHVPLYL 78
Score = 72.9 bits (179), Expect = 9e-16
Identities = 28/103 (27%), Positives = 48/103 (46%), Gaps = 8/103 (7%)
Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
SS + ++ + IL +N+P +E++E F FG L V LP+ VEF+
Sbjct: 2 SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-------GITAIVEFL 54
Query: 737 TKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
EA++A + L + + L LEWA +K+ ++
Sbjct: 55 EPLEARKAFRHL-AYSKFHHVPLYLEWAPIGVFGAAPQKKDSQ 96
Score = 58.3 bits (141), Expect = 1e-10
Identities = 16/104 (15%), Positives = 30/104 (28%), Gaps = 11/104 (10%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
T + KNL + I+ F + G + V + V+F
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG-----------ITAIVEFLEPLE 58
Query: 640 LNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQ 683
+A + L S + L+ + + A K +
Sbjct: 59 ARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAE 102
Score = 41.7 bits (98), Expect = 9e-05
Identities = 8/66 (12%), Positives = 22/66 (33%), Gaps = 5/66 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+++ F G++ V L + A + + +A+ A + +
Sbjct: 20 AGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPLEARKAFRHLAYSKFHHV 74
Query: 87 RIKVEK 92
+ +E
Sbjct: 75 PLYLEW 80
Score = 39.0 bits (91), Expect = 6e-04
Identities = 15/62 (24%), Positives = 21/62 (33%), Gaps = 2/62 (3%)
Query: 218 PVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTT-FLGMAYIGFKDEKNCNKAL 275
R I+ KNLPAG +++ F L V A + F + KA
Sbjct: 4 GSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAF 63
Query: 276 NK 277
Sbjct: 64 RH 65
>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 = 117 bits (296), Expect = 1e-30
Identities = 38/183 (20%), Positives = 76/183 (41%), Gaps = 17/183 (9%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
LY+ N+ F TE+++ F + +T A + + F++F + +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE 701
QA+ D + ++L+ ++R K+ + +P +
Sbjct: 66 QAMA------FDGIIFQ----GQSLK-----IRRPHDYQPLPGAHKLFIGGLPNYLNDDQ 110
Query: 702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
V+EL +FG LK L K +GL +G+ F E++ N +A+ L L ++L++
Sbjct: 111 VKELLTSFGPLKAFNLVKDS-ATGLSKGYAFCEYVDINVTDQAIAGL-NGMQLGDKKLLV 168
Query: 762 EWA 764
+ A
Sbjct: 169 QRA 171
Score = 85.0 bits (211), Expect = 2e-19
Identities = 37/197 (18%), Positives = 68/197 (34%), Gaps = 37/197 (18%)
Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP-----IDKETDKTKGFALVTFLM 387
+ + R++V N+ + +TE+ + F L + + + ++ K FA + F
Sbjct: 1 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60
Query: 388 PEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSK 447
+ TQA DG +F G+ L +P + + G
Sbjct: 61 VDETTQAMA-FDGIIFQGQ--SLKIRRPH-DYQPLPGAHK-------------------- 96
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFN 501
+ + LP +K L FG L + TGL E++ N A
Sbjct: 97 --LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154
Query: 502 SLAYTKFKEVPLYLEWA 518
L + + L ++ A
Sbjct: 155 GLNGMQLGDKKLLVQRA 171
Score = 80.7 bits (200), Expect = 7e-18
Identities = 31/196 (15%), Positives = 67/196 (34%), Gaps = 48/196 (24%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKP-LPLASVRTTF------------LGMAYIGFKDEKNCN 272
+ V N+P G+ ++ + +F + L + A++ F+
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 273 KALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAED 332
+A+ + ++G+ L I + D +
Sbjct: 66 QAMAFDGIIFQGQSLKI-RRPHDY----------------------------------QP 90
Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
+ + ++F+ L + +D + +L +GPL L D T +KG+A ++
Sbjct: 91 LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 150
Query: 393 QAYQHLDGTVFLGRML 408
QA L+G + L
Sbjct: 151 QAIAGLNGMQLGDKKL 166
Score = 64.2 bits (157), Expect = 4e-12
Identities = 17/89 (19%), Positives = 38/89 (42%), Gaps = 5/89 (5%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
+ L+I L +D ++ GP+ + + + D + G S GY F ++
Sbjct: 89 QPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK--DSAT-GL--SKGYAFCEY 143
Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSN 663
+QA+ L L + ++ ++R++
Sbjct: 144 VDINVTDQAIAGLNGMQLGDKKLLVQRAS 172
Score = 42.2 bits (100), Expect = 2e-04
Identities = 11/65 (16%), Positives = 25/65 (38%), Gaps = 1/65 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
+ +Q+K G + L + G + +AF Y + A+ N + +
Sbjct: 106 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 165
Query: 88 IKVEK 92
+ V++
Sbjct: 166 LLVQR 170
Score = 38.0 bits (89), Expect = 0.004
Identities = 11/83 (13%), Positives = 28/83 (33%), Gaps = 7/83 (8%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYT------TEGKFRRFAFIGYHREDQAQAALDYFNN 80
+ IT+E + F + + + + + FAF+ + D+ A+ F+
Sbjct: 14 FGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDG 72
Query: 81 TYVFSSRIKVEKCSNLGDTTKPK 103
+K+ + +
Sbjct: 73 IIFQGQSLKIRRPHDYQPLPGAH 95
>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 = 116 bits (294), Expect = 2e-30
Identities = 41/187 (21%), Positives = 81/187 (43%), Gaps = 17/187 (9%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
+++ + +E +R F++ G + + V R D S G FV FYTR++
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLR--DRSQ-NPPQSKGCCFVTFYTRKAA 60
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
+A L N + + S K+ + I + ++
Sbjct: 61 LEAQNALHNMKVLPGMHHPIQMK----------PADSEKNNAVEDRKLFIGMISKKCTEN 110
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG--RR 758
++ +F +FG+++ R+ + GL RG FV F T+ A+ A+KA+ Q+ + G
Sbjct: 111 DIRVMFSSFGQIEECRILRGP--DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSP 168
Query: 759 LVLEWAE 765
+V+++A+
Sbjct: 169 MVVKFAD 175
Score = 91.9 bits (229), Expect = 1e-21
Identities = 48/194 (24%), Positives = 87/194 (44%), Gaps = 31/194 (15%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKET--DKTKGFALVTFLMPEHAT 392
++ ++FV + T +E DL +LFE+YG + E+ + D+ ++KG VTF + A
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILV 452
+A L L M H I KP ++E N + +RKL F +
Sbjct: 62 EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVE------DRKL--F-------------I 100
Query: 453 KNLPYRTLPTDLKALFEPFGDL--GRVLVPPYGIT---GLVEFLQKNQAKAAFNSLAYTK 507
+ + D++ +F FG + R+L P G++ V F + A+ A ++ +
Sbjct: 101 GMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQ 160
Query: 508 FKEV---PLYLEWA 518
E P+ +++A
Sbjct: 161 TMEGCSSPMVVKFA 174
Score = 68.4 bits (168), Expect = 2e-13
Identities = 29/192 (15%), Positives = 57/192 (29%), Gaps = 47/192 (24%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVR---------TTFLGMAYIGFKDEKNCNKA- 274
+ V +P +KDL+ F+ + + G ++ F K +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 275 --LNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAED 332
L+ K K + +
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEK---------------------------------NN 91
Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
E ++F+ +S TE+D+ +F +G + E + ++G A VTF A
Sbjct: 92 AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQ 150
Query: 393 QAYQHLDGTVFL 404
A + + +
Sbjct: 151 TAIKAMHQAQTM 162
Score = 65.3 bits (160), Expect = 2e-12
Identities = 41/211 (19%), Positives = 61/211 (28%), Gaps = 63/211 (29%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL--------VEFLQKNQAKAAFNSL 503
V +P DL+ LFE +G + + V V F + A A N+L
Sbjct: 8 VGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNAL 67
Query: 504 AYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVP 563
K + + + E E++K
Sbjct: 68 HNMKVLP-----------------GMHHPIQMKPADSEKNNAVEDRK------------- 97
Query: 564 EVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQ 623
L+I ++ TE+ IR F G I + R D G
Sbjct: 98 -------------------LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD----GL 134
Query: 624 FLSMGYGFVQFYTRESLNQALKVLQNSSLDE 654
S G FV F TR A+K + + E
Sbjct: 135 --SRGCAFVTFTTRAMAQTAIKAMHQAQTME 163
Score = 58.8 bits (143), Expect = 3e-10
Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 1/97 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGSGLHRGFGFVEFITKNEAKRAM 745
K+ V +P + ++ ELF+ +G + + + + + +G FV F T+ A A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 746 KALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFG 782
AL L G ++ + + + G
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIG 101
Score = 48.4 bits (116), Expect = 1e-06
Identities = 11/57 (19%), Positives = 23/57 (40%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF 84
K T+ ++ F G + + ++ +G R AF+ + AQ A+ +
Sbjct: 106 KCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTM 162
Score = 48.0 bits (115), Expect = 1e-06
Identities = 10/65 (15%), Positives = 26/65 (40%), Gaps = 3/65 (4%)
Query: 29 ITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+++ L+ FE+ G V ++ + + + + F+ ++ A A + +N V
Sbjct: 15 WSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLP 74
Query: 86 SRIKV 90
Sbjct: 75 GMHHP 79
>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 = 112 bits (281), Expect = 1e-27
Identities = 39/213 (18%), Positives = 77/213 (36%), Gaps = 35/213 (16%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
+ E+ L++ NL + TE+ +R F++ G + V + R + G+
Sbjct: 12 LKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR-----------GF 60
Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKIL 689
GF++ +R A L + L + ++ + G+ +
Sbjct: 61 GFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH--------------------GAALT 100
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV-GSGLHRGFGFVEFITKNEAKRAMKAL 748
V+N+ +E+ F FG ++ + +V G G GFVEF K A++A++
Sbjct: 101 VKNLSPVVSNELLEQAFSQFGPVEKAVV---VVDDRGRATGKGFVEFAAKPPARKALERC 157
Query: 749 CQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYF 781
L E + +D +
Sbjct: 158 GDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLM 190
Score = 77.0 bits (190), Expect = 9e-16
Identities = 45/178 (25%), Positives = 64/178 (35%), Gaps = 42/178 (23%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
+ + R+FV NL +TE+D +LFE+YG +EV + D+ GF +
Sbjct: 17 KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTL 70
Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRII 450
A A LDGT+ R L ++ A +
Sbjct: 71 AEIAKAELDGTILKSRPL-------------------------------RIRFATHGAAL 99
Query: 451 LVKNLPYRTLPTDLKALFEPFGDL--GRVLVPPYGIT---GLVEFLQKNQAKAAFNSL 503
VKNL L+ F FG + V+V G G VEF K A+ A
Sbjct: 100 TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERC 157
Score = 65.9 bits (161), Expect = 5e-12
Identities = 38/208 (18%), Positives = 71/208 (34%), Gaps = 46/208 (22%)
Query: 221 KRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF-LGMAYIGFKDEKNCNKALNK- 277
Q + V NLP + ++D K F+ + V G +I + A +
Sbjct: 19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAEL 78
Query: 278 NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESG 337
+ + K + L ++FA
Sbjct: 79 DGTILKSRPLR--------------------------------------IRFAT---HGA 97
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+ V+NLS V+ + L + F ++GP+ + ++ +D + + G V F A +A +
Sbjct: 98 ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALER 156
Query: 398 L-DGTVFLGRMLHLIPGKPKENEGNVDG 424
DG L + +P E + DG
Sbjct: 157 CGDGAFLLTTTPRPVIVEPMEQFDDEDG 184
Score = 43.1 bits (102), Expect = 2e-04
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 5/66 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
IT+E K FE G ++V + + R F FI A+ A + T + S
Sbjct: 32 TDITEEDFKRLFERYGEPSEVFI-----NRDRGFGFIRLESRTLAEIAKAELDGTILKSR 86
Query: 87 RIKVEK 92
+++
Sbjct: 87 PLRIRF 92
Score = 42.4 bits (100), Expect = 3e-04
Identities = 21/73 (28%), Positives = 30/73 (41%), Gaps = 6/73 (8%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKF 508
V NLP D K LFE +G+ V + + G + + A+ A L T
Sbjct: 27 VGNLPTDITEEDFKRLFERYGEPSEVFINRDRGF---GFIRLESRTLAEIAKAELDGTIL 83
Query: 509 KEVPLYLEWAPEG 521
K PL + +A G
Sbjct: 84 KSRPLRIRFATHG 96
Score = 42.0 bits (99), Expect = 4e-04
Identities = 10/59 (16%), Positives = 23/59 (38%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
++ E L+ F + G V + G+ F+ + + A+ AL+ + +
Sbjct: 108 VSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTT 166
>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 = 107 bits (269), Expect = 4e-27
Identities = 44/185 (23%), Positives = 86/185 (46%), Gaps = 20/185 (10%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
LY+ NL+ TED ++++F+ GPIA++ + K+ K ++ Y FV+++ N
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNK------NVNYAFVEYHQSHDAN 55
Query: 642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE 701
AL+ L ++ + +++ + + S + + V ++
Sbjct: 56 IALQTLNGKQIENNIVKINWAFQ------------SQQSSSDDTFNLFVGDLNVNVDDET 103
Query: 702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
+ FK F + M +G RG+GFV F ++++A+ AM ++ Q L GR L +
Sbjct: 104 LRNAFKDFPSYLSGHVMWDMQ-TGSSRGYGFVSFTSQDDAQNAMDSM-QGQDLNGRPLRI 161
Query: 762 EWAEE 766
WA +
Sbjct: 162 NWAAK 166
Score = 75.6 bits (187), Expect = 4e-16
Identities = 31/189 (16%), Positives = 64/189 (33%), Gaps = 41/189 (21%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVR------TTFLGMAYIGFKDEKNCNKALNK- 277
+ V NL + + LK YF+ P+A+++ + A++ + + N AL
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 278 NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESG 337
N + + I + + +
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDD---------------------------------TF 88
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+FV +L+ V ++ L F+ + + D +T ++G+ V+F + A A
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 398 LDGTVFLGR 406
+ G GR
Sbjct: 149 MQGQDLNGR 157
Score = 74.5 bits (184), Expect = 1e-15
Identities = 38/225 (16%), Positives = 74/225 (32%), Gaps = 67/225 (29%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--------PYGITGLVEFLQKNQAKAA 499
R++ V NL LK F+ G + + + Y VE+ Q + A A
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYA---FVEYHQSHDANIA 57
Query: 500 FNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQ 559
+L + + + + WA
Sbjct: 58 LQTLNGKQIENNIVKINWA----------------------------------------- 76
Query: 560 QGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 619
+ ++ + L++ +LN N ++++R FK S V D +
Sbjct: 77 ----------FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW--DMQ 124
Query: 620 SPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
+ G S GYGFV F +++ A+ +Q L+ + + + +
Sbjct: 125 T-GS--SRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 71.0 bits (175), Expect = 1e-14
Identities = 41/191 (21%), Positives = 68/191 (35%), Gaps = 40/191 (20%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NL +TED L + F+ GP+A + + IDK +K +A V + A A Q L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 399 DGTVFLGRMLHL-----IPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVK 453
+G ++ + ++ N+ F V
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNL---------------F-------------VG 93
Query: 454 NLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSLAYTK 507
+L L+ F+ F V TG V F ++ A+ A +S+
Sbjct: 94 DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD 153
Query: 508 FKEVPLYLEWA 518
PL + WA
Sbjct: 154 LNGRPLRINWA 164
Score = 47.5 bits (114), Expect = 2e-06
Identities = 16/68 (23%), Positives = 32/68 (47%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
IT++ LK F+ G + ++++ K +AF+ YH+ A AL N + ++
Sbjct: 10 KAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENN 69
Query: 87 RIKVEKCS 94
+K+
Sbjct: 70 IVKINWAF 77
Score = 35.6 bits (83), Expect = 0.021
Identities = 11/63 (17%), Positives = 28/63 (44%), Gaps = 1/63 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
+ E L+ F++ + + + + G R + F+ + +D AQ A+D +
Sbjct: 99 VDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP 158
Query: 88 IKV 90
+++
Sbjct: 159 LRI 161
>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 = 107 bits (270), Expect = 6e-27
Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 19/189 (10%)
Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
+ +EPE L+I L+F +T++S+R HF++ G + V +DP + + S G+GF
Sbjct: 5 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV--MRDPNT-KR--SRGFGF 59
Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVR 691
V + T E ++ A+ + +D +E KR A + + A T KI V
Sbjct: 60 VTYATVEEVDAAMNA-RPHKVDGRVVEPKR--------AVSREDSQRPGAHLTVKKIFVG 110
Query: 692 NIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQS 751
I ++ + + F+ +G+++ + + GSG RGF FV F + K + Q
Sbjct: 111 GIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFDDHDSVD---KIVIQK 166
Query: 752 TH-LYGRRL 759
H + G
Sbjct: 167 YHTVNGHNC 175
Score = 76.6 bits (189), Expect = 4e-16
Identities = 30/151 (19%), Positives = 59/151 (39%), Gaps = 22/151 (14%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
++ + ++F+ LS+ T++ L FE++G L + ++ D T +++GF VT+ E
Sbjct: 8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGK-VHCCISERKLDAFNQVVEARSKRI 449
A VDG+ V + + D+ K+
Sbjct: 68 VDAAM--------------------NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK- 106
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP 480
I V + T L+ FE +G + + +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 137
Score = 72.3 bits (178), Expect = 1e-14
Identities = 37/212 (17%), Positives = 68/212 (32%), Gaps = 38/212 (17%)
Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASV-----RTTFL--GMAYIGFK 266
S++P Q + + L + L+++F+ L T G ++ +
Sbjct: 4 SESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 267 DEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDS 326
+ + A+N G+ + K S+EDS
Sbjct: 64 TVEEVDAAMNARPHKVDGRVVEP----------------------------KRAVSREDS 95
Query: 327 VQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFL 386
Q +IFV + E L FE+YG + + + D+ + K +GFA VTF
Sbjct: 96 -QRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154
Query: 387 MPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
+ + G + K+
Sbjct: 155 DHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQE 185
Score = 51.5 bits (124), Expect = 1e-07
Identities = 12/93 (12%), Positives = 40/93 (43%), Gaps = 6/93 (6%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
+ +++ + ++ E +R +F++ G I + + + G+
Sbjct: 94 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKR-----GF 148
Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKRS 662
FV F +S+++ + + +++ H E++++
Sbjct: 149 AFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA 180
Score = 50.4 bits (121), Expect = 3e-07
Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 2/74 (2%)
Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 733
K +S +Q K+ + + F+ + F+ +G L + + + RGFGFV
Sbjct: 3 KSESPKEPEQLR-KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-TKRSRGFGFV 60
Query: 734 EFITKNEAKRAMKA 747
+ T E AM A
Sbjct: 61 TYATVEEVDAAMNA 74
Score = 40.7 bits (96), Expect = 6e-04
Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAAL 75
+ L+ FE+ G + +++ GK R FAF+ + D +
Sbjct: 116 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 37.7 bits (88), Expect = 0.006
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALD 76
++ T E L++ FE+ GT+TD + + R F F+ Y ++ AA++
Sbjct: 23 FETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Score = 33.8 bits (78), Expect = 0.11
Identities = 21/112 (18%), Positives = 37/112 (33%), Gaps = 14/112 (12%)
Query: 202 KDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFK--------PLPLASV 253
K + S P + V K I V + ++ L+ YF+ +
Sbjct: 87 KRAVSREDSQRPGAHLTVKK-----IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRG 141
Query: 254 RTTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYK-YSKDNSAKYSGAA 304
G A++ F D + +K + + G + K SK A S +
Sbjct: 142 SGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQ 193
>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 = 106 bits (268), Expect = 6e-27
Identities = 36/169 (21%), Positives = 71/169 (42%), Gaps = 20/169 (11%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
+T L + L + T+ + F+ GPI + + R S GY FV F +
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGY-----SYGYAFVDFTSEMD 57
Query: 640 LNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQ 699
+A+KVL ++ ++++ + ES + + V N+P
Sbjct: 58 SQRAIKVLNGITVRNKRLKVSYARPGGESI--------------KDTNLYVTNLPRTITD 103
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+++ +F +G + + + + +G RG FV + + EA+ A+ AL
Sbjct: 104 DQLDTIFGKYGSIVQKNILRDKL-TGRPRGVAFVRYNKREEAQEAISAL 151
Score = 89.6 bits (223), Expect = 6e-21
Identities = 37/193 (19%), Positives = 69/193 (35%), Gaps = 33/193 (17%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
A + + V L +T+ +L LF GP+ + D +T + G+A V F + +
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVK 453
A + L+G + L + +P + N + V
Sbjct: 61 AIKVLNGITVRNKRLKVSYARP---------------GGESIKDTN----------LYVT 95
Query: 454 NLPYRTLPTDLKALFEPFGDL--GRVLV-PPYGIT---GLVEFLQKNQAKAAFNSL--AY 505
NLP L +F +G + +L G V + ++ +A+ A ++L
Sbjct: 96 NLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
Query: 506 TKFKEVPLYLEWA 518
+ PL + A
Sbjct: 156 PEGGSQPLSVRLA 168
Score = 74.1 bits (183), Expect = 1e-15
Identities = 41/187 (21%), Positives = 74/187 (39%), Gaps = 44/187 (23%)
Query: 229 VKNLPAGVKKKDLKAYFKPL-PLASV-----RTTF--LGMAYIGFKDEKNCNKALNK-NK 279
V LP + ++L A F+ + P+ + T G A++ F E + +A+ N
Sbjct: 8 VNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNG 67
Query: 280 SFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRI 339
+ K+L + + A+ G + + N +
Sbjct: 68 ITVRNKRLKV------SYARPGGESIKDTN-----------------------------L 92
Query: 340 FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLD 399
+V NL T+T+D L +F KYG + + + DK T + +G A V + E A +A L+
Sbjct: 93 YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Query: 400 GTVFLGR 406
+ G
Sbjct: 153 NVIPEGG 159
Score = 73.4 bits (181), Expect = 3e-15
Identities = 43/214 (20%), Positives = 66/214 (30%), Gaps = 64/214 (29%)
Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAA 499
S ++V LP +L ALF G + + TG V+F + ++ A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 500 FNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQ 559
L + L + +A G E K
Sbjct: 62 IKVLNGITVRNKRLKVSYA-----------RPGGESIK---------------------- 88
Query: 560 QGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 619
DT LY+ NL T+D + F K G I + R D
Sbjct: 89 --------------------DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR--DKL 126
Query: 620 SPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLD 653
+ G+ G FV++ RE +A+ L N +
Sbjct: 127 T-GR--PRGVAFVRYNKREEAQEAISALNNVIPE 157
Score = 46.0 bits (110), Expect = 6e-06
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+T +L A F G + ++ T G +AF+ + E +Q A+ N V
Sbjct: 13 QDMTDRELYALFRAIGPINTCRIMRDYKT--GYSYGYAFVDFTSEMDSQRAIKVLNGITV 70
Query: 84 FSSRIKV 90
+ R+KV
Sbjct: 71 RNKRLKV 77
Score = 41.4 bits (98), Expect = 3e-04
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYV 83
IT +QL F + G++ + G+ R AF+ Y++ ++AQ A+ NN
Sbjct: 101 ITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIP 156
>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 = 104 bits (262), Expect = 4e-26
Identities = 42/168 (25%), Positives = 69/168 (41%), Gaps = 20/168 (11%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L N T++ R F G I S + R K S+GYGFV + +
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQ-----SLGYGFVNYIDPKDA 57
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
+A+ L L I++ + + + + V +P Q
Sbjct: 58 EKAINTLNGLRLQTKTIKVSYARPSSA--------------SIRDANLYVSGLPKTMTQK 103
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
E+E+LF +G + R+ +G+ RG GF+ F + EA+ A+K L
Sbjct: 104 ELEQLFSQYGRIITSRILVDQ-VTGVSRGVGFIRFDKRIEAEEAIKGL 150
Score = 87.2 bits (217), Expect = 4e-20
Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 33/188 (17%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ V L +T+++ LF G + L DK T ++ G+ V ++ P+ A +A L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 399 DGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYR 458
+G + + + +P S + N + V LP
Sbjct: 65 NGLRLQTKTIKVSYARP---------------SSASIRDAN----------LYVSGLPKT 99
Query: 459 TLPTDLKALFEPFGDL--GRVLV-PPYGIT---GLVEFLQKNQAKAAFNSL--AYTKFKE 510
+L+ LF +G + R+LV G++ G + F ++ +A+ A L
Sbjct: 100 MTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGAT 159
Query: 511 VPLYLEWA 518
P+ +++A
Sbjct: 160 EPITVKFA 167
Score = 69.9 bits (172), Expect = 4e-14
Identities = 37/187 (19%), Positives = 75/187 (40%), Gaps = 44/187 (23%)
Query: 229 VKNLPAGVKKKDLKAYFKPL-PLASVR-----TTF--LGMAYIGFKDEKNCNKALNK-NK 279
V LP + +++ ++ F + + S + T LG ++ + D K+ KA+N N
Sbjct: 7 VNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG 66
Query: 280 SFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRI 339
+ K + + + A+ S A+ + N +
Sbjct: 67 LRLQTKTIKV------SYARPSSASIRDAN-----------------------------L 91
Query: 340 FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLD 399
+V L T+T+ +L +LF +YG + + +D+ T ++G + F A +A + L+
Sbjct: 92 YVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 151
Query: 400 GTVFLGR 406
G G
Sbjct: 152 GQKPSGA 158
Score = 68.4 bits (168), Expect = 2e-13
Identities = 37/214 (17%), Positives = 68/214 (31%), Gaps = 64/214 (29%)
Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAA 499
SK ++V LP + ++LF G++ + ITG V ++ A+ A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 500 FNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQ 559
N+L + + + + +A S ++ N
Sbjct: 61 INTLNGLRLQTKTIKVSYA---------RPSSASIRDAN--------------------- 90
Query: 560 QGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 619
LY+ L T+ + + F + G I + + D
Sbjct: 91 -----------------------LYVSGLPKTMTQKELEQLFSQYGRIITSRILV--DQV 125
Query: 620 SPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLD 653
+ G S G GF++F R +A+K L
Sbjct: 126 T-GV--SRGVGFIRFDKRIEAEEAIKGLNGQKPS 156
Score = 44.9 bits (107), Expect = 2e-05
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 5/67 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+TQE+ ++ F G + +L K T G+ + F+ Y A+ A++ N +
Sbjct: 12 QNMTQEEFRSLFGSIGEIESCKLVRDKIT--GQSLGYGFVNYIDPKDAEKAINTLNGLRL 69
Query: 84 FSSRIKV 90
+ IKV
Sbjct: 70 QTKTIKV 76
Score = 36.8 bits (86), Expect = 0.011
Identities = 12/56 (21%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+TQ++L+ F + G + ++ G R FI + + +A+ A+ N
Sbjct: 100 MTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKP 155
>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 = 105 bits (265), Expect = 4e-26
Identities = 40/189 (21%), Positives = 76/189 (40%), Gaps = 21/189 (11%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
P +LY+ +L+ + TE + F GPI S+ V R + S+GY +V F
Sbjct: 11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRR-----SLGYAYVNFQ 65
Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPF 695
+AL + + + + S R ++ K I ++N+
Sbjct: 66 QPADAERALDTMNFDVIKGKPVRIMWSQR------------DPSLRKSGVGNIFIKNLDK 113
Query: 696 QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLY 755
+ + F AFG + ++ + +G+GFV F T+ A+RA++ + L
Sbjct: 114 SIDNKALYDTFSAFGNILSCKV---VCDENGSKGYGFVHFETQEAAERAIEKM-NGMLLN 169
Query: 756 GRRLVLEWA 764
R++ +
Sbjct: 170 DRKVFVGRF 178
Score = 74.6 bits (184), Expect = 3e-15
Identities = 46/240 (19%), Positives = 79/240 (32%), Gaps = 49/240 (20%)
Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
+ ++V +L VTE L + F GP+ + + D T ++ G+A V F P
Sbjct: 9 SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 68
Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRI 449
A +A ++ V G+ + + S RK N
Sbjct: 69 DAERALDTMNFDVIKGKPVRI-------------MWSQRDPSLRKSGVGN---------- 105
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDL--GRVLVPP-----YGITGLVEFLQKNQAKAAFNS 502
I +KNL L F FG++ +V+ YG V F + A+ A
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGF---VHFETQEAAERAIEK 162
Query: 503 LAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGV 562
+ + +++ K + E E E G K+ + + G
Sbjct: 163 MNGMLLNDRKVFVGRF----------------KSRKEREAELGARAKEFYPYDVPDYAGS 206
Score = 71.2 bits (175), Expect = 4e-14
Identities = 45/251 (17%), Positives = 77/251 (30%), Gaps = 64/251 (25%)
Query: 439 NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQ 492
N + + V +L L F P G + + V IT V F Q
Sbjct: 7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 493 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKEN 552
A+ A +++ + K P+ + W+ ++ K
Sbjct: 67 PADAERALDTMNFDVIKGKPVRIMWS---------QRDPSLRKSG--------------- 102
Query: 553 TAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 612
++IKNL+ + ++ F G I S V
Sbjct: 103 ---------------------------VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKV 135
Query: 613 ARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATT 672
D S GYGFV F T+E+ +A++ + L++ ++ + R E EA
Sbjct: 136 VC--DENG-----SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 188
Query: 673 VKRKSSNVAKQ 683
R
Sbjct: 189 GARAKEFYPYD 199
Score = 42.3 bits (100), Expect = 2e-04
Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 10/75 (13%)
Query: 19 DLDEVEFIYKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAAL 75
DL +T+ L KF G + +++ T + +A++ + + A+ AL
Sbjct: 22 DLH-----PDVTEAMLYEKFSPAGPILSIRVCRDMIT--RRSLGYAYVNFQQPADAERAL 74
Query: 76 DYFNNTYVFSSRIKV 90
D N + +++
Sbjct: 75 DTMNFDVIKGKPVRI 89
Score = 37.6 bits (88), Expect = 0.007
Identities = 10/64 (15%), Positives = 27/64 (42%), Gaps = 1/64 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
I + L F G + ++ E + + F+ + ++ A+ A++ N + ++
Sbjct: 115 IDNKALYDTFSAFGNILSCKVV-CDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 173
Query: 89 KVEK 92
V +
Sbjct: 174 FVGR 177
Score = 29.2 bits (66), Expect = 4.0
Identities = 18/103 (17%), Positives = 38/103 (36%), Gaps = 9/103 (8%)
Query: 221 KRQYHTIVVKNLPAGVKKKDLKAYFKPLP-LASVR-----TTFLGMAYIGFKDEKNCNKA 274
K I +KNL + K L F + S + G ++ F+ ++ +A
Sbjct: 100 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERA 159
Query: 275 LNK-NKSFWKGKQL--NIYKYSKDNSAKYSGAADDNNNASMEN 314
+ K N +++ +K K+ A+ A + + +
Sbjct: 160 IEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPD 202
>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 = 103 bits (260), Expect = 6e-26
Identities = 42/169 (24%), Positives = 78/169 (46%), Gaps = 22/169 (13%)
Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
+ ++I LN+++TED++R +F K G + + + KDP + G+ S G+GF+ F
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKI--MKDPAT-GR--SRGFGFLSFEKP 55
Query: 638 ESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQA 697
S+++ +K +H ++ + ++ KR + KI V I
Sbjct: 56 SSVDEVVK-------TQHILD----GKVID-----PKRAIPRDEQDKTGKIFVGGIGPDV 99
Query: 698 KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ E EE F +G + +L +G RGFGFV + + + R +
Sbjct: 100 RPKEFEEFFSQWGTIIDAQLMLDK-DTGQSRGFGFVTYDSADAVDRVCQ 147
Score = 72.6 bits (179), Expect = 5e-15
Identities = 29/146 (19%), Positives = 61/146 (41%), Gaps = 27/146 (18%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
ES ++F+ L++ TED+L + F KYG + ++ + D T +++GF ++F P +
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKN 454
+ H++ GK +D K A + + ++ + I V
Sbjct: 62 VK----------TQHILDGKV------IDPKR----------AIPRDEQDKTGK-IFVGG 94
Query: 455 LPYRTLPTDLKALFEPFGDLGRVLVP 480
+ P + + F +G + +
Sbjct: 95 IGPDVRPKEFEEFFSQWGTIIDAQLM 120
Score = 70.6 bits (174), Expect = 2e-14
Identities = 19/86 (22%), Positives = 43/86 (50%), Gaps = 1/86 (1%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
++ ++G+IFV + V + + F ++G + + L +DK+T +++GF VT+ +
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141
Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPK 416
+ Q F R + + +P+
Sbjct: 142 VDRVCQ-NKFIDFKDRKIEIKRAEPR 166
Score = 53.3 bits (129), Expect = 2e-08
Identities = 14/88 (15%), Positives = 36/88 (40%), Gaps = 6/88 (6%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
E + +++ + + F + G I + KD G+GFV +
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQS-----RGFGFVTY 136
Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRS 662
+ +++++ + + + +IE+KR+
Sbjct: 137 DSADAVDRVCQ-NKFIDFKDRKIEIKRA 163
Score = 40.2 bits (95), Expect = 6e-04
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAAL 75
+ ++ + F + GT+ D QL + G+ R F F+ Y D
Sbjct: 99 VRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC 146
Score = 37.1 bits (87), Expect = 0.008
Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAAL 75
+ T++ L+ F + GTVTD+++ G+ R F F+ + + +
Sbjct: 13 WDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
>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 = 100 bits (251), Expect = 2e-25
Identities = 27/90 (30%), Positives = 43/90 (47%)
Query: 332 DIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
D+ + V NL+Y + D L ++FEKYG + +V +P + T +GFA V F A
Sbjct: 9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68
Query: 392 TQAYQHLDGTVFLGRMLHLIPGKPKENEGN 421
A +DG GR L + + + +
Sbjct: 69 QDAEAAMDGAELDGRELRVQVARYGRRDLS 98
Score = 75.0 bits (185), Expect = 1e-16
Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 2/92 (2%)
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
SS + V N+ ++ + +F+ +G + V +P++ + RGF FV
Sbjct: 3 SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPH-TKAPRGFAFVR 61
Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
F + +A+ A A+ L GR L ++ A
Sbjct: 62 FHDRRDAQDAEAAM-DGAELDGRELRVQVARY 92
Score = 63.8 bits (156), Expect = 1e-12
Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
+ + TL + NL + ++ DS+RR F+K G + V + ++P + G+ FV+F
Sbjct: 8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIP--REPHT-KA--PRGFAFVRF 62
Query: 635 YTRESLNQALKVLQNSSLDEHQI 657
+ R A + + LD ++
Sbjct: 63 HDRRDAQDAEAAMDGAELDGREL 85
Score = 51.5 bits (124), Expect = 3e-08
Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 5/69 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
Y+ + + L+ FE+ G V DV + +T R FAF+ +H AQ A + +
Sbjct: 23 YRTSPDSLRRVFEKYGRVGDVYIPREPHT--KAPRGFAFVRFHDRRDAQDAEAAMDGAEL 80
Query: 84 FSSRIKVEK 92
++V+
Sbjct: 81 DGRELRVQV 89
Score = 44.5 bits (106), Expect = 6e-06
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 6/60 (10%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
+ V NL YRT P L+ +FE +G +G V +P T V F + A+ A ++
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 98.3 bits (245), Expect = 2e-24
Identities = 29/88 (32%), Positives = 45/88 (51%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
D+ + V NL+Y + D L ++FEKYG + +V +P D+ T +++GFA V F
Sbjct: 42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101
Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
A A +DG V GR L + +
Sbjct: 102 AEDAMDAMDGAVLDGRELRVQMARYGRP 129
Score = 75.5 bits (186), Expect = 2e-16
Identities = 23/120 (19%), Positives = 47/120 (39%), Gaps = 8/120 (6%)
Query: 661 RSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK 720
+ ++ + + + V N+ ++ + +F+ +G + V +P+
Sbjct: 23 SMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD 82
Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRY 780
+ RGF FV F K +A+ AM A+ L GR L ++ A R + +
Sbjct: 83 RY-TKESRGFAFVRFHDKRDAEDAMDAM-DGAVLDGRELRVQMARYG------RPPDSHH 134
Score = 60.9 bits (148), Expect = 3e-11
Identities = 22/84 (26%), Positives = 44/84 (52%), Gaps = 5/84 (5%)
Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
+ E T+L + NL + ++ D++RR F+K G + V + R D + + S G+ FV+
Sbjct: 41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR--DRYT-KE--SRGFAFVR 95
Query: 634 FYTRESLNQALKVLQNSSLDEHQI 657
F+ + A+ + + LD ++
Sbjct: 96 FHDKRDAEDAMDAMDGAVLDGREL 119
Score = 50.9 bits (122), Expect = 8e-08
Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
Y+ + + L+ FE+ G V DV + +YT + R FAF+ +H + A+ A+D + +
Sbjct: 57 YRTSPDTLRRVFEKYGRVGDVYIPRDRYT--KESRGFAFVRFHDKRDAEDAMDAMDGAVL 114
Query: 84 FSSRIKVEK 92
++V+
Sbjct: 115 DGRELRVQM 123
Score = 45.1 bits (107), Expect = 7e-06
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
+ V NL YRT P L+ +FE +G +G V +P T V F K A+ A +++
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
>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 = 96.9 bits (242), Expect = 3e-24
Identities = 35/90 (38%), Positives = 56/90 (62%), Gaps = 2/90 (2%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
+ L+IKNLNF++TE++++ F K G I S T+ K G LSMG+GFV++ E
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTI--SKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEA 670
+ALK LQ ++D H++E++ S R + +
Sbjct: 64 QKALKQLQGHTVDGHKLEVRISERATKPAS 93
Score = 80.8 bits (200), Expect = 9e-19
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 3/87 (3%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKT---KGFALVTFLMPEH 390
+ S +F++NL+++ TE+ L +F K G + + K GF V + PE
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKE 417
A +A + L G G L + +
Sbjct: 63 AQKALKQLQGHTVDGHKLEVRISERAT 89
Score = 68.8 bits (169), Expect = 2e-14
Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 3/86 (3%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHR--GFGFVEFITKNEAK 742
S + ++N+ F + ++ +F G +K + KK +G+ GFGFVE+ +A+
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 743 RAMKALCQSTHLYGRRLVLEWAEEAD 768
+A+K L Q + G +L + +E A
Sbjct: 65 KALKQL-QGHTVDGHKLEVRISERAT 89
Score = 45.3 bits (108), Expect = 3e-06
Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 4/68 (5%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRR----FAFIGYHREDQAQAALDYFNNTY 82
+ T+E LK F + G + + F F+ Y + +QAQ AL
Sbjct: 15 FSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHT 74
Query: 83 VFSSRIKV 90
V +++V
Sbjct: 75 VDGHKLEV 82
Score = 37.6 bits (88), Expect = 0.001
Identities = 16/78 (20%), Positives = 28/78 (35%), Gaps = 9/78 (11%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLV-----PPYGIT----GLVEFLQKNQAKAAF 500
+ +KNL + T LK +F G + + + G VE+ + QA+ A
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 501 NSLAYTKFKEVPLYLEWA 518
L L + +
Sbjct: 68 KQLQGHTVDGHKLEVRIS 85
>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 = 94.9 bits (237), Expect = 8e-24
Identities = 23/75 (30%), Positives = 36/75 (48%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
+ S +++R L T+ DL KL + YG + +DK T+K KG+ V F P A +
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62
Query: 394 AYQHLDGTVFLGRML 408
A L + +M
Sbjct: 63 AVTALKASGVQAQMA 77
Score = 58.7 bits (143), Expect = 4e-11
Identities = 13/75 (17%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
S + +R + ++ +L + +G++ + + +G+GFV+F + + A++A
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKT-TNKCKGYGFVDFDSPSAAQKA 63
Query: 745 MKALCQSTHLYGRRL 759
+ AL +++ + +
Sbjct: 64 VTAL-KASGVQAQMA 77
Score = 56.8 bits (138), Expect = 2e-10
Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
+ LYI+ L +T+ + + + G I S D + + GYGFV F +
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAI--LDKTT-NK--CKGYGFVDFDS 56
Query: 637 RESLNQALKVLQNSSLD 653
+ +A+ L+ S +
Sbjct: 57 PSAAQKAVTALKASGVQ 73
Score = 44.4 bits (106), Expect = 5e-06
Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 5/72 (6%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
T + L + G + + K T K + + F+ + AQ A+ + V
Sbjct: 15 PGTTDQDLVKLCQPYGKIVSTKAILDKTT--NKCKGYGFVDFDSPSAAQKAVTALKASGV 72
Query: 84 FSSRIKVEKCSN 95
+ K S+
Sbjct: 73 QAQMAKQSGPSS 84
Score = 39.0 bits (92), Expect = 3e-04
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 6/58 (10%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 503
++ L T DL L +P+G + T V+F + A+ A +L
Sbjct: 10 IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>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 = 97.2 bits (242), Expect = 1e-23
Identities = 39/167 (23%), Positives = 59/167 (35%), Gaps = 21/167 (12%)
Query: 255 TTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMEN 314
T G D K + Y+ DN DD
Sbjct: 10 KTLKGETTTEAVDAATAEKVFKQ--------------YANDNGVDGEWTYDDATKTFTVT 55
Query: 315 IKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKET 374
+ H D+ + V NL+Y + D L ++FEKYG + +V +P D+ T
Sbjct: 56 EGSHHHHH-------HMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYT 108
Query: 375 DKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGN 421
+++GFA V F A A +DG V GR L + + +
Sbjct: 109 KESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDS 155
Score = 70.6 bits (173), Expect = 2e-14
Identities = 25/140 (17%), Positives = 55/140 (39%), Gaps = 3/140 (2%)
Query: 627 MGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGS 686
G + + + K N + + + + + + ++ + +
Sbjct: 13 KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKT-FTVTEGSHHHHHHMDVEGMT 71
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ V N+ ++ + +F+ +G + V +P+ + RGF FV F K +A+ AM
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY-TKESRGFAFVRFHDKRDAEDAMD 130
Query: 747 ALCQSTHLYGRRLVLEWAEE 766
A+ L GR L ++ A
Sbjct: 131 AM-DGAVLDGRELRVQMARY 149
Score = 67.9 bits (166), Expect = 2e-13
Identities = 25/136 (18%), Positives = 55/136 (40%), Gaps = 5/136 (3%)
Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREP 577
+ + E ++ + + + +D + E + +
Sbjct: 8 NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67
Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
E T+L + NL + ++ D++RR F+K G + V + R D + + S G+ FV+F+ +
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR--DRYT-KE--SRGFAFVRFHDK 122
Query: 638 ESLNQALKVLQNSSLD 653
A+ + + LD
Sbjct: 123 RDAEDAMDAMDGAVLD 138
Score = 48.7 bits (116), Expect = 7e-07
Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
Y+ + + L+ FE+ G V DV + +YT + R FAF+ +H + A+ A+D + +
Sbjct: 80 YRTSPDTLRRVFEKYGRVGDVYIPRDRYT--KESRGFAFVRFHDKRDAEDAMDAMDGAVL 137
Query: 84 FSSRIKVEK 92
++V+
Sbjct: 138 DGRELRVQM 146
Score = 43.7 bits (103), Expect = 4e-05
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
+ V NL YRT P L+ +FE +G +G V +P T V F K A+ A +++
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Score = 29.0 bits (65), Expect = 3.8
Identities = 20/130 (15%), Positives = 45/130 (34%), Gaps = 12/130 (9%)
Query: 169 GEEKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIV 228
E + ++ Q A+ + D E+ + + ++
Sbjct: 18 TEAVDAATAEKVFKQYANDNGVDGEW---TYDDATKTFTVTEGSHHHHHHMDVEGMTSLK 74
Query: 229 VKNLPAGVKKKDLKAYFKPL-PLASV-----RTT--FLGMAYIGFKDEKNCNKALNK-NK 279
V NL L+ F+ + V R T G A++ F D+++ A++ +
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 280 SFWKGKQLNI 289
+ G++L +
Sbjct: 135 AVLDGRELRV 144
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 94.7 bits (236), Expect = 1e-23
Identities = 18/87 (20%), Positives = 42/87 (48%), Gaps = 1/87 (1%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
E ++F+ L ++ T+++L ++ + +G + ++ L ++ K KG A V + A+Q
Sbjct: 15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQ 73
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEG 420
A +DG ++ + + G
Sbjct: 74 AVMKMDGMTIKENIIKVAISNSGPSSG 100
Score = 73.9 bits (182), Expect = 3e-16
Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 3/82 (3%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
K+ + +PF + E+EE+ KA G +K +RL +G +G +VE+ +++A +A
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR--AGKPKGLAYVEYENESQASQA 74
Query: 745 MKALCQSTHLYGRRLVLEWAEE 766
+ + + + + +
Sbjct: 75 VMKM-DGMTIKENIIKVAISNS 95
Score = 58.4 bits (142), Expect = 8e-11
Identities = 16/89 (17%), Positives = 36/89 (40%), Gaps = 6/89 (6%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
L+I L F+ T++ + K G + + + + K G +V++
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGK------PKGLAYVEY 65
Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSN 663
+QA+ + ++ E+ I++ SN
Sbjct: 66 ENESQASQAVMKMDGMTIKENIIKVAISN 94
Score = 53.4 bits (129), Expect = 4e-09
Identities = 19/66 (28%), Positives = 33/66 (50%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ T+E+L+ + GTV D++L GK + A++ Y E QA A+ + + +
Sbjct: 27 FSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKEN 86
Query: 87 RIKVEK 92
IKV
Sbjct: 87 IIKVAI 92
Score = 41.5 bits (98), Expect = 8e-05
Identities = 12/64 (18%), Positives = 27/64 (42%), Gaps = 7/64 (10%)
Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP------PYGITGLVEFLQKNQAKAA 499
K + + LP+ +L+ + + G + + + P G+ VE+ ++QA A
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGL-AYVEYENESQASQA 74
Query: 500 FNSL 503
+
Sbjct: 75 VMKM 78
Score = 28.0 bits (63), Expect = 3.7
Identities = 14/73 (19%), Positives = 32/73 (43%), Gaps = 8/73 (10%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF------LGMAYIGFKDEKNCNKALNK 277
H + + LP K++L+ K + +R G+AY+ +++E ++A+ K
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMK 77
Query: 278 -NKSFWKGKQLNI 289
+ K + +
Sbjct: 78 MDGMTIKENIIKV 90
>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 = 95.6 bits (238), Expect = 2e-23
Identities = 25/115 (21%), Positives = 42/115 (36%), Gaps = 1/115 (0%)
Query: 303 AADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGP 362
A S A + + + ++V N+ Y T DL F G
Sbjct: 3 APCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGS 62
Query: 363 LAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
+ + + DK + KG+A + F A +D TVF GR + ++P +
Sbjct: 63 INRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKVLPKRTNM 116
Score = 69.7 bits (171), Expect = 2e-14
Identities = 25/130 (19%), Positives = 52/130 (40%), Gaps = 6/130 (4%)
Query: 545 GEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKC 604
+ T + E EE++ ++Y+ N+++ ST + HF C
Sbjct: 1 AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60
Query: 605 GPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
G I +T+ K P GY +++F R S++ A+ + + I++
Sbjct: 61 GSINRITILCDKFSGHP-----KGYAYIEFAERNSVDAAVA-MDETVFRGRTIKVLPKRT 114
Query: 665 NLESEATTVK 674
N+ ++T +
Sbjct: 115 NMPGISSTDR 124
Score = 60.1 bits (146), Expect = 4e-11
Identities = 18/112 (16%), Positives = 43/112 (38%), Gaps = 5/112 (4%)
Query: 656 QIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFV 715
Q + +E + + + V N+ + + ++E F + G + +
Sbjct: 7 QTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRI 66
Query: 716 RLPK-KMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
+ K SG +G+ ++EF +N A+ A+ ++ GR + +
Sbjct: 67 TILCDKF--SGHPKGYAYIEFAERNSVDAAV-AMDETV-FRGRTIKVLPKRT 114
Score = 42.0 bits (99), Expect = 7e-05
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 6/63 (9%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 496
+ KR + V N+ Y + DL+A F G + R+ + +G +EF ++N
Sbjct: 32 KEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSV 91
Query: 497 KAA 499
AA
Sbjct: 92 DAA 94
Score = 41.6 bits (98), Expect = 1e-04
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
Y T + L+A F G++ + + K++ G + +A+I + + AA+ + V
Sbjct: 46 YGSTAQDLEAHFSSCGSINRITILCDKFS--GHPKGYAYIEFAERNSVDAAVAM--DETV 101
Query: 84 FSSR-IKV 90
F R IKV
Sbjct: 102 FRGRTIKV 109
Score = 37.8 bits (88), Expect = 0.003
Identities = 18/100 (18%), Positives = 45/100 (45%), Gaps = 8/100 (8%)
Query: 198 KTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASV--- 253
+K A ++ P+S + ++ V N+ G +DL+A+F + +
Sbjct: 10 HSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITIL 69
Query: 254 --RTT--FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNI 289
+ + G AYI F + + + A+ +++ ++G+ + +
Sbjct: 70 CDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKV 109
>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 = 94.7 bits (236), Expect = 2e-23
Identities = 23/97 (23%), Positives = 44/97 (45%), Gaps = 6/97 (6%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
D+ E +F+RNLS+ E+ L ++ +++G L V + + +T+ +KG A F+ E
Sbjct: 10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69
Query: 391 ATQAYQHLD------GTVFLGRMLHLIPGKPKENEGN 421
A + G GR L + ++ +
Sbjct: 70 AQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106
Score = 76.2 bits (188), Expect = 6e-17
Identities = 24/100 (24%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 674 KRKSSNVAK--QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFG 731
SS + G + +RN+ F +++ + E+ + FG+LK+VR+ + +G
Sbjct: 2 SSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPD-TEHSKGCA 60
Query: 732 FVEFITKNEAKRAMKALCQSTH-----LYGRRLVLEWAEE 766
F +F+T+ A++ + A L GR+L ++ A
Sbjct: 61 FAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 100
Score = 64.7 bits (158), Expect = 7e-13
Identities = 19/82 (23%), Positives = 36/82 (43%), Gaps = 5/82 (6%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
+ T++I+NL+F+S E+++ ++ G + V V P + S G
Sbjct: 5 SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVV--LHPDT-EH--SKGC 59
Query: 630 GFVQFYTRESLNQALKVLQNSS 651
F QF T+E+ + L +
Sbjct: 60 AFAQFMTQEAAQKCLAAASLEA 81
Score = 41.6 bits (98), Expect = 9e-05
Identities = 9/56 (16%), Positives = 22/56 (39%), Gaps = 1/56 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNT 81
+ +E L ++ G + V++ + + AF + ++ AQ L +
Sbjct: 25 FDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLE 80
Score = 40.0 bits (94), Expect = 3e-04
Identities = 12/67 (17%), Positives = 27/67 (40%), Gaps = 6/67 (8%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 496
+ + + ++NL + + L + + FGDL V V + T +F+ + A
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 497 KAAFNSL 503
+ +
Sbjct: 71 QKCLAAA 77
>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 = 95.7 bits (238), Expect = 4e-23
Identities = 25/121 (20%), Positives = 56/121 (46%), Gaps = 3/121 (2%)
Query: 304 ADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPL 363
+D N ++ + + + ++ + E +FV ++ ED++ + F YG +
Sbjct: 40 SDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEI 99
Query: 364 AEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHL---IPGKPKENEG 420
+ L +D+ T +KG+ALV + + A A + L+G +G+ + + PK +
Sbjct: 100 KNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKK 159
Query: 421 N 421
+
Sbjct: 160 S 160
Score = 72.6 bits (178), Expect = 5e-15
Identities = 28/131 (21%), Positives = 56/131 (42%), Gaps = 7/131 (5%)
Query: 649 NSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKA 708
+S+ E +R + E ++S G + V +I +A++ E++E F
Sbjct: 41 DSNTREAIHSYERVRNEDDDELEPGPQRSV-----EGWILFVTSIHEEAQEDEIQEKFCD 95
Query: 709 FGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEAD 768
+GE+K + L +G +G+ VE+ T +A A +AL + G+ + ++W
Sbjct: 96 YGEIKNIHLNLDR-RTGFSKGYALVEYETHKQALAAKEAL-NGAEIMGQTIQVDWCFVKG 153
Query: 769 NVEDIRKRTNR 779
+ R
Sbjct: 154 PKRVKKSEKRR 164
Score = 64.9 bits (158), Expect = 2e-12
Identities = 26/143 (18%), Positives = 56/143 (39%), Gaps = 5/143 (3%)
Query: 515 LEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 574
++ A E E ++ + KEK + G + + V +++ E
Sbjct: 7 IDNAEEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGP 66
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
+ L++ +++ + ED I+ F G I ++ + D ++ G S GY V++
Sbjct: 67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL--DRRT-GF--SKGYALVEY 121
Query: 635 YTRESLNQALKVLQNSSLDEHQI 657
T + A + L + + I
Sbjct: 122 ETHKQALAAKEALNGAEIMGQTI 144
Score = 51.4 bits (123), Expect = 1e-07
Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ +++++ KF + G + ++ L G + +A + Y QA AA + N +
Sbjct: 82 EEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG 141
Query: 86 SRIKVEKC 93
I+V+ C
Sbjct: 142 QTIQVDWC 149
Score = 42.5 bits (100), Expect = 1e-04
Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 502
I+ V ++ +++ F +G++ + + TG LVE+ QA AA +
Sbjct: 74 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 503 LAYTKFKEVPLYLEWA 518
L + + ++W
Sbjct: 134 LNGAEIMGQTIQVDWC 149
>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 = 92.3 bits (230), Expect = 1e-22
Identities = 30/94 (31%), Positives = 47/94 (50%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
++ I V NLS E DL +LF +G ++ + L DK T ++KGFA ++F E
Sbjct: 10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69
Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDG 424
A +A + G + +L++ KP N G G
Sbjct: 70 AARAIAGVSGFGYDHLILNVEWAKPSTNSGPSSG 103
Score = 73.4 bits (181), Expect = 5e-16
Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 2/85 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
+ I V N+ ++++++ELF+ FG + + L K +G +GF F+ F + +A RA
Sbjct: 15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKT-TGQSKGFAFISFHRREDAARA 73
Query: 745 MKALCQSTHLYGRRLVLEWAEEADN 769
+ + L +EWA+ + N
Sbjct: 74 IAGV-SGFGYDHLILNVEWAKPSTN 97
Score = 63.4 bits (155), Expect = 2e-12
Identities = 20/79 (25%), Positives = 41/79 (51%), Gaps = 5/79 (6%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
R + + T+ + NL+ ++ E ++ F+ G I+ + +A+ D + GQ S G+ F+ F
Sbjct: 10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAK--DKTT-GQ--SKGFAFISF 64
Query: 635 YTRESLNQALKVLQNSSLD 653
+ RE +A+ + D
Sbjct: 65 HRREDAARAIAGVSGFGYD 83
Score = 49.1 bits (118), Expect = 2e-07
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 5/69 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+ L+ F G+++ + L K T G+ + FAFI +HR + A A+ +
Sbjct: 25 EDTRETDLQELFRPFGSISRIYLAKDKTT--GQSKGFAFISFHRREDAARAIAGVSGFGY 82
Query: 84 FSSRIKVEK 92
+ VE
Sbjct: 83 DHLILNVEW 91
Score = 46.4 bits (111), Expect = 1e-06
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 503
I V NL T TDL+ LF PFG + R+ + TG + F ++ A A +
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 504 AYTKFKEVPLYLEWA 518
+ + + L +EWA
Sbjct: 78 SGFGYDHLILNVEWA 92
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 91.7 bits (228), Expect = 2e-22
Identities = 20/72 (27%), Positives = 32/72 (44%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+ L+ V E L + KYG + EV + + T K G A V F A + ++
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67
Query: 398 LDGTVFLGRMLH 409
L T +G ++H
Sbjct: 68 LHLTSVMGNIIH 79
Score = 70.1 bits (172), Expect = 8e-15
Identities = 15/81 (18%), Positives = 29/81 (35%), Gaps = 5/81 (6%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
P + LN N E ++ +K G + V + + +G V F +
Sbjct: 3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRK-----HLGLARVLFTS 57
Query: 637 RESLNQALKVLQNSSLDEHQI 657
+ +K L +S+ + I
Sbjct: 58 TRGAKETVKNLHLTSVMGNII 78
Score = 60.1 bits (146), Expect = 3e-11
Identities = 13/75 (17%), Positives = 33/75 (44%), Gaps = 2/75 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
++ + +++ ++++ + +GE++ V + + H G V F + AK
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPR-TRKHLGLARVLFTSTRGAKET 64
Query: 745 MKALCQSTHLYGRRL 759
+K L T + G +
Sbjct: 65 VKNL-HLTSVMGNII 78
Score = 52.8 bits (127), Expect = 1e-08
Identities = 13/87 (14%), Positives = 30/87 (34%), Gaps = 9/87 (10%)
Query: 7 GPVVPRN-HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIG 64
G + + + L+ + + LK + G V +V++ K A +
Sbjct: 2 GQIPLKEVTFARLN-------DNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVL 54
Query: 65 YHREDQAQAALDYFNNTYVFSSRIKVE 91
+ A+ + + T V + I +
Sbjct: 55 FTSTRGAKETVKNLHLTSVMGNIIHAQ 81
Score = 43.5 bits (103), Expect = 2e-05
Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 6/81 (7%)
Query: 447 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAF 500
+ + L T LK + +G++ V + + T V F AK
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65
Query: 501 NSLAYTKFKEVPLYLEWAPEG 521
+L T ++ + +G
Sbjct: 66 KNLHLTSVMGNIIHAQLDIKG 86
Score = 35.8 bits (83), Expect = 0.007
Identities = 10/81 (12%), Positives = 26/81 (32%), Gaps = 12/81 (14%)
Query: 218 PVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF-------LGMAYIGFKDEK 269
+ + + L V++ LK + + V LG+A + F +
Sbjct: 3 QIPLK---EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTR 59
Query: 270 NCNKALNK-NKSFWKGKQLNI 289
+ + + + G ++
Sbjct: 60 GAKETVKNLHLTSVMGNIIHA 80
>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 = 90.3 bits (225), Expect = 5e-22
Identities = 25/88 (28%), Positives = 49/88 (55%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
+ S ++V +L + +TED L +FE +G + ++L D +T ++KG+ +TF E A +
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGN 421
A + L+G GR + + + + G+
Sbjct: 63 ALEQLNGFELAGRPMRVGHVTERLDGGS 90
Score = 69.1 bits (170), Expect = 1e-14
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 2/81 (2%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
S + V ++ F + + +F+ FG++ + L K +G +G+GF+ F A+RA+
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSD-TGRSKGYGFITFSDSECARRAL 64
Query: 746 KALCQSTHLYGRRLVLEWAEE 766
+ L L GR + + E
Sbjct: 65 EQL-NGFELAGRPMRVGHVTE 84
Score = 54.9 bits (133), Expect = 1e-09
Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
+ LY+ +L+FN TED +R F+ G I ++ + KD + G+ S GYGF+ F
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLM--KDSDT-GR--SKGYGFITFSDS 57
Query: 638 ESLNQALKVLQNSSLD 653
E +AL+ L L
Sbjct: 58 ECARRALEQLNGFELA 73
Score = 48.7 bits (117), Expect = 2e-07
Identities = 15/65 (23%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ IT++ L+ FE G + ++ L ++ G+ + + FI + + A+ AL+ N +
Sbjct: 15 FNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAG 74
Query: 86 SRIKV 90
++V
Sbjct: 75 RPMRV 79
Score = 38.3 bits (90), Expect = 7e-04
Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
+ V +L + L+ +FEPFG + +++ TG + F A+ A L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
>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 = 89.2 bits (222), Expect = 1e-21
Identities = 25/73 (34%), Positives = 43/73 (58%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
+ + V LS TE DL ++F KYGP+A+V + D+++ +++GFA V F + A +A
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 396 QHLDGTVFLGRML 408
+ +G GR +
Sbjct: 75 ERANGMELDGRRI 87
Score = 65.7 bits (161), Expect = 2e-13
Identities = 19/90 (21%), Positives = 34/90 (37%), Gaps = 2/90 (2%)
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
+ + V + + ++ E+F +G + V + S RGF FV
Sbjct: 5 SSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-SRRSRGFAFVY 63
Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
F ++AK A + L GRR+ +
Sbjct: 64 FENVDDAKEAKERANGME-LDGRRIRVSGP 92
Score = 65.7 bits (161), Expect = 2e-13
Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 5/82 (6%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
P+P+ L + L+ +TE +R F K GPIA V++ D +S + S G+ FV F
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIV--YDQQS-RR--SRGFAFVYFE 65
Query: 636 TRESLNQALKVLQNSSLDEHQI 657
+ +A + LD +I
Sbjct: 66 NVDDAKEAKERANGMELDGRRI 87
Score = 49.9 bits (120), Expect = 6e-08
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
T+ L+ F + G + DV + Y + + R FAF+ + D A+ A + N +
Sbjct: 25 LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG 84
Query: 86 SRIKVEK 92
RI+V
Sbjct: 85 RRIRVSG 91
Score = 41.0 bits (97), Expect = 8e-05
Identities = 13/60 (21%), Positives = 21/60 (35%), Gaps = 6/60 (10%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
+ V L T DL+ +F +G + V + + V F + AK A
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
>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 = 88.9 bits (221), Expect = 1e-21
Identities = 26/88 (29%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
+ + R+FV NL +TE+++ KLFEKYG EV + D KGF +
Sbjct: 10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTL 63
Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
A A LD G+ L + +
Sbjct: 64 AEIAKVELDNMPLRGKQLRVRFACHSAS 91
Score = 73.8 bits (182), Expect = 3e-16
Identities = 22/87 (25%), Positives = 44/87 (50%), Gaps = 8/87 (9%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
S++ V N+P + E+ +LF+ +G+ V + K +GFGF+ T+ A+ A
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-------DKGFGFIRLETRTLAEIA 67
Query: 745 MKALCQSTHLYGRRLVLEWAEEADNVE 771
L + L G++L + +A + ++
Sbjct: 68 KVEL-DNMPLRGKQLRVRFACHSASLT 93
Score = 68.8 bits (169), Expect = 2e-14
Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 11/93 (11%)
Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
E+ + L++ NL + TE+ +R+ F+K G V + + K G+GF
Sbjct: 7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-----------GFGF 55
Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
++ TR A L N L Q+ ++ +
Sbjct: 56 IRLETRTLAEIAKVELDNMPLRGKQLRVRFACH 88
Score = 49.2 bits (118), Expect = 1e-07
Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 6/75 (8%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYT 506
+ V NLP +++ LFE +G G V + + G + + A+ A L
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGF---GFIRLETRTLAEIAKVELDNM 74
Query: 507 KFKEVPLYLEWAPEG 521
+ L + +A
Sbjct: 75 PLRGKQLRVRFACHS 89
Score = 44.6 bits (106), Expect = 6e-06
Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
IT+E+++ FE+ G +V + K + F FI A+ A +N +
Sbjct: 25 PDITEEEMRKLFEKYGKAGEVFIH-----KDKGFGFIRLETRTLAEIAKVELDNMPLRGK 79
Query: 87 RIKVE 91
+++V
Sbjct: 80 QLRVR 84
Score = 30.7 bits (70), Expect = 0.41
Identities = 17/93 (18%), Positives = 38/93 (40%), Gaps = 4/93 (4%)
Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVR-TTFLGMAYIGFKDEKNCN 272
S Q + V NLP + +++++ F+ V G +I +
Sbjct: 6 SGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAE 65
Query: 273 KALNK-NKSFWKGKQLNIYKYSKDNSAKYSGAA 304
A + + +GKQL + +++ +++ SG +
Sbjct: 66 IAKVELDNMPLRGKQLRV-RFACHSASLTSGPS 97
>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 = 89.8 bits (223), Expect = 2e-21
Identities = 25/73 (34%), Positives = 43/73 (58%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
+ + V LS TE DL ++F KYGP+A+V + D+++ +++GFA V F + A +A
Sbjct: 46 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
Query: 396 QHLDGTVFLGRML 408
+ +G GR +
Sbjct: 106 ERANGMELDGRRI 118
Score = 69.8 bits (171), Expect = 2e-14
Identities = 20/106 (18%), Positives = 40/106 (37%), Gaps = 2/106 (1%)
Query: 661 RSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK 720
S + + + + V + + ++ E+F +G + V +
Sbjct: 22 ASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD 81
Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
S RGF FV F ++AK A + L GRR+ ++++
Sbjct: 82 QQ-SRRSRGFAFVYFENVDDAKEAKERA-NGMELDGRRIRVDFSIT 125
Score = 69.0 bits (169), Expect = 4e-14
Identities = 25/88 (28%), Positives = 40/88 (45%), Gaps = 5/88 (5%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
P+P+ L + L+ +TE +R F K GPIA V++ D +S + S G+
Sbjct: 36 HVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVY--DQQS-RR--SRGF 90
Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQI 657
FV F + +A + LD +I
Sbjct: 91 AFVYFENVDDAKEAKERANGMELDGRRI 118
Score = 49.7 bits (119), Expect = 2e-07
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 5/69 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
T+ L+ F + G + DV + + + + R FAF+ + D A+ A + N +
Sbjct: 56 LYTTERDLREVFSKYGPIADVSIVYDQQS--RRSRGFAFVYFENVDDAKEAKERANGMEL 113
Query: 84 FSSRIKVEK 92
RI+V+
Sbjct: 114 DGRRIRVDF 122
Score = 42.0 bits (99), Expect = 9e-05
Identities = 13/64 (20%), Positives = 21/64 (32%), Gaps = 6/64 (9%)
Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAA 499
+ V L T DL+ +F +G + V + + V F + AK A
Sbjct: 45 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104
Query: 500 FNSL 503
Sbjct: 105 KERA 108
>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 = 88.8 bits (221), Expect = 2e-21
Identities = 26/85 (30%), Positives = 47/85 (55%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
++ G++FV LS+ E L ++F KYG ++EV++ D+ET +++GF VTF + A
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKEN 418
A ++G GR + + +
Sbjct: 70 AMMAMNGKSVDGRQIRVDQAGKSSD 94
Score = 66.1 bits (162), Expect = 2e-13
Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 2/81 (2%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
K+ V + F + +E++F +G++ V + K + RGFGFV F ++AK AM
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRE-TQRSRGFGFVTFENIDDAKDAM 71
Query: 746 KALCQSTHLYGRRLVLEWAEE 766
A+ + GR++ ++ A +
Sbjct: 72 MAM-NGKSVDGRQIRVDQAGK 91
Score = 63.4 bits (155), Expect = 2e-12
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 5/88 (5%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
+ L++ L+F++ E S+ + F K G I+ V V KD ++ + S G+GFV F
Sbjct: 8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVV--KDRET-QR--SRGFGFVTFE 62
Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSN 663
+ A+ + S+D QI + ++
Sbjct: 63 NIDDAKDAMMAMNGKSVDGRQIRVDQAG 90
Score = 42.2 bits (100), Expect = 4e-05
Identities = 15/69 (21%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+ ++ L+ F + G +++V + + T + R F F+ + D A+ A+ N V
Sbjct: 22 FDTNEQSLEQVFSKYGQISEVVVVKDRET--QRSRGFGFVTFENIDDAKDAMMAMNGKSV 79
Query: 84 FSSRIKVEK 92
+I+V++
Sbjct: 80 DGRQIRVDQ 88
Score = 36.5 bits (85), Expect = 0.004
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
+ V L + T L+ +F +G + V+V T G V F + AK A ++
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
>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 = 88.0 bits (219), Expect = 3e-21
Identities = 23/73 (31%), Positives = 43/73 (58%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
++V NL +++T +DL ++F KYG + +V + DK+T K+KG A + FL + A
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75
Query: 396 QHLDGTVFLGRML 408
+ ++ GR++
Sbjct: 76 RAINNKQLFGRVI 88
Score = 66.5 bits (163), Expect = 1e-13
Identities = 19/81 (23%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
+ S + V N+PF +++ +F +G++ V + K + +G F+ F+ K+ A+
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDK-DTRKSKGVAFILFLDKDSAQN 73
Query: 744 AMKALCQSTHLYGRRLVLEWA 764
+A+ + L+GR + A
Sbjct: 74 CTRAI-NNKQLFGRVIKASIA 93
Score = 58.4 bits (142), Expect = 6e-11
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
+T+Y+ NL F+ T + + R F K G + VT+ + KD + S G F+ F
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKD---TRK--SKGVAFILFL 66
Query: 636 TRESLNQALKVLQNSSLD 653
++S + + N L
Sbjct: 67 DKDSAQNCTRAINNKQLF 84
Score = 51.5 bits (124), Expect = 2e-08
Identities = 20/69 (28%), Positives = 28/69 (40%), Gaps = 5/69 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+ +T L F + G V V + K T K + AFI + +D AQ NN +
Sbjct: 26 FSLTNNDLYRIFSKYGKVVKVTIMKDKDT--RKSKGVAFILFLDKDSAQNCTRAINNKQL 83
Query: 84 FSSRIKVEK 92
F IK
Sbjct: 84 FGRVIKASI 92
Score = 41.4 bits (98), Expect = 6e-05
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQA 496
A SK + V NLP+ DL +F +G + +V + T + FL K+ A
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 497 KAAFNSL 503
+ ++
Sbjct: 72 QNCTRAI 78
>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 = 89.5 bits (222), Expect = 4e-21
Identities = 23/98 (23%), Positives = 48/98 (48%)
Query: 321 KSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGF 380
+ D+ + + + +S ++V NLS+ TE+ + +LF K G + ++I+ +DK GF
Sbjct: 24 HFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGF 83
Query: 381 ALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
V + A A ++++GT R++ +
Sbjct: 84 CFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE 121
Score = 76.4 bits (188), Expect = 2e-16
Identities = 26/87 (29%), Positives = 46/87 (52%), Gaps = 5/87 (5%)
Query: 571 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYG 630
E++E+ + TLY+ NL+F +TE+ I F K G I + + K K+ G+
Sbjct: 30 EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTA-----CGFC 84
Query: 631 FVQFYTRESLNQALKVLQNSSLDEHQI 657
FV++Y+R A++ + + LD+ I
Sbjct: 85 FVEYYSRADAENAMRYINGTRLDDRII 111
Score = 71.0 bits (174), Expect = 1e-14
Identities = 22/108 (20%), Positives = 45/108 (41%), Gaps = 10/108 (9%)
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
+ + + V N+ F + ++ ELF G++K + + + GF FVE
Sbjct: 29 NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KKTACGFCFVE 87
Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFG 782
+ ++ +A+ AM+ + T L R + +W + R +G
Sbjct: 88 YYSRADAENAMRYI-NGTRLDDRIIRTDWDA--------GFKEGRQYG 126
Score = 51.7 bits (124), Expect = 7e-08
Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 1/67 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ T+EQ+ F + G + + + F F+ Y+ A+ A+ Y N T +
Sbjct: 49 FYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD 108
Query: 86 SRIKVEK 92
I+ +
Sbjct: 109 RIIRTDW 115
Score = 49.4 bits (118), Expect = 4e-07
Identities = 16/95 (16%), Positives = 35/95 (36%), Gaps = 6/95 (6%)
Query: 431 SERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL--- 487
+ D Q + + V NL + T + LF GD+ ++++ +
Sbjct: 23 QHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82
Query: 488 ---VEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP 519
VE+ + A+ A + T+ + + +W
Sbjct: 83 FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA 117
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 87.7 bits (218), Expect = 5e-21
Identities = 25/95 (26%), Positives = 39/95 (41%), Gaps = 8/95 (8%)
Query: 324 EDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
E + R+FVR V E +L ++F +GP+ EV + GFA V
Sbjct: 19 SHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFV 70
Query: 384 TFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
F E A +A + + G F + L ++ K
Sbjct: 71 EFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105
Score = 68.9 bits (169), Expect = 2e-14
Identities = 22/117 (18%), Positives = 45/117 (38%), Gaps = 14/117 (11%)
Query: 660 KRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPK 719
+ + + + +++ VR P ++SE+ E+F FG +K V++
Sbjct: 6 HHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN 65
Query: 720 KMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKR 776
GF FVEF A +A++ + + L + +++ R R
Sbjct: 66 ---------GFAFVEFEEAESAAKAIEEV-HGKSFANQPLEVVYSKLPAK----RYR 108
Score = 61.5 bits (150), Expect = 9e-12
Identities = 17/95 (17%), Positives = 34/95 (35%), Gaps = 13/95 (13%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
+ +T L+++ + E + F GP+ V + G+
Sbjct: 21 MHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------------GF 67
Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
FV+F ES +A++ + S +E+ S
Sbjct: 68 AFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKL 102
Score = 45.7 bits (109), Expect = 3e-06
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 2/69 (2%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 509
+ V+ P ++L +F PFG + V + G VEF + A A + F
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-G-FAFVEFEEAESAAKAIEEVHGKSFA 91
Query: 510 EVPLYLEWA 518
PL + ++
Sbjct: 92 NQPLEVVYS 100
Score = 41.5 bits (98), Expect = 8e-05
Identities = 10/65 (15%), Positives = 26/65 (40%), Gaps = 7/65 (10%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ + +L F G + +V++ FAF+ + + A A++ + +
Sbjct: 41 LDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQ 93
Query: 87 RIKVE 91
++V
Sbjct: 94 PLEVV 98
Score = 30.3 bits (69), Expect = 0.63
Identities = 15/92 (16%), Positives = 38/92 (41%), Gaps = 3/92 (3%)
Query: 200 KSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTFL 258
++ P + + + V+ P V++ +L F P P+ V+
Sbjct: 7 HHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-N 65
Query: 259 GMAYIGFKDEKNCNKALNK-NKSFWKGKQLNI 289
G A++ F++ ++ KA+ + + + + L +
Sbjct: 66 GFAFVEFEEAESAAKAIEEVHGKSFANQPLEV 97
>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 = 86.4 bits (215), Expect = 8e-21
Identities = 20/85 (23%), Positives = 43/85 (50%), Gaps = 1/85 (1%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDK-ETDKTKGFALVTFLMPEHATQ 393
+ ++ + L+ VT+D + ++F YG + + +P+++ +KG+A V F P+ A +
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKEN 418
A +H+DG G+ +
Sbjct: 63 ALKHMDGGQIDGQEITATAVLAPWP 87
Score = 73.3 bits (181), Expect = 3e-16
Identities = 17/94 (18%), Positives = 43/94 (45%), Gaps = 10/94 (10%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+K+ + + + + E+F +G++K + +P + + L +G+ +VEF +EA++A+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 746 KALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
K + + G+ + + R
Sbjct: 65 KHM-DGGQIDGQEI---------TATAVLAPWPR 88
Score = 61.8 bits (151), Expect = 4e-12
Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 4/79 (5%)
Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
T ++I L N T+D I F G I + + + P S GY +V+F +
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMP--VERMHPHL--SKGYAYVEFENPD 58
Query: 639 SLNQALKVLQNSSLDEHQI 657
+ALK + +D +I
Sbjct: 59 EAEKALKHMDGGQIDGQEI 77
Score = 49.8 bits (120), Expect = 7e-08
Identities = 9/69 (13%), Positives = 27/69 (39%), Gaps = 4/69 (5%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+T++ + F G + + + + + +A++ + D+A+ AL + + +
Sbjct: 14 RNVTKDHIMEIFSTYGKIKMIDMPVERMHP-HLSKGYAYVEFENPDEAEKALKHMDGGQI 72
Query: 84 FSSRIKVEK 92
I
Sbjct: 73 DGQEITATA 81
Score = 37.5 bits (88), Expect = 0.001
Identities = 10/62 (16%), Positives = 22/62 (35%), Gaps = 9/62 (14%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--------PYGITGLVEFLQKNQAKAAFN 501
+ + L + +F +G + + +P G VEF ++A+ A
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKG-YAYVEFENPDEAEKALK 65
Query: 502 SL 503
+
Sbjct: 66 HM 67
Score = 27.9 bits (63), Expect = 3.5
Identities = 13/74 (17%), Positives = 25/74 (33%), Gaps = 10/74 (13%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVR------TTFL--GMAYIGFKDEKNCNKALN 276
+ + L V K + F + + L G AY+ F++ KAL
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 277 K-NKSFWKGKQLNI 289
+ G+++
Sbjct: 66 HMDGGQIDGQEITA 79
>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 = 87.0 bits (216), Expect = 1e-20
Identities = 21/99 (21%), Positives = 48/99 (48%)
Query: 311 SMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPI 370
++ + + + ++ + E +FV ++ ED++ + F YG + + L +
Sbjct: 1 AIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL 60
Query: 371 DKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLH 409
D+ T +KG+ALV + + A A + L+G +G+ +
Sbjct: 61 DRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ 99
Score = 71.9 bits (177), Expect = 2e-15
Identities = 27/113 (23%), Positives = 51/113 (45%), Gaps = 9/113 (7%)
Query: 654 EHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK 713
H E R+ + E E + G + V +I +A++ E++E F +GE+K
Sbjct: 2 IHSYERVRNEDDDELEPGPQRSVE-------GWILFVTSIHEEAQEDEIQEKFCDYGEIK 54
Query: 714 FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
+ L +G +G+ VE+ T +A A +AL + G+ + ++W
Sbjct: 55 NIHLNLDR-RTGFSKGYALVEYETHKQALAAKEAL-NGAEIMGQTIQVDWCFV 105
Score = 53.8 bits (130), Expect = 4e-09
Identities = 22/98 (22%), Positives = 43/98 (43%), Gaps = 12/98 (12%)
Query: 567 ENVEEDEEREPEPDT-------TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 619
E V +++ E EP L++ +++ + ED I+ F G I ++ + D +
Sbjct: 6 ERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL--DRR 63
Query: 620 SPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI 657
+ G S GY V++ T + A + L + + I
Sbjct: 64 T-GF--SKGYALVEYETHKQALAAKEALNGAEIMGQTI 98
Score = 51.5 bits (124), Expect = 3e-08
Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ +++++ KF + G + ++ L G + +A + Y QA AA + N +
Sbjct: 36 EEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG 95
Query: 86 SRIKVEKC 93
I+V+ C
Sbjct: 96 QTIQVDWC 103
Score = 40.7 bits (96), Expect = 2e-04
Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 502
I+ V ++ +++ F +G++ + + TG LVE+ QA AA +
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 503 LAYTKFKEVPLYLEWA 518
L + + ++W
Sbjct: 88 LNGAEIMGQTIQVDWC 103
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 86.5 bits (215), Expect = 1e-20
Identities = 21/76 (27%), Positives = 39/76 (51%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
E +FV + TE+D+ F +YG + + L +D+ T KG+ LV + + A A
Sbjct: 22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81
Query: 395 YQHLDGTVFLGRMLHL 410
+ L+G +G+ + +
Sbjct: 82 MEGLNGQDLMGQPISV 97
Score = 73.1 bits (180), Expect = 8e-16
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 2/82 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G + V + +A + ++ + F +GE+K + L +G +G+ VE+ T EA+ A
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQAA 81
Query: 745 MKALCQSTHLYGRRLVLEWAEE 766
M+ L L G+ + ++W
Sbjct: 82 MEGL-NGQDLMGQPISVDWCFV 102
Score = 51.9 bits (125), Expect = 2e-08
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ T+E + KF E G + ++ L G + + + Y +AQAA++ N +
Sbjct: 33 EEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG 92
Query: 86 SRIKVEKC 93
I V+ C
Sbjct: 93 QPISVDWC 100
Score = 51.5 bits (124), Expect = 2e-08
Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 10/99 (10%)
Query: 564 EVEENVEEDEEREPEPD-----TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP 618
+ + E + EP P L++ ++ +TE+ I F + G I ++ + D
Sbjct: 2 REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL--DR 59
Query: 619 KSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI 657
++ G GY V++ T + A++ L L I
Sbjct: 60 RT-GY--LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 95
Score = 41.1 bits (97), Expect = 1e-04
Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 6/76 (7%)
Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 502
I+ V + D+ F +G++ + + TG LVE+ +A+AA
Sbjct: 25 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84
Query: 503 LAYTKFKEVPLYLEWA 518
L P+ ++W
Sbjct: 85 LNGQDLMGQPISVDWC 100
>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 = 86.6 bits (215), Expect = 1e-20
Identities = 26/91 (28%), Positives = 48/91 (52%)
Query: 328 QFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLM 387
+ A R++V +L + +TED L +FE +G + + L +D ET ++KG+ +TF
Sbjct: 18 NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 77
Query: 388 PEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
E A +A + L+G GR + + + +
Sbjct: 78 SECAKKALEQLNGFELAGRPMKVGHVTERTD 108
Score = 68.5 bits (168), Expect = 3e-14
Identities = 21/109 (19%), Positives = 49/109 (44%), Gaps = 7/109 (6%)
Query: 661 RSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK 720
+ + A +++ S+ ++ V ++ F + + +F+ FG ++ ++L
Sbjct: 7 HHSHMAAAMANNLQKGSAG-----PMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMD 61
Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
+G +G+GF+ F AK+A++ L L GR + + E +
Sbjct: 62 SE-TGRSKGYGFITFSDSECAKKALEQL-NGFELAGRPMKVGHVTERTD 108
Score = 56.9 bits (138), Expect = 3e-10
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 5/80 (6%)
Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
++ LY+ +L+FN TED +R F+ G I S+ + D ++ G+ S GYGF+
Sbjct: 20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLM--MDSET-GR--SKGYGFIT 74
Query: 634 FYTRESLNQALKVLQNSSLD 653
F E +AL+ L L
Sbjct: 75 FSDSECAKKALEQLNGFELA 94
Score = 46.9 bits (112), Expect = 1e-06
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ IT++ L+ FE G + +QL +E G+ + + FI + + A+ AL+ N +
Sbjct: 36 FNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAG 95
Query: 86 SRIKV 90
+KV
Sbjct: 96 RPMKV 100
Score = 41.1 bits (97), Expect = 1e-04
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 6/60 (10%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
+ V +L + L+ +FEPFG + + + TG + F AK A L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
>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 = 85.6 bits (213), Expect = 2e-20
Identities = 25/84 (29%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
A++ I+V N+ Y T ++L F G + V + DK + KGFA + F E
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKE 417
+ LD ++F GR + +IP +
Sbjct: 64 SLA-LDESLFRGRQIKVIPKRTNR 86
Score = 64.1 bits (157), Expect = 6e-13
Identities = 25/92 (27%), Positives = 44/92 (47%), Gaps = 14/92 (15%)
Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD---PKSPGQFLSMGYGFVQF 634
++Y+ N+++ +T + + HF CG + VT+ K PK G+ +++F
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPK--------GFAYIEF 55
Query: 635 YTRESLNQALKVLQNSSLDEHQI--ELKRSNR 664
+ES+ +L L S QI KR+NR
Sbjct: 56 SDKESVRTSLA-LDESLFRGRQIKVIPKRTNR 86
Score = 60.6 bits (148), Expect = 1e-11
Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 5/81 (6%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGSGLHRGFGFVEFITKNEAKRAM 745
I V N+ + A E+E F G + V + K SG +GF ++EF K + ++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF--SGHPKGFAYIEFSDKESVRTSL 65
Query: 746 KALCQSTHLYGRRLVLEWAEE 766
AL +S GR++ +
Sbjct: 66 -ALDESL-FRGRQIKVIPKRT 84
Score = 43.7 bits (104), Expect = 1e-05
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 9/74 (12%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
Y T E+L+A F G+V V + K++ G + FA+I + ++ + +L + +
Sbjct: 16 YGATAEELEAHFHGCGSVNRVTILCDKFS--GHPKGFAYIEFSDKESVRTSLAL--DESL 71
Query: 84 FSSR-IKV-EKCSN 95
F R IKV K +N
Sbjct: 72 FRGRQIKVIPKRTN 85
Score = 41.7 bits (99), Expect = 5e-05
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 6/61 (9%)
Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKA 498
R I V N+ Y +L+A F G + RV + +G +EF K +
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63
Query: 499 A 499
+
Sbjct: 64 S 64
Score = 31.3 bits (72), Expect = 0.20
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 8/72 (11%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASV-----RTT--FLGMAYIGFKDEKNCNKALNK 277
+I V N+ G ++L+A+F + V + + G AYI F D+++ +L
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 67
Query: 278 NKSFWKGKQLNI 289
++S ++G+Q+ +
Sbjct: 68 DESLFRGRQIKV 79
>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 = 85.4 bits (212), Expect = 2e-20
Identities = 20/86 (23%), Positives = 40/86 (46%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
S +++ ++ Y TE+ + L GP+ + + D +T ++KG+A + F E + A
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 396 QHLDGTVFLGRMLHLIPGKPKENEGN 421
++L+G R L + G
Sbjct: 62 RNLNGYQLGSRFLKCGYSSNSDISGV 87
Score = 68.0 bits (167), Expect = 3e-14
Identities = 15/95 (15%), Positives = 40/95 (42%), Gaps = 2/95 (2%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ + +IP+ + ++ +L G + +++ +G +G+ F+EF + A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQ-TGRSKGYAFIEFRDLESSASAV 61
Query: 746 KALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRY 780
+ L L R L ++ +D + + +
Sbjct: 62 RNL-NGYQLGSRFLKCGYSSNSDISGVSLEHHHHH 95
Score = 56.1 bits (136), Expect = 5e-10
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
P +Y+ ++ ++ TE+ I GP+ ++ + DP++ G+ S GY F++F E
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMF--DPQT-GR--SKGYAFIEFRDLE 55
Query: 639 SLNQALKVLQNSSLDEHQI 657
S A++ L L +
Sbjct: 56 SSASAVRNLNGYQLGSRFL 74
Score = 49.9 bits (120), Expect = 7e-08
Identities = 16/83 (19%), Positives = 36/83 (43%), Gaps = 1/83 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y T+EQ+ G V ++++ + + G+ + +AFI + + + +A+ N + S
Sbjct: 12 YDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGS 71
Query: 86 SRIKVEKCSNLGDTTKPKSWSKY 108
+K SN + +
Sbjct: 72 RFLKCGYSSNSDISGVSLEHHHH 94
Score = 33.7 bits (78), Expect = 0.037
Identities = 11/62 (17%), Positives = 24/62 (38%), Gaps = 6/62 (9%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFN 501
R++ + ++PY + L G + + + TG +EF + +A
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 502 SL 503
+L
Sbjct: 63 NL 64
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 86.8 bits (215), Expect = 3e-20
Identities = 22/100 (22%), Positives = 41/100 (41%), Gaps = 1/100 (1%)
Query: 309 NASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVIL 368
+ S ++V L+ V + L F +G + ++ +
Sbjct: 37 TCVNCTERHVDGGSGGSGGSGGSA-TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 95
Query: 369 PIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRML 408
P+D ET+K +GFA V F + E A A +++ + GR +
Sbjct: 96 PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI 135
Score = 76.0 bits (187), Expect = 2e-16
Identities = 22/104 (21%), Positives = 43/104 (41%), Gaps = 2/104 (1%)
Query: 661 RSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK 720
+ + + S + T + V + + + F FG++ +++P
Sbjct: 39 VNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD 98
Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
+ HRGF FVEF +A A+ + +S L+GR + + A
Sbjct: 99 YE-TEKHRGFAFVEFELAEDAAAAIDNMNESE-LFGRTIRVNLA 140
Score = 60.2 bits (146), Expect = 5e-11
Identities = 15/100 (15%), Positives = 30/100 (30%), Gaps = 5/100 (5%)
Query: 554 AEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA 613
+ + + LY+ L + + F G I + +
Sbjct: 37 TCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIP 96
Query: 614 RKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLD 653
D ++ + G+ FV+F E A+ + S L
Sbjct: 97 --LDYET-EK--HRGFAFVEFELAEDAAAAIDNMNESELF 131
Score = 49.8 bits (119), Expect = 2e-07
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
++ + L A F G +TD+Q+ E K R FAF+ + + A AA+D N + +F
Sbjct: 73 EEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG 132
Query: 86 SRIKVEK 92
I+V
Sbjct: 133 RTIRVNL 139
Score = 44.0 bits (104), Expect = 2e-05
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 496
A +KR++ V L L A F PFGD+ + +P T VEF A
Sbjct: 59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 118
Query: 497 KAAFNSL 503
AA +++
Sbjct: 119 AAAIDNM 125
>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 = 85.3 bits (212), Expect = 3e-20
Identities = 23/88 (26%), Positives = 44/88 (50%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
++V L+ V + L F +G + ++ +P+D ET+K +GFA V F + E A
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGN 421
A +++ + GR + + KP + +
Sbjct: 70 AIDNMNESELFGRTIRVNLAKPMRIKES 97
Score = 71.1 bits (175), Expect = 3e-15
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 2/81 (2%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ V + + + F FG++ +++P + HRGF FVEF +A A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-TEKHRGFAFVEFELAEDAAAAI 71
Query: 746 KALCQSTHLYGRRLVLEWAEE 766
+ + L+GR + + A+
Sbjct: 72 DNM-NESELFGRTIRVNLAKP 91
Score = 54.9 bits (133), Expect = 1e-09
Identities = 15/76 (19%), Positives = 27/76 (35%), Gaps = 5/76 (6%)
Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
LY+ L + + F G I + + D ++ + G+ FV+F
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIP--LDYET-EK--HRGFAFVEFELA 64
Query: 638 ESLNQALKVLQNSSLD 653
E A+ + S L
Sbjct: 65 EDAAAAIDNMNESELF 80
Score = 48.4 bits (116), Expect = 3e-07
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
++ + L A F G +TD+Q+ E K R FAF+ + + A AA+D N + +F
Sbjct: 22 EEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG 81
Query: 86 SRIKVEK 92
I+V
Sbjct: 82 RTIRVNL 88
Score = 43.7 bits (104), Expect = 1e-05
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 496
A +KR++ V L L A F PFGD+ + +P T VEF A
Sbjct: 8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67
Query: 497 KAAFNSL 503
AA +++
Sbjct: 68 AAAIDNM 74
>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 = 88.4 bits (219), Expect = 4e-20
Identities = 43/207 (20%), Positives = 78/207 (37%), Gaps = 29/207 (14%)
Query: 450 ILVKNL-PYRTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTK 507
+LV NL P R P L LF +GD+ RV + LV+ NQA+ A + L K
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 65
Query: 508 FKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEE 567
P+ + + K++ E ++ + ++ + ++
Sbjct: 66 LHGKPIRITLS------------------KHQNVQLPREGQEDQGLTKDYGNSPLHRFKK 107
Query: 568 NVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 627
++ + P TL++ N+ + +E+ ++ F G + +KD
Sbjct: 108 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR--------- 158
Query: 628 GYGFVQFYTRESLNQALKVLQNSSLDE 654
+Q + E QAL L N L E
Sbjct: 159 KMALIQMGSVEEAVQALIDLHNHDLGE 185
Score = 81.9 bits (202), Expect = 6e-18
Identities = 32/208 (15%), Positives = 59/208 (28%), Gaps = 39/208 (18%)
Query: 580 DTTLYIKNLN-FNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
++ L + NLN T S+ F G + V + K VQ
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----------KENALVQMADGN 52
Query: 639 SLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSK----------- 687
A+ L L I + S + S
Sbjct: 53 QAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKN 112
Query: 688 ----------ILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFI 736
+ + NIP + +++ LF + G +K + +K R ++
Sbjct: 113 FQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK------DRKMALIQMG 166
Query: 737 TKNEAKRAMKALCQSTHLYGRRLVLEWA 764
+ EA +A+ L L + ++
Sbjct: 167 SVEEAVQALIDLHNHDLGENHHLRVSFS 194
Score = 80.3 bits (198), Expect = 2e-17
Identities = 43/197 (21%), Positives = 66/197 (33%), Gaps = 19/197 (9%)
Query: 336 SGRIFVRNLS-YTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+ + V NL+ VT L LF YG + V + +K K ALV A A
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLA 57
Query: 395 YQHLDGTVFLGRMLHLIPGK----PKENEGNVDGKVHCCISERKLDAFNQVVEARSKR-- 448
HL+G G+ + + K EG D + L F + +
Sbjct: 58 MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117
Query: 449 ----IILVKNLPYRTLPTDLKALFEPFGDL--GRVLVPPYGITGLVEFLQKNQAKAAFNS 502
+ + N+P DLK LF G + G L++ +A A
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALID 177
Query: 503 LAYTKFKE-VPLYLEWA 518
L E L + ++
Sbjct: 178 LHNHDLGENHHLRVSFS 194
Score = 79.2 bits (195), Expect = 6e-17
Identities = 39/183 (21%), Positives = 66/183 (36%), Gaps = 11/183 (6%)
Query: 225 HTIVVKNL-PAGVKKKDLKAYFKPL-PLASVRTTF--LGMAYIGFKDEKNCNKALNK-NK 279
++V NL P V + L F + V+ F A + D A++ N
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNG 63
Query: 280 SFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAK-HWKSQEDSVQFAEDIAESGR 338
GK + I SK + + ++ + + + H + S F S
Sbjct: 64 HKLHGKPIRI-TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT 122
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ + N+ +V+E+DL LF G ++ K K + AL+ E A QA L
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGG----VVKGFKFFQKDRKMALIQMGSVEEAVQALIDL 178
Query: 399 DGT 401
Sbjct: 179 HNH 181
Score = 45.7 bits (108), Expect = 2e-05
Identities = 20/127 (15%), Positives = 39/127 (30%), Gaps = 17/127 (13%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
++T + L F G V V++ + + A + +QAQ A+ + N +
Sbjct: 15 RVTPQSLFILFGVYGDVQRVKILFNKKE----NALVQMADGNQAQLAMSHLNGHKLHGKP 70
Query: 88 IKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTF 147
I++ + SK+ + + +D K F
Sbjct: 71 IRI-------------TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117
Query: 148 SDFLQLH 154
LH
Sbjct: 118 PPSATLH 124
Score = 39.5 bits (92), Expect = 0.002
Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 4/63 (6%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR- 87
+++E LK F G V + + K A I ++A AL +N + +
Sbjct: 132 VSEEDLKVLFSSNGGVVKGFKFFQKDRKM---ALIQMGSVEEAVQALIDLHNHDLGENHH 188
Query: 88 IKV 90
++V
Sbjct: 189 LRV 191
Score = 29.9 bits (67), Expect = 2.6
Identities = 18/78 (23%), Positives = 28/78 (35%), Gaps = 7/78 (8%)
Query: 223 QYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL----GMAYIGFKDEKNCNKALNK- 277
T+ + N+P V ++DLK F F MA I + +AL
Sbjct: 119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDL 178
Query: 278 -NKSFWKGKQLNIYKYSK 294
N + L + +SK
Sbjct: 179 HNHDLGENHHLRV-SFSK 195
>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 = 85.9 bits (213), Expect = 4e-20
Identities = 22/100 (22%), Positives = 43/100 (43%)
Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
Q+ + E +FV + TE+D+ F +YG + + L +D+ T KG+
Sbjct: 8 EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 67
Query: 382 LVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGN 421
LV + + A A + L+G +G+ + + +
Sbjct: 68 LVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKG 107
Score = 72.0 bits (177), Expect = 3e-15
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 2/82 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G + V + +A + ++ + F +GE+K + L +G +G+ VE+ T EA+ A
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQAA 80
Query: 745 MKALCQSTHLYGRRLVLEWAEE 766
M+ L L G+ + ++W
Sbjct: 81 MEGL-NGQDLMGQPISVDWCFV 101
Score = 54.7 bits (132), Expect = 3e-09
Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 5/80 (6%)
Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
L++ ++ +TE+ I F + G I ++ + D ++ G GY V++ T
Sbjct: 20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL--DRRT-GY--LKGYTLVEYETY 74
Query: 638 ESLNQALKVLQNSSLDEHQI 657
+ A++ L L I
Sbjct: 75 KEAQAAMEGLNGQDLMGQPI 94
Score = 50.8 bits (122), Expect = 7e-08
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+ T+E + KF E G + ++ L + T G + + + Y +AQAA++ N +
Sbjct: 32 EEATEEDIHDKFAEYGEIKNIHLNLDRRT--GYLKGYTLVEYETYKEAQAAMEGLNGQDL 89
Query: 84 FSSRIKVEKC 93
I V+ C
Sbjct: 90 MGQPISVDWC 99
Score = 42.4 bits (100), Expect = 6e-05
Identities = 15/77 (19%), Positives = 29/77 (37%), Gaps = 8/77 (10%)
Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAAFN 501
I+ V + D+ F +G++ + + G LVE+ +A+AA
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY-TLVEYETYKEAQAAME 82
Query: 502 SLAYTKFKEVPLYLEWA 518
L P+ ++W
Sbjct: 83 GLNGQDLMGQPISVDWC 99
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 85.5 bits (212), Expect = 4e-20
Identities = 26/96 (27%), Positives = 43/96 (44%), Gaps = 8/96 (8%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAE--------VILPIDKETDKTKGFAL 382
+D +++ IFV+ L VT + + F++ G + + L D+ET K KG A
Sbjct: 2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61
Query: 383 VTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
V+F P A A DG F G + + + +
Sbjct: 62 VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRAD 97
Score = 57.8 bits (140), Expect = 2e-10
Identities = 17/89 (19%), Positives = 33/89 (37%), Gaps = 7/89 (7%)
Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP-----GQFLSMG 628
E++ + T++++ L N T +S+ +FK+ G I + + G+ G
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK--LKG 58
Query: 629 YGFVQFYTRESLNQALKVLQNSSLDEHQI 657
V F S A+ + I
Sbjct: 59 EATVSFDDPPSAKAAIDWFDGKEFSGNPI 87
Score = 54.7 bits (132), Expect = 3e-09
Identities = 17/89 (19%), Positives = 29/89 (32%), Gaps = 10/89 (11%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKF--------VRLPKKMVGSGLHRGFGFVEFIT 737
+ I V+ + V + FK G +K + L +G +G V F
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRE-TGKLKGEATVSFDD 66
Query: 738 KNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
AK A+ G + + +A
Sbjct: 67 PPSAKAAIDWF-DGKEFSGNPIKVSFATR 94
Score = 43.9 bits (104), Expect = 1e-05
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 9/75 (12%)
Query: 27 YKITQEQLKAKFEEKGTVT--------DVQLKYTTE-GKFRRFAFIGYHREDQAQAALDY 77
+T E + F++ G + + L E GK + A + + A+AA+D+
Sbjct: 17 ENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDW 76
Query: 78 FNNTYVFSSRIKVEK 92
F+ + IKV
Sbjct: 77 FDGKEFSGNPIKVSF 91
Score = 27.7 bits (62), Expect = 5.6
Identities = 17/109 (15%), Positives = 28/109 (25%), Gaps = 22/109 (20%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------------GLVEFLQKNQ 495
I V+ L + F+ G + + V F
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 496 AKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEE 544
AKAA + +F P+ + A ++ N G E
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVS--------FATRRADFNRGGGNGRGGLE 110
>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 = 84.8 bits (210), Expect = 6e-20
Identities = 29/107 (27%), Positives = 50/107 (46%), Gaps = 8/107 (7%)
Query: 323 QEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAE--------VILPIDKET 374
S ++ +++ I+V+ L+ +VT DDL F++ G + + + +DKET
Sbjct: 2 SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61
Query: 375 DKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGN 421
K KG A V++ P A A + DG F G L + + K +
Sbjct: 62 GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 108
Score = 55.1 bits (133), Expect = 2e-09
Identities = 14/105 (13%), Positives = 36/105 (34%), Gaps = 7/105 (6%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP-----GQF 624
+ E ++ +Y++ LN + T D + FK+CG + + G+
Sbjct: 5 SSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGK- 63
Query: 625 LSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESE 669
G V + + A++ ++++ + +
Sbjct: 64 -PKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 107
Score = 54.0 bits (130), Expect = 5e-09
Identities = 17/92 (18%), Positives = 32/92 (34%), Gaps = 8/92 (8%)
Query: 682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELK---FVRLPK-KMV---GSGLHRGFGFVE 734
S I V+ + ++ + FK G +K P + +G +G V
Sbjct: 12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 71
Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
+ AK A++ G +L + A +
Sbjct: 72 YEDPPTAKAAVEWF-DGKDFQGSKLKVSLARK 102
Score = 46.2 bits (110), Expect = 2e-06
Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 9/75 (12%)
Query: 27 YKITQEQLKAKFEEKGTVT--------DVQLKYTTE-GKFRRFAFIGYHREDQAQAALDY 77
+T + L F++ G V + + E GK + A + Y A+AA+++
Sbjct: 25 DSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEW 84
Query: 78 FNNTYVFSSRIKVEK 92
F+ S++KV
Sbjct: 85 FDGKDFQGSKLKVSL 99
Score = 29.7 bits (67), Expect = 1.3
Identities = 16/90 (17%), Positives = 23/90 (25%), Gaps = 14/90 (15%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------------GLV 488
E I V+ L DL F+ G + + V
Sbjct: 11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70
Query: 489 EFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 518
+ AKAA F+ L + A
Sbjct: 71 SYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 100
>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 = 85.0 bits (211), Expect = 6e-20
Identities = 25/83 (30%), Positives = 42/83 (50%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
+ ++++NLS VTE DL LF ++ + T + +G A +TF E A QA
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
Query: 396 QHLDGTVFLGRMLHLIPGKPKEN 418
++G G++L + GK K+
Sbjct: 85 HLVNGYKLYGKILVIEFGKNKKQ 107
Score = 72.7 bits (179), Expect = 1e-15
Identities = 25/103 (24%), Positives = 47/103 (45%), Gaps = 2/103 (1%)
Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM 721
S+ + E + SS + + ++N+ + + ++ LF F E K + +M
Sbjct: 2 SSGSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM 61
Query: 722 VGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
+G RG F+ F K A +A+ + LYG+ LV+E+
Sbjct: 62 -MTGRMRGQAFITFPNKEIAWQALHLV-NGYKLYGKILVIEFG 102
Score = 59.6 bits (145), Expect = 5e-11
Identities = 18/95 (18%), Positives = 35/95 (36%), Gaps = 5/95 (5%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
EP+ LY+KNL+ TE + F + + + + G F+ F
Sbjct: 22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPI--QFRMMTG---RMRGQAFITFPN 76
Query: 637 RESLNQALKVLQNSSLDEHQIELKRSNRNLESEAT 671
+E QAL ++ L + ++ + +
Sbjct: 77 KEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSSG 111
Score = 49.2 bits (118), Expect = 2e-07
Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 1/66 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
++T+ L + F +++ G+ R AFI + ++ A AL N ++
Sbjct: 35 PRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYG 94
Query: 86 SRIKVE 91
+ +E
Sbjct: 95 KILVIE 100
Score = 45.0 bits (107), Expect = 7e-06
Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 6/92 (6%)
Query: 433 RKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL----- 487
RK+ F+ +++ +KNL R DL +LF F + + +TG
Sbjct: 11 RKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQA 70
Query: 488 -VEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 518
+ F K A A + + K L +E+
Sbjct: 71 FITFPNKEIAWQALHLVNGYKLYGKILVIEFG 102
Score = 34.6 bits (80), Expect = 0.023
Identities = 24/111 (21%), Positives = 44/111 (39%), Gaps = 10/111 (9%)
Query: 201 SKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTFL- 258
S ++ + P+ + + +KNL V ++DL + F F
Sbjct: 2 SSGSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM 61
Query: 259 ------GMAYIGFKDEKNCNKALNK-NKSFWKGKQLNIYKYSKDNSAKYSG 302
G A+I F +++ +AL+ N GK L I ++ K+ + SG
Sbjct: 62 MTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVI-EFGKNKKQRSSG 111
>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 = 83.7 bits (208), Expect = 8e-20
Identities = 21/74 (28%), Positives = 39/74 (52%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
++V L+ V + L F +G + ++ +P+D ET+K +GFA V F + E A A
Sbjct: 6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65
Query: 395 YQHLDGTVFLGRML 408
+++ + GR +
Sbjct: 66 IDNMNESELFGRTI 79
Score = 73.3 bits (181), Expect = 3e-16
Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 2/82 (2%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
T + V + + + F FG++ +++P + HRGF FVEF +A
Sbjct: 6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-TEKHRGFAFVEFELAEDAAA 64
Query: 744 AMKALCQSTHLYGRRLVLEWAE 765
A+ + + L+GR + + A+
Sbjct: 65 AIDNM-NESELFGRTIRVNLAK 85
Score = 54.1 bits (131), Expect = 2e-09
Identities = 15/76 (19%), Positives = 27/76 (35%), Gaps = 5/76 (6%)
Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
LY+ L + + F G I + + D ++ + G+ FV+F
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIP--LDYET-EK--HRGFAFVEFELA 59
Query: 638 ESLNQALKVLQNSSLD 653
E A+ + S L
Sbjct: 60 EDAAAAIDNMNESELF 75
Score = 49.1 bits (118), Expect = 9e-08
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
++ + L A F G +TD+Q+ E K R FAF+ + + A AA+D N + +F
Sbjct: 17 EEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG 76
Query: 86 SRIKVEK 92
I+V
Sbjct: 77 RTIRVNL 83
Score = 44.4 bits (106), Expect = 5e-06
Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAK 497
A +KR++ V L L A F PFGD+ + +P T VEF A
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63
Query: 498 AAFNSL 503
AA +++
Sbjct: 64 AAIDNM 69
>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 = 84.3 bits (209), Expect = 1e-19
Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 3/91 (3%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+ +++RNL Y +T +++ +F KYGP+ ++ + +T+G A V + A A
Sbjct: 7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNA 63
Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGNVDGK 425
HL G R L ++ +D K
Sbjct: 64 VDHLSGFNVSNRYLVVLYYNANRAFQKMDTK 94
Score = 71.2 bits (175), Expect = 4e-15
Identities = 19/108 (17%), Positives = 45/108 (41%), Gaps = 13/108 (12%)
Query: 683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 742
+ + +RN+P++ E+ ++F +G ++ +R+ + RG +V + +AK
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN----TPETRGTAYVVYEDIFDAK 61
Query: 743 RAMKALCQSTHLYGRRLVLEWAEEADNVEDIR--------KRTNRYFG 782
A+ L ++ R LV+ + + + K +G
Sbjct: 62 NAVDHL-SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYG 108
Score = 65.5 bits (160), Expect = 3e-13
Identities = 23/107 (21%), Positives = 41/107 (38%), Gaps = 8/107 (7%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
PE + LYI+NL + T + + F K GPI + V P++ G +V +
Sbjct: 5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETR------GTAYVVYED 56
Query: 637 RESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQ 683
A+ L ++ + + N N + K+K +
Sbjct: 57 IFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLL 103
Score = 55.5 bits (134), Expect = 1e-09
Identities = 22/107 (20%), Positives = 44/107 (41%), Gaps = 5/107 (4%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQAKAAFNSLA 504
RI+ ++NLPY+ ++ +F +G + ++ V T V + AK A + L+
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 505 YTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEE--GEEGEEEK 549
L + + + + K +E+ K +E G + K
Sbjct: 69 GFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK 115
Score = 49.7 bits (119), Expect = 1e-07
Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
YKIT E++ F + G + +++ T + R A++ Y A+ A+D+ + V +
Sbjct: 18 YKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNR 75
Query: 87 RIKVE 91
+ V
Sbjct: 76 YLVVL 80
Score = 27.7 bits (62), Expect = 5.8
Identities = 11/58 (18%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTFL----GMAYIGFKDEKNCNKALNK 277
+ ++NLP + +++ F P+ +R G AY+ ++D + A++
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDH 66
>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 = 83.1 bits (206), Expect = 2e-19
Identities = 25/88 (28%), Positives = 38/88 (43%), Gaps = 8/88 (9%)
Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAE--------VILPIDKETDKTKGFA 381
+++ IFV+ L VT + + F++ G + + L D+ET K KG A
Sbjct: 7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 66
Query: 382 LVTFLMPEHATQAYQHLDGTVFLGRMLH 409
V+F P A A DG F G +
Sbjct: 67 TVSFDDPPSAKAAIDWFDGKEFSGNPIK 94
Score = 56.2 bits (136), Expect = 4e-10
Identities = 16/93 (17%), Positives = 30/93 (32%), Gaps = 7/93 (7%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP-----GQF 624
+ T++++ L N T +S+ +FK+ G I + + G+
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK- 61
Query: 625 LSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI 657
G V F S A+ + I
Sbjct: 62 -LKGEATVSFDDPPSAKAAIDWFDGKEFSGNPI 93
Score = 51.2 bits (123), Expect = 3e-08
Identities = 17/97 (17%), Positives = 31/97 (31%), Gaps = 8/97 (8%)
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK---FVRLPK-KMV---GSGLH 727
+ + + I V+ + V + FK G +K P + +G
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62
Query: 728 RGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
+G V F AK A+ G + + +A
Sbjct: 63 KGEATVSFDDPPSAKAAIDWF-DGKEFSGNPIKVSFA 98
Score = 45.8 bits (109), Expect = 2e-06
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 9/75 (12%)
Query: 27 YKITQEQLKAKFEEKGTVTD--------VQLKYTTE-GKFRRFAFIGYHREDQAQAALDY 77
+T E + F++ G + + L E GK + A + + A+AA+D+
Sbjct: 23 ENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDW 82
Query: 78 FNNTYVFSSRIKVEK 92
F+ + IKV
Sbjct: 83 FDGKEFSGNPIKVSF 97
>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 = 87.4 bits (216), Expect = 2e-19
Identities = 41/212 (19%), Positives = 68/212 (32%), Gaps = 10/212 (4%)
Query: 205 APSDPSVPPVSKAPVHKRQYHTIVVKNL-PAGVKKKDLKAYFKPL-PLASVRTTF--LGM 260
P + ++ + ++V NL P V + L F + V+ F
Sbjct: 15 VPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN 74
Query: 261 AYIGFKDEKNCNKALNK-NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKH 319
A + D A++ N GK + I N +D H
Sbjct: 75 ALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLH 134
Query: 320 WKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKG 379
+ S F S + + N+ +V+E+DL LF G ++ K K +
Sbjct: 135 RFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGG----VVKGFKFFQKDRK 190
Query: 380 FALVTFLMPEHATQAYQHLDGT-VFLGRMLHL 410
AL+ E A QA L + L +
Sbjct: 191 MALIQMGSVEEAVQALIDLHNHDLGENHHLRV 222
Score = 87.0 bits (215), Expect = 2e-19
Identities = 46/209 (22%), Positives = 79/209 (37%), Gaps = 29/209 (13%)
Query: 448 RIILVKNL-PYRTLPTDLKALFEPFGDLGRVLVPPYGI-TGLVEFLQKNQAKAAFNSLAY 505
++LV NL P R P L LF +GD+ RV + LV+ NQA+ A + L
Sbjct: 35 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNG 94
Query: 506 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEV 565
K P+ + + + + EG+E + K+ ++ P
Sbjct: 95 HKLHGKPIRITLSK-------------HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGS 141
Query: 566 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
+ + + P TL++ N+ + +E+ ++ F G + +KD
Sbjct: 142 K-----NFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR------- 189
Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDE 654
+Q + E QAL L N L E
Sbjct: 190 --KMALIQMGSVEEAVQALIDLHNHDLGE 216
Score = 83.5 bits (206), Expect = 3e-18
Identities = 32/212 (15%), Positives = 59/212 (27%), Gaps = 39/212 (18%)
Query: 576 EPEPDTTLYIKNLN-FNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
++ L + NLN T S+ F G + V + K VQ
Sbjct: 30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK----------ENALVQM 79
Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSK------- 687
A+ L L I + S + S
Sbjct: 80 ADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKP 139
Query: 688 --------------ILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGF 732
+ + NIP + +++ LF + G +K + +K R
Sbjct: 140 GSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK------DRKMAL 193
Query: 733 VEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
++ + EA +A+ L L + ++
Sbjct: 194 IQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 225
Score = 80.0 bits (197), Expect = 5e-17
Identities = 45/199 (22%), Positives = 66/199 (33%), Gaps = 19/199 (9%)
Query: 334 AESGRIFVRNLS-YTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
A + + V NL+ VT L LF YG + V K K ALV A
Sbjct: 32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQ 86
Query: 393 QAYQHLDGTVFLGRMLHLIPGK----PKENEGNVDGKVHCCISERKLDAFNQVVEARSKR 448
A HL+G G+ + + K EG D + L F + +
Sbjct: 87 LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 146
Query: 449 I------ILVKNLPYRTLPTDLKALFEPFGDL--GRVLVPPYGITGLVEFLQKNQAKAAF 500
I + + N+P DLK LF G + G L++ +A A
Sbjct: 147 IFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQAL 206
Query: 501 NSLAYTKFKE-VPLYLEWA 518
L E L + ++
Sbjct: 207 IDLHNHDLGENHHLRVSFS 225
Score = 41.5 bits (97), Expect = 5e-04
Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 4/77 (5%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
++T + L F G V V++ + + A + +QAQ A+ + N +
Sbjct: 46 RVTPQSLFILFGVYGDVQRVKILFNKKE----NALVQMADGNQAQLAMSHLNGHKLHGKP 101
Query: 88 IKVEKCSNLGDTTKPKS 104
I++ + +
Sbjct: 102 IRITLSKHQNVQLPREG 118
Score = 39.6 bits (92), Expect = 0.002
Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 4/63 (6%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR- 87
+++E LK F G V + + K A I ++A AL +N + +
Sbjct: 163 VSEEDLKVLFSSNGGVVKGFKFFQKDRKM---ALIQMGSVEEAVQALIDLHNHDLGENHH 219
Query: 88 IKV 90
++V
Sbjct: 220 LRV 222
>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 = 85.5 bits (211), Expect = 4e-19
Identities = 26/194 (13%), Positives = 61/194 (31%), Gaps = 35/194 (18%)
Query: 579 PDTTLYIKNLN-FNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
L + L+ D + F G + V + K G V+
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP----------GAAMVEMADG 52
Query: 638 ESLNQALKVLQNSSLDEHQIELKRSNRNLESEA-----------------------TTVK 674
++++A+ L N+ + ++ + S + +T +
Sbjct: 53 YAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPE 112
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
+ + N + + + N P + + E+ G + + K G G +E
Sbjct: 113 QAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSV-KVFSGKSERSSSGLLE 171
Query: 735 FITKNEAKRAMKAL 748
+ +K++A + L
Sbjct: 172 WDSKSDALETLGFL 185
Score = 84.0 bits (207), Expect = 1e-18
Identities = 24/209 (11%), Positives = 60/209 (28%), Gaps = 23/209 (11%)
Query: 448 RIILVKNLPYRTL-PTDLKALFEPFGDLGRVLVPPYGI-TGLVEFLQKNQAKAAFNSLAY 505
+++V L + + +F +G++ +V +VE A L
Sbjct: 5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNN 64
Query: 506 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEV 565
+ + + K+ G+ E + ++ ++
Sbjct: 65 NFMFGQKMNVCVS----------------KQPAIMPGQSYGLEDGSCSYKDFSESRNNRF 108
Query: 566 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
+ + R P L+ N TE++ + G +V K
Sbjct: 109 STPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSV--KVFSGKSE--- 163
Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDE 654
G +++ ++ + L L + +
Sbjct: 164 RSSSGLLEWDSKSDALETLGFLNHYQMKN 192
Score = 79.7 bits (196), Expect = 4e-17
Identities = 35/196 (17%), Positives = 64/196 (32%), Gaps = 24/196 (12%)
Query: 334 AESGRIFVRNLSY-TVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
A+S + V L + D + +F YG + +V K G A+V
Sbjct: 2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVD 56
Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCC------ISERKLDAFNQVVEARS 446
+A HL+ G+ +++ K + SE + + F+ +A
Sbjct: 57 RAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAK 116
Query: 447 KRI------ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKN 494
RI + N P + + + G V + GL+E+ K+
Sbjct: 117 NRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKS 176
Query: 495 QAKAAFNSLAYTKFKE 510
A L + + K
Sbjct: 177 DALETLGFLNHYQMKN 192
Score = 79.7 bits (196), Expect = 4e-17
Identities = 25/188 (13%), Positives = 58/188 (30%), Gaps = 7/188 (3%)
Query: 226 TIVVKNL-PAGVKKKDLKAYFKPL-PLASVRTTF--LGMAYIGFKDEKNCNKA---LNKN 278
++V L + + + F + V+ G A + D ++A LN N
Sbjct: 6 VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNN 65
Query: 279 KSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGR 338
F + + + K + G D + + + + S + S
Sbjct: 66 FMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNV 125
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ N VTE++ ++ ++ G + + + L+ + A + L
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185
Query: 399 DGTVFLGR 406
+
Sbjct: 186 NHYQMKNP 193
Score = 44.3 bits (104), Expect = 4e-05
Identities = 8/64 (12%), Positives = 23/64 (35%), Gaps = 1/64 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLK-YTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
+T+E +E G +K ++ + + + + + A L + N+ + +
Sbjct: 135 VTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPN 194
Query: 88 IKVE 91
Sbjct: 195 GPYP 198
Score = 41.6 bits (97), Expect = 3e-04
Identities = 18/117 (15%), Positives = 36/117 (30%), Gaps = 6/117 (5%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
K+ +++ F G V V+ + G A + A+ + NN ++F +
Sbjct: 16 KMNCDRVFNVFCLYGNVEKVKFMKSKPG----AAMVEMADGYAVDRAITHLNNNFMFGQK 71
Query: 88 IKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKND 144
+ V P S +Y+ + PE ++ S
Sbjct: 72 MNVCVSKQ--PAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVL 126
>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 = 82.3 bits (204), Expect = 4e-19
Identities = 27/84 (32%), Positives = 42/84 (50%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+FV N+ Y TE+ L +F + GP+ L D+ET K KG+ + E A A
Sbjct: 7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66
Query: 395 YQHLDGTVFLGRMLHLIPGKPKEN 418
++L+G F GR L + ++N
Sbjct: 67 MRNLNGREFSGRALRVDNAASEKN 90
Score = 64.6 bits (158), Expect = 6e-13
Identities = 24/98 (24%), Positives = 47/98 (47%), Gaps = 2/98 (2%)
Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
++ + V NIP++A + +++++F G + RL +G +G+GF E+ +
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR-ETGKPKGYGFCEYQDQET 62
Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTN 778
A AM+ L GR L ++ A N E+++
Sbjct: 63 ALSAMRNL-NGREFSGRALRVDNAASEKNKEELKSLGT 99
Score = 51.5 bits (124), Expect = 2e-08
Identities = 16/84 (19%), Positives = 38/84 (45%), Gaps = 11/84 (13%)
Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD---PKSPGQFLSMGY 629
+ ++++ N+ + +TE+ ++ F + GP+ S + ++ PK GY
Sbjct: 1 DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPK--------GY 52
Query: 630 GFVQFYTRESLNQALKVLQNSSLD 653
GF ++ +E+ A++ L
Sbjct: 53 GFCEYQDQETALSAMRNLNGREFS 76
Score = 48.8 bits (117), Expect = 2e-07
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 1/85 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y+ T+EQLK F E G V +L Y E GK + + F Y ++ A +A+ N
Sbjct: 18 YEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSG 77
Query: 86 SRIKVEKCSNLGDTTKPKSWSKYAP 110
++V+ ++ + + KS AP
Sbjct: 78 RALRVDNAASEKNKEELKSLGTGAP 102
Score = 34.9 bits (81), Expect = 0.018
Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKA 498
RS R + V N+PY LK +F G + + TG E+ + A +
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 499 AFNSL 503
A +L
Sbjct: 66 AMRNL 70
>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 = 81.9 bits (203), Expect = 4e-19
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 4/88 (4%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
ES + + NLSY+ TE+ L ++FEK I + K+KG+A + F E A +
Sbjct: 13 GESKTLVLSNLSYSATEETLQEVFEKATF----IKVPQNQNGKSKGYAFIEFASFEDAKE 68
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGN 421
A + GR + L P+ + +
Sbjct: 69 ALNSCNKREIEGRAIRLELQGPRGSPNS 96
Score = 64.6 bits (158), Expect = 6e-13
Identities = 22/92 (23%), Positives = 44/92 (47%), Gaps = 7/92 (7%)
Query: 676 KSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
S N SK L + N+ + A + ++E+F+ +++P+ +G +G+ F+E
Sbjct: 5 SSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATF---IKVPQNQ--NGKSKGYAFIE 59
Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
F + +AK A+ + + GR + LE
Sbjct: 60 FASFEDAKEALNSC-NKREIEGRAIRLELQGP 90
Score = 61.9 bits (151), Expect = 5e-12
Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 9/84 (10%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
TL + NL++++TE++++ F+K + V + ++ KS GY
Sbjct: 5 SSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATF---IKVPQNQNGKSK------GY 55
Query: 630 GFVQFYTRESLNQALKVLQNSSLD 653
F++F + E +AL ++
Sbjct: 56 AFIEFASFEDAKEALNSCNKREIE 79
Score = 46.1 bits (110), Expect = 2e-06
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 3/66 (4%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
Y T+E L+ FE+ + V GK + +AFI + + A+ AL+ N +
Sbjct: 25 YSATEETLQEVFEKATFI-KVPQNQN--GKSKGYAFIEFASFEDAKEALNSCNKREIEGR 81
Query: 87 RIKVEK 92
I++E
Sbjct: 82 AIRLEL 87
Score = 36.1 bits (84), Expect = 0.005
Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 11/73 (15%)
Query: 437 AFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP------PYGITGLVEF 490
+ N SK ++ + NL Y L+ +FE + VP G +EF
Sbjct: 6 SGNSTWSGESKTLV-LSNLSYSATEETLQEVFEKATF---IKVPQNQNGKSKGY-AFIEF 60
Query: 491 LQKNQAKAAFNSL 503
AK A NS
Sbjct: 61 ASFEDAKEALNSC 73
>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 = 81.2 bits (201), Expect = 8e-19
Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 2/85 (2%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
+ R+ V N+ + + DL ++F ++G + +V + ++ +KGF VTF A +
Sbjct: 13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADR 70
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKEN 418
A + L GTV GR + + +
Sbjct: 71 AREKLHGTVVEGRKIEVNNATARVM 95
Score = 71.9 bits (177), Expect = 2e-15
Identities = 27/90 (30%), Positives = 48/90 (53%), Gaps = 4/90 (4%)
Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
++ +K T ++ V NIPF+ + ++ ++F FG++ V + GS +GFGFV F
Sbjct: 7 GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFVTFE 63
Query: 737 TKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
+A RA + L T + GR++ + A
Sbjct: 64 NSADADRAREKL-HGTVVEGRKIEVNNATA 92
Score = 58.5 bits (142), Expect = 8e-11
Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 7/82 (8%)
Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
L++ N+ F + +R+ F + G I V + + S G+GF
Sbjct: 7 GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-------SKGFGF 59
Query: 632 VQFYTRESLNQALKVLQNSSLD 653
V F ++A + L + ++
Sbjct: 60 VTFENSADADRAREKLHGTVVE 81
Score = 46.5 bits (111), Expect = 1e-06
Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 1/66 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
++ L+ F + G + DV++ + G + F F+ + A A + + T V
Sbjct: 25 FRFRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADADRAREKLHGTVVEGR 83
Query: 87 RIKVEK 92
+I+V
Sbjct: 84 KIEVNN 89
Score = 39.6 bits (93), Expect = 4e-04
Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 12/62 (19%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------GLVEFLQKNQAKAAFN 501
+ V N+P+R DL+ +F FG + V + I G V F A A
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEI----IFNERGSKGFGFVTFENSADADRARE 73
Query: 502 SL 503
L
Sbjct: 74 KL 75
>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 = 81.3 bits (201), Expect = 1e-18
Identities = 20/95 (21%), Positives = 42/95 (44%), Gaps = 1/95 (1%)
Query: 324 EDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
+ E + ++ V NL + V++ D+ +LF ++G L + + D + ++ G A V
Sbjct: 23 DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADV 81
Query: 384 TFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
F A +A + G GR + + + +
Sbjct: 82 HFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 116
Score = 67.0 bits (164), Expect = 2e-13
Identities = 26/92 (28%), Positives = 42/92 (45%), Gaps = 3/92 (3%)
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
+TG+K+LV N+ F ++++ELF FG LK + SG G V
Sbjct: 25 GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR--SGRSLGTADVH 82
Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
F + +A +AMK + L GR + ++
Sbjct: 83 FERRADALKAMKQY-KGVPLDGRPMDIQLVAS 113
Score = 63.2 bits (154), Expect = 3e-12
Identities = 20/98 (20%), Positives = 39/98 (39%), Gaps = 6/98 (6%)
Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
E L + NL+F ++ I+ F + G + V + G+ S+G V
Sbjct: 28 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS----GR--SLGTADV 81
Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEA 670
F R +A+K + LD ++++ ++ E
Sbjct: 82 HFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEH 119
Score = 53.1 bits (128), Expect = 9e-09
Identities = 10/65 (15%), Positives = 26/65 (40%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ ++ ++ F E GT+ + Y G+ A + + R A A+ + +
Sbjct: 45 FGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGR 104
Query: 87 RIKVE 91
+ ++
Sbjct: 105 PMDIQ 109
Score = 42.4 bits (100), Expect = 6e-05
Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 5/76 (6%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSLA 504
+LV NL + D++ LF FG L + V G T V F ++ A A
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 505 YTKFKEVPLYLEWAPE 520
P+ ++
Sbjct: 98 GVPLDGRPMDIQLVAS 113
Score = 32.0 bits (73), Expect = 0.25
Identities = 16/100 (16%), Positives = 30/100 (30%), Gaps = 8/100 (8%)
Query: 198 KTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTT 256
+ ++V NL GV D++ F L
Sbjct: 9 QMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVD 68
Query: 257 F------LGMAYIGFKDEKNCNKALNK-NKSFWKGKQLNI 289
+ LG A + F+ + KA+ + G+ ++I
Sbjct: 69 YDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI 108
>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 = 80.8 bits (200), Expect = 1e-18
Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
G++F+ L+ E L +F K+GP++EV+L D+ T K++GFA +TF P A A
Sbjct: 6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNA 64
Query: 395 YQHLDGTVFLGRML 408
+ ++G G+ +
Sbjct: 65 AKDMNGKSLHGKAI 78
Score = 68.1 bits (167), Expect = 4e-14
Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 6/89 (6%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
E + L+I LN + E ++ F K GPI+ V + + + KS G+ F+ F
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSR------GFAFITFE 56
Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSNR 664
A K + SL I+++++ +
Sbjct: 57 NPADAKNAAKDMNGKSLHGKAIKVEQAKK 85
Score = 63.1 bits (154), Expect = 3e-12
Identities = 22/101 (21%), Positives = 42/101 (41%), Gaps = 3/101 (2%)
Query: 680 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN 739
V K+ + + + + ++ +F G + V L K + RGF F+ F
Sbjct: 2 VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR--TSKSRGFAFITFENPA 59
Query: 740 EAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRY 780
+AK A K + L+G+ + +E A++ R+R
Sbjct: 60 DAKNAAKDM-NGKSLHGKAIKVEQAKKPSFQSGGRRRPPAS 99
Score = 48.9 bits (117), Expect = 3e-07
Identities = 20/66 (30%), Positives = 31/66 (46%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ ++ LKA F + G +++V L K R FAFI + A+ A N +
Sbjct: 17 RETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGK 76
Query: 87 RIKVEK 92
IKVE+
Sbjct: 77 AIKVEQ 82
Score = 37.3 bits (87), Expect = 0.003
Identities = 17/71 (23%), Positives = 24/71 (33%), Gaps = 13/71 (18%)
Query: 442 VEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT---------GLVEFLQ 492
VEA + + L T LKA+F G + VL+ I + F
Sbjct: 2 VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLL----IKDRTSKSRGFAFITFEN 57
Query: 493 KNQAKAAFNSL 503
AK A +
Sbjct: 58 PADAKNAAKDM 68
>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 = 80.0 bits (198), Expect = 1e-18
Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 8/86 (9%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
S ++ V N+S T T +L FE+YGP+ E + K +A V E A +A
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAI 61
Query: 396 QHLDGTVFLGRMLHLIPGKPKENEGN 421
+ LD T F G+ +H+ + +
Sbjct: 62 RGLDNTEFQGKRMHVQLSTSRLRTAS 87
Score = 70.7 bits (174), Expect = 3e-15
Identities = 17/90 (18%), Positives = 37/90 (41%), Gaps = 10/90 (11%)
Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
SS + + +K+ V NI E+ F+ +G + + + + FV
Sbjct: 2 SSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---------KDYAFVHME 52
Query: 737 TKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
+A A++ L +T G+R+ ++ +
Sbjct: 53 RAEDAVEAIRGL-DNTEFQGKRMHVQLSTS 81
Score = 54.9 bits (133), Expect = 1e-09
Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 13/77 (16%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
+ T L++ N++ T +R F++ GP+ + + Y FV
Sbjct: 7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-------------DYAFVHMER 53
Query: 637 RESLNQALKVLQNSSLD 653
E +A++ L N+
Sbjct: 54 AEDAVEAIRGLDNTEFQ 70
Score = 48.4 bits (116), Expect = 2e-07
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
T ++L+AKFEE G V + + + +AF+ R + A A+ +NT
Sbjct: 20 PTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRGLDNTEFQGK 72
Query: 87 RIKVE 91
R+ V+
Sbjct: 73 RMHVQ 77
Score = 39.1 bits (92), Expect = 4e-04
Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 4/75 (5%)
Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSL 503
++ + V N+ +L+A FE +G + +V Y V + A A L
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY---AFVHMERAEDAVEAIRGL 64
Query: 504 AYTKFKEVPLYLEWA 518
T+F+ ++++ +
Sbjct: 65 DNTEFQGKRMHVQLS 79
>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 = 79.8 bits (198), Expect = 2e-18
Identities = 18/83 (21%), Positives = 36/83 (43%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
+ +FV +L+ V ++ L F+ + + D +T ++G+ V+F + A A
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 396 QHLDGTVFLGRMLHLIPGKPKEN 418
+ G GR L + E+
Sbjct: 61 DSMQGQDLNGRPLRINWAAKLEH 83
Score = 60.6 bits (148), Expect = 9e-12
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 2/83 (2%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ V ++ + FK F + M +G RG+GFV F ++++A+ AM
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM-QTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 747 ALCQSTHLYGRRLVLEWAEEADN 769
++ Q L GR L + WA + ++
Sbjct: 62 SM-QGQDLNGRPLRINWAAKLEH 83
Score = 53.7 bits (130), Expect = 2e-09
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ +LN N ++++R FK S V D ++ G S GYGFV F +++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW--DMQT-GS--SRGYGFVSFTSQDDAQN 58
Query: 643 ALKVLQNSSLDEHQI 657
A+ +Q L+ +
Sbjct: 59 AMDSMQGQDLNGRPL 73
Score = 42.1 bits (100), Expect = 3e-05
Identities = 11/65 (16%), Positives = 28/65 (43%), Gaps = 1/65 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ E L+ F++ + + + + G R + F+ + +D AQ A+D +
Sbjct: 11 VNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG 70
Query: 86 SRIKV 90
+++
Sbjct: 71 RPLRI 75
Score = 34.8 bits (81), Expect = 0.011
Identities = 17/75 (22%), Positives = 27/75 (36%), Gaps = 6/75 (8%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
+ V +L L+ F+ F V T G V F ++ A+ A +S+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 504 AYTKFKEVPLYLEWA 518
PL + WA
Sbjct: 64 QGQDLNGRPLRINWA 78
>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 = 80.4 bits (199), Expect = 2e-18
Identities = 21/87 (24%), Positives = 39/87 (44%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+ ++V L V+E L +LF + GP+ +P D+ T + +G+ V FL E A A
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73
Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGN 421
+ +D G+ + + +
Sbjct: 74 IKIMDMIKLYGKPIRVNKASAHNKNLS 100
Score = 72.3 bits (178), Expect = 1e-15
Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 2/81 (2%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ + V + + + + ELF G + +PK V +G H+G+GFVEF+++ +A A+
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRV-TGQHQGYGFVEFLSEEDADYAI 74
Query: 746 KALCQSTHLYGRRLVLEWAEE 766
K + LYG+ + + A
Sbjct: 75 KIM-DMIKLYGKPIRVNKASA 94
Score = 59.6 bits (145), Expect = 4e-11
Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
E D T+Y+ L+ +E + F + GP+ + + + + GYGFV+F
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQ-----HQGYGFVEF 64
Query: 635 YTRESLNQALKVLQNSSLD 653
+ E + A+K++ L
Sbjct: 65 LSEEDADYAIKIMDMIKLY 83
Score = 50.0 bits (120), Expect = 9e-08
Identities = 20/91 (21%), Positives = 40/91 (43%), Gaps = 9/91 (9%)
Query: 6 SGPVVPRNHISLL---DLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFA 61
SGP+ RN + + LD K+++ L F + G V + + G+ + +
Sbjct: 6 SGPISERNQDATVYVGGLD-----EKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60
Query: 62 FIGYHREDQAQAALDYFNNTYVFSSRIKVEK 92
F+ + E+ A A+ + ++ I+V K
Sbjct: 61 FVEFLSEEDADYAIKIMDMIKLYGKPIRVNK 91
Score = 43.0 bits (102), Expect = 2e-05
Identities = 19/88 (21%), Positives = 30/88 (34%), Gaps = 6/88 (6%)
Query: 437 AFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEF 490
+ + E + V L + L LF G + +P +TG VEF
Sbjct: 5 SSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64
Query: 491 LQKNQAKAAFNSLAYTKFKEVPLYLEWA 518
L + A A + K P+ + A
Sbjct: 65 LSEEDADYAIKIMDMIKLYGKPIRVNKA 92
>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 = 79.6 bits (197), Expect = 4e-18
Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
S +FV+ LS TE+ L + F+ + D+ET +KGF V F E A A
Sbjct: 14 PSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGN 421
+ ++ G + L KPK G+
Sbjct: 71 KEAMEDGEIDGNKVTLDWAKPKGEGGS 97
Score = 62.7 bits (153), Expect = 2e-12
Identities = 22/92 (23%), Positives = 43/92 (46%), Gaps = 5/92 (5%)
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
N Q + V+ + + E L ++F R+ +G +GFGFV+
Sbjct: 5 SSGPNARSQPSKTLFVKGLSEDTTE---ETLKESFDGSVRARIVTDRE-TGSSKGFGFVD 60
Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
F ++ +AK A +A+ + + G ++ L+WA+
Sbjct: 61 FNSEEDAKAAKEAM-EDGEIDGNKVTLDWAKP 91
Score = 55.7 bits (135), Expect = 7e-10
Identities = 19/88 (21%), Positives = 42/88 (47%), Gaps = 8/88 (9%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
+P TL++K L+ ++TE++++ F + D ++ G S G+
Sbjct: 5 SSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIV--TDRET-GS--SKGF 56
Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQI 657
GFV F + E A + +++ +D +++
Sbjct: 57 GFVDFNSEEDAKAAKEAMEDGEIDGNKV 84
Score = 39.5 bits (93), Expect = 3e-04
Identities = 13/67 (19%), Positives = 31/67 (46%), Gaps = 4/67 (5%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
T+E LK F+ ++ E G + F F+ ++ E+ A+AA + + +
Sbjct: 25 EDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDG 81
Query: 86 SRIKVEK 92
+++ ++
Sbjct: 82 NKVTLDW 88
Score = 30.3 bits (69), Expect = 0.59
Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 9/60 (15%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
+ VK L T LK E F R + TG V+F + AKAA ++
Sbjct: 18 LFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Score = 27.6 bits (62), Expect = 5.5
Identities = 15/74 (20%), Positives = 27/74 (36%), Gaps = 6/74 (8%)
Query: 222 RQYHTIVVKNLPAGVKKKDLKAYFKPLPLASV---RTT--FLGMAYIGFKDEKNCNKALN 276
+ T+ VK L ++ LK F A + R T G ++ F E++ A
Sbjct: 13 QPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 277 K-NKSFWKGKQLNI 289
G ++ +
Sbjct: 73 AMEDGEIDGNKVTL 86
>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 = 79.7 bits (197), Expect = 4e-18
Identities = 20/98 (20%), Positives = 41/98 (41%), Gaps = 1/98 (1%)
Query: 321 KSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGF 380
+E + + ++ +F L+ + DL F G + +V + D+ + ++KG
Sbjct: 10 PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI 69
Query: 381 ALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
A V F + A L G LG + + + ++N
Sbjct: 70 AYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKN 106
Score = 68.1 bits (167), Expect = 5e-14
Identities = 16/118 (13%), Positives = 34/118 (28%), Gaps = 12/118 (10%)
Query: 558 NQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 617
+ ++ E T++ L + F G + V + ++
Sbjct: 3 SGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN 62
Query: 618 ---PKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATT 672
K G +V+F +S+ A+ L L I ++ S +
Sbjct: 63 SRRSK--------GIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNRLSGP 111
Score = 56.9 bits (138), Expect = 4e-10
Identities = 16/108 (14%), Positives = 42/108 (38%), Gaps = 3/108 (2%)
Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM 721
S+ + + + ++ + + + + ++E+ F A G+++ VR+
Sbjct: 2 SSGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR 61
Query: 722 VGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
S +G +VEF A+ L G ++++ ++ N
Sbjct: 62 N-SRRSKGIAYVEFCEIQSVPLAIG--LTGQRLLGVPIIVQASQAEKN 106
Score = 44.2 bits (105), Expect = 1e-05
Identities = 19/97 (19%), Positives = 39/97 (40%), Gaps = 8/97 (8%)
Query: 201 SKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASV-----R 254
S ++ P PV +R T+ L A ++ +DL+ +F + + V R
Sbjct: 2 SSGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR 61
Query: 255 TT--FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNI 289
+ G+AY+ F + ++ A+ G + +
Sbjct: 62 NSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIV 98
Score = 41.9 bits (99), Expect = 7e-05
Identities = 11/67 (16%), Positives = 23/67 (34%), Gaps = 2/67 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+I L+ F G V DV++ + + A++ + A+ +
Sbjct: 35 ARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLG 93
Query: 86 SRIKVEK 92
I V+
Sbjct: 94 VPIIVQA 100
Score = 38.1 bits (89), Expect = 0.002
Identities = 15/63 (23%), Positives = 21/63 (33%), Gaps = 6/63 (9%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 496
E R R + L R P DL+ F G + V + + VEF +
Sbjct: 21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80
Query: 497 KAA 499
A
Sbjct: 81 PLA 83
>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 = 78.5 bits (194), Expect = 8e-18
Identities = 22/75 (29%), Positives = 31/75 (41%), Gaps = 3/75 (4%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
RI+V NL + D+ +F KYG + ++ L + FA V F P A
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAED 76
Query: 394 AYQHLDGTVFLGRML 408
A DG + G L
Sbjct: 77 AVYGRDGYDYDGYRL 91
Score = 72.0 bits (177), Expect = 2e-15
Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 5/83 (6%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
+I V N+P + ++E++F +G ++ + L + G F FVEF +A+
Sbjct: 21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG----PPFAFVEFEDPRDAED 76
Query: 744 AMKALCQSTHLYGRRLVLEWAEE 766
A+ G RL +E+
Sbjct: 77 AVYGR-DGYDYDGYRLRVEFPRS 98
Score = 64.3 bits (157), Expect = 1e-12
Identities = 18/93 (19%), Positives = 31/93 (33%), Gaps = 10/93 (10%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
D +Y+ NL + I F K G I + + ++ + FV+F
Sbjct: 17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP--------PFAFVEF 68
Query: 635 YTRESLNQALKVLQNSSLDEHQI--ELKRSNRN 665
A+ D +++ E RS R
Sbjct: 69 EDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRG 101
Score = 52.7 bits (127), Expect = 1e-08
Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 2/65 (3%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
I + ++ F + G + D+ LK G FAF+ + A+ A+ +
Sbjct: 32 PDIRTKDIEDVFYKYGAIRDIDLKNRRGG--PPFAFVEFEDPRDAEDAVYGRDGYDYDGY 89
Query: 87 RIKVE 91
R++VE
Sbjct: 90 RLRVE 94
Score = 41.2 bits (97), Expect = 1e-04
Identities = 18/84 (21%), Positives = 31/84 (36%), Gaps = 9/84 (10%)
Query: 444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLV------PPYGITGLVEFLQKNQAK 497
+ I V NLP D++ +F +G + + + PP+ VEF A+
Sbjct: 19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAF---VEFEDPRDAE 75
Query: 498 AAFNSLAYTKFKEVPLYLEWAPEG 521
A + L +E+ G
Sbjct: 76 DAVYGRDGYDYDGYRLRVEFPRSG 99
Score = 27.3 bits (61), Expect = 8.1
Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 6/68 (8%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASV----RTTFLGMAYIGFKDEKNCNKALNK-NK 279
I V NLP ++ KD++ F + + R A++ F+D ++ A+ +
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDG 83
Query: 280 SFWKGKQL 287
+ G +L
Sbjct: 84 YDYDGYRL 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 = 78.1 bits (193), Expect = 8e-18
Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 7/90 (7%)
Query: 331 EDIAESGR-IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
ED S + ++VRNL + +E+ + K F P A K + +A V F E
Sbjct: 9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVE------RVKKIRDYAFVHFSNRE 62
Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
A +A + L+G V G + + KP + +
Sbjct: 63 DAVEAMKALNGKVLDGSPIEVTLAKPVDKD 92
Score = 71.5 bits (176), Expect = 2e-15
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 11/90 (12%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
+E LY++NL +++E+ I + F P A V + + Y
Sbjct: 5 SSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR-----------DY 53
Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIEL 659
FV F RE +A+K L LD IE+
Sbjct: 54 AFVHFSNREDAVEAMKALNGKVLDGSPIEV 83
Score = 65.4 bits (160), Expect = 3e-13
Identities = 24/85 (28%), Positives = 35/85 (41%), Gaps = 9/85 (10%)
Query: 686 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
KIL VRN+ + +E+ F R+ K R + FV F + +A A
Sbjct: 15 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-------IRDYAFVHFSNREDAVEA 67
Query: 745 MKALCQSTHLYGRRLVLEWAEEADN 769
MKAL L G + + A+ D
Sbjct: 68 MKAL-NGKVLDGSPIEVTLAKPVDK 91
Score = 50.7 bits (122), Expect = 5e-08
Identities = 13/65 (20%), Positives = 27/65 (41%), Gaps = 5/65 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
++E ++ +F ++K K R +AF+ + + A A+ N + S
Sbjct: 25 LSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAFVHFSNREDAVEAMKALNGKVLDGS 79
Query: 87 RIKVE 91
I+V
Sbjct: 80 PIEVT 84
Score = 42.6 bits (101), Expect = 3e-05
Identities = 15/73 (20%), Positives = 24/73 (32%)
Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY 505
S +I+ V+NL T ++ F V V F + A A +L
Sbjct: 14 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNG 73
Query: 506 TKFKEVPLYLEWA 518
P+ + A
Sbjct: 74 KVLDGSPIEVTLA 86
Score = 30.7 bits (70), Expect = 0.43
Identities = 12/67 (17%), Positives = 29/67 (43%), Gaps = 3/67 (4%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTFL-GMAYIGFKDEKNCNKALNK-NKSFW 282
+ V+NL ++ ++ F + P A R + A++ F + ++ +A+ N
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVL 76
Query: 283 KGKQLNI 289
G + +
Sbjct: 77 DGSPIEV 83
>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 = 78.5 bits (194), Expect = 8e-18
Identities = 19/96 (19%), Positives = 37/96 (38%), Gaps = 3/96 (3%)
Query: 324 EDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
ED V+ + +F+ NL+ + +L + ++ + +D T + F V
Sbjct: 6 EDPVE-GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYV 63
Query: 384 TFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
F E +A + L G G + L K ++
Sbjct: 64 DFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDGT 98
Score = 70.0 bits (172), Expect = 7e-15
Identities = 19/94 (20%), Positives = 39/94 (41%), Gaps = 7/94 (7%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
+ E E L+I NLN N + ++ + + V + + +
Sbjct: 7 DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGT------NRKF 60
Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKRSN 663
G+V F + E L +AL+ L + ++I+L++
Sbjct: 61 GYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK 93
Score = 57.3 bits (139), Expect = 2e-10
Identities = 13/83 (15%), Positives = 34/83 (40%), Gaps = 4/83 (4%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ + N+ +E++ + + G+ R FG+V+F + + ++A++
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTN--RKFGYVDFESAEDLEKALE 76
Query: 747 ALCQSTHLYGRRLVLEWAEEADN 769
++G + LE + D
Sbjct: 77 L--TGLKVFGNEIKLEKPKGRDG 97
Score = 50.7 bits (122), Expect = 4e-08
Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 1/66 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ +LK E D+ + G R+F ++ + + + AL+ VF +
Sbjct: 27 PNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGN 85
Query: 87 RIKVEK 92
IK+EK
Sbjct: 86 EIKLEK 91
Score = 31.8 bits (73), Expect = 0.18
Identities = 16/90 (17%), Positives = 27/90 (30%), Gaps = 13/90 (14%)
Query: 207 SDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRT-------TFLG 259
DP S P + + NL +LK L + T
Sbjct: 6 EDPVEGSESTTP------FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK 59
Query: 260 MAYIGFKDEKNCNKALNKNKSFWKGKQLNI 289
Y+ F+ ++ KAL G ++ +
Sbjct: 60 FGYVDFESAEDLEKALELTGLKVFGNEIKL 89
Score = 31.1 bits (71), Expect = 0.36
Identities = 15/86 (17%), Positives = 26/86 (30%), Gaps = 12/86 (13%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLV--PPYGIT---GLVEFLQKNQAKAAFNSLAYT 506
+ NL +LK + V G G V+F + A L
Sbjct: 22 IGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGL 80
Query: 507 KFKEVPLYLEWAPEGVFAEAKEKSKG 532
K + LE + ++ ++G
Sbjct: 81 KVFGNEIKLEK------PKGRDGTRG 100
>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 = 78.0 bits (193), Expect = 9e-18
Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
I+V NL Y+ T + + +LF ++G + V L D+ET K KGF V E ++A
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAK 61
Query: 398 LDGTVFLGRMLHLIPGKPKEN 418
LD T F+GR + + PK++
Sbjct: 62 LDNTDFMGRTIRVTEANPKKS 82
Score = 60.6 bits (148), Expect = 9e-12
Identities = 24/94 (25%), Positives = 42/94 (44%), Gaps = 6/94 (6%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
I V N+ + A +V+ELF FG++ V+L + +GFGFVE + A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDR-ETKKPKGFGFVEM-QEESVSEAIA 60
Query: 747 ALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRY 780
L +T GR + + A + + + +
Sbjct: 61 KL-DNTDFMGRTIRVTEANPK---KSLEHHHHHH 90
Score = 42.5 bits (101), Expect = 2e-05
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 6/67 (8%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
Y T EQ+K F + G V +V+L + T K + F F+ +E+ A+ +NT
Sbjct: 11 YSATSEQVKELFSQFGKVFNVKLIYDRET--KKPKGFGFVEM-QEESVSEAIAKLDNTDF 67
Query: 84 FSSRIKV 90
I+V
Sbjct: 68 MGRTIRV 74
Score = 41.4 bits (98), Expect = 6e-05
Identities = 17/76 (22%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
+Y+ NL +++T + ++ F + G + +V + ++ + G+GFV+ ES++
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRE---TKK--PKGFGFVEMQE-ESVS 56
Query: 642 QALKVLQNSSLDEHQI 657
+A+ L N+ I
Sbjct: 57 EAIAKLDNTDFMGRTI 72
Score = 33.3 bits (77), Expect = 0.042
Identities = 17/60 (28%), Positives = 21/60 (35%), Gaps = 7/60 (11%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
I V NL Y +K LF FG + V + T VE Q+ A L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAKL 62
>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 = 78.5 bits (194), Expect = 9e-18
Identities = 23/88 (26%), Positives = 40/88 (45%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
+D + +FV +LS +T +D+ F +G +++ + D T K+KG+ V+F
Sbjct: 10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 69
Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
A A Q + G GR + K
Sbjct: 70 AENAIQQMGGQWLGGRQIRTNWATRKPP 97
Score = 59.7 bits (145), Expect = 4e-11
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ V ++ + +++ F FG + R+ K M +G +G+GFV F K +A+ A++
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMA-TGKSKGYGFVSFFNKWDAENAIQ 75
Query: 747 ALCQSTHLYGRRLVLEWAEE 766
+ L GR++ WA
Sbjct: 76 QM-GGQWLGGRQIRTNWATR 94
Score = 58.9 bits (143), Expect = 7e-11
Identities = 23/113 (20%), Positives = 49/113 (43%), Gaps = 5/113 (4%)
Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
++++ +++ +L+ T + I+ F G I+ V + D + G+ S GYGFV
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVK--DMAT-GK--SKGYGFV 62
Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTG 685
F+ + A++ + L QI + R + +T + + +G
Sbjct: 63 SFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115
Score = 42.7 bits (101), Expect = 3e-05
Identities = 14/65 (21%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+IT E +KA F G ++D ++ GK + + F+ + + A+ A+ ++
Sbjct: 25 PEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG 84
Query: 86 SRIKV 90
+I+
Sbjct: 85 RQIRT 89
Score = 35.8 bits (83), Expect = 0.009
Identities = 19/75 (25%), Positives = 26/75 (34%), Gaps = 6/75 (8%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
+ V +L D+KA F PFG + V T G V F K A+ A +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 504 AYTKFKEVPLYLEWA 518
+ WA
Sbjct: 78 GGQWLGGRQIRTNWA 92
>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 = 77.7 bits (192), Expect = 1e-17
Identities = 20/83 (24%), Positives = 33/83 (39%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
I V+N+ +TV+ D++ F Y + + E G A+V F + AT A
Sbjct: 14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 395 YQHLDGTVFLGRMLHLIPGKPKE 417
L+ R + L+ G
Sbjct: 74 VIDLNDRPIGSRKVKLVLGSGPS 96
Score = 67.7 bits (166), Expect = 4e-14
Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 4/89 (4%)
Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFGFVEF 735
++ K + I V+N+PF E+ + F + + V L G+ G V F
Sbjct: 7 GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE--KGMPTGEAMVAF 64
Query: 736 ITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
+++EA A+ L + R++ L
Sbjct: 65 ESRDEATAAVIDL-NDRPIGSRKVKLVLG 92
Score = 63.1 bits (154), Expect = 2e-12
Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 5/87 (5%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
T + ++N+ F + D I F I +V K + K G G V F +
Sbjct: 12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPG-SVCLKYNEK--GM--PTGEAMVAFES 66
Query: 637 RESLNQALKVLQNSSLDEHQIELKRSN 663
R+ A+ L + + +++L +
Sbjct: 67 RDEATAAVIDLNDRPIGSRKVKLVLGS 93
Score = 51.5 bits (124), Expect = 2e-08
Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ ++ +++ F + V LKY +G A + + D+A AA+ N+ + S
Sbjct: 25 FTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS 84
Query: 86 SRIKVEKCS 94
++K+ S
Sbjct: 85 RKVKLVLGS 93
Score = 43.8 bits (104), Expect = 1e-05
Identities = 13/83 (15%), Positives = 27/83 (32%), Gaps = 9/83 (10%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL--------GMAYIGFKDEKNCNKALN 276
I V+N+P V ++ +F + G A + F+ A+
Sbjct: 16 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75
Query: 277 K-NKSFWKGKQLNIYKYSKDNSA 298
N +++ + S +S
Sbjct: 76 DLNDRPIGSRKVKLVLGSGPSSG 98
Score = 41.1 bits (97), Expect = 8e-05
Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 6/64 (9%)
Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAA 499
II V+N+P+ ++ F + + + Y G +V F +++A AA
Sbjct: 14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 500 FNSL 503
L
Sbjct: 74 VIDL 77
>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 = 78.1 bits (193), Expect = 1e-17
Identities = 20/87 (22%), Positives = 42/87 (48%), Gaps = 1/87 (1%)
Query: 324 EDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
+ + G++ V NL + V++ D+ +LF ++G L + + D + ++ G A V
Sbjct: 17 DSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADV 75
Query: 384 TFLMPEHATQAYQHLDGTVFLGRMLHL 410
F A +A + +G GR +++
Sbjct: 76 HFERKADALKAMKQYNGVPLDGRPMNI 102
Score = 65.8 bits (161), Expect = 3e-13
Identities = 27/91 (29%), Positives = 40/91 (43%), Gaps = 3/91 (3%)
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
+TG K+LV N+ F ++++ELF FG LK + SG G V
Sbjct: 19 GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR--SGRSLGTADVH 76
Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAE 765
F K +A +AMK L GR + ++
Sbjct: 77 FERKADALKAMKQY-NGVPLDGRPMNIQLVT 106
Score = 62.3 bits (152), Expect = 4e-12
Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 6/81 (7%)
Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
E L + NL+F ++ I+ F + G + V + G+ S+G V
Sbjct: 22 GGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS----GR--SLGTADV 75
Query: 633 QFYTRESLNQALKVLQNSSLD 653
F + +A+K LD
Sbjct: 76 HFERKADALKAMKQYNGVPLD 96
Score = 52.7 bits (127), Expect = 1e-08
Identities = 11/65 (16%), Positives = 28/65 (43%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ ++ ++ F E GT+ + Y G+ A + + R+ A A+ +N +
Sbjct: 39 FGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 98
Query: 87 RIKVE 91
+ ++
Sbjct: 99 PMNIQ 103
Score = 41.5 bits (98), Expect = 9e-05
Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 5/59 (8%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSL 503
+LV NL + D++ LF FG L + V G T V F +K A A
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 90
Score = 30.7 bits (70), Expect = 0.45
Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 8/82 (9%)
Query: 216 KAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF------LGMAYIGFKDE 268
++V NL GV D++ F L + LG A + F+ +
Sbjct: 21 GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERK 80
Query: 269 KNCNKALNK-NKSFWKGKQLNI 289
+ KA+ + N G+ +NI
Sbjct: 81 ADALKAMKQYNGVPLDGRPMNI 102
>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 = 77.2 bits (191), Expect = 1e-17
Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 2/82 (2%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGP--LAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
+++ NL++ T++DLT+ G + E+ ++ ++KGFALV + +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 396 QHLDGTVFLGRMLHLIPGKPKE 417
L G+ + P E
Sbjct: 63 DLLPKRELHGQNPVVTPSNKLE 84
Score = 53.4 bits (129), Expect = 3e-09
Identities = 13/82 (15%), Positives = 36/82 (43%), Gaps = 4/82 (4%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
+ + N+ + ++ E + G ++ ++ + +G +GF V ++ +K+
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA-NGQSKGFALVGVGSEASSKKL 61
Query: 745 MKALCQSTHLYGRRLVLEWAEE 766
M L L+G+ V+ + +
Sbjct: 62 MDLL-PKRELHGQNPVVTPSNK 82
Score = 45.7 bits (109), Expect = 2e-06
Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 7/77 (9%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGP--IASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
LYI NL + +T++ + G I + + GQ S G+ V + S
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA---NGQ--SKGFALVGVGSEASS 58
Query: 641 NQALKVLQNSSLDEHQI 657
+ + +L L
Sbjct: 59 KKLMDLLPKRELHGQNP 75
Score = 41.4 bits (98), Expect = 7e-05
Identities = 11/73 (15%), Positives = 25/73 (34%), Gaps = 7/73 (9%)
Query: 27 YKITQEQLKAKFEEKGT--VTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNT 81
+ T E L G + +++ + G+ + FA +G E ++ +D
Sbjct: 11 WWTTDEDLTEAVHSLGVNDILEIKFFENRAN--GQSKGFALVGVGSEASSKKLMDLLPKR 68
Query: 82 YVFSSRIKVEKCS 94
+ V +
Sbjct: 69 ELHGQNPVVTPSN 81
Score = 31.4 bits (72), Expect = 0.22
Identities = 12/62 (19%), Positives = 20/62 (32%), Gaps = 8/62 (12%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFG--DLGRVLVPPYGITG------LVEFLQKNQAKAAFN 501
+ + NL + T DL G D+ + G LV + +K +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 502 SL 503
L
Sbjct: 64 LL 65
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 77.7 bits (192), Expect = 2e-17
Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
E+ ++ R+ V N+ + + DL ++F ++G + +V + ++ +KGF VTF
Sbjct: 24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSAD 81
Query: 391 ATQAYQHLDGTVFLGRML 408
A +A + L GTV GR +
Sbjct: 82 ADRAREKLHGTVVEGRKI 99
Score = 64.6 bits (158), Expect = 6e-13
Identities = 30/108 (27%), Positives = 51/108 (47%), Gaps = 6/108 (5%)
Query: 661 RSNRNLESEATTVKRKSS--NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLP 718
S+ + + V R S K ++ V NIPF+ + ++ ++F FG++ V +
Sbjct: 3 SSHHHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII 62
Query: 719 KKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
GS +GFGFV F +A RA + L T + GR++ + A
Sbjct: 63 FNERGS---KGFGFVTFENSADADRAREKLHG-TVVEGRKIEVNNATA 106
Score = 57.3 bits (139), Expect = 2e-10
Identities = 18/89 (20%), Positives = 35/89 (39%), Gaps = 7/89 (7%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
L++ N+ F + +R+ F + G I V + + S G+
Sbjct: 19 SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-------SKGF 71
Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIE 658
GFV F ++A + L + ++ +IE
Sbjct: 72 GFVTFENSADADRAREKLHGTVVEGRKIE 100
Score = 44.6 bits (106), Expect = 6e-06
Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 1/66 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
++ L+ F + G + DV++ + G + F F+ + A A + + T V
Sbjct: 39 FRFRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADADRAREKLHGTVVEGR 97
Query: 87 RIKVEK 92
+I+V
Sbjct: 98 KIEVNN 103
Score = 39.6 bits (93), Expect = 4e-04
Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 13/79 (16%)
Query: 433 RKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------- 485
+ N +++ KR+ V N+P+R DL+ +F FG + V + I
Sbjct: 16 PRGSHMNTENKSQPKRL-HVSNIPFRFRDPDLRQMFGQFGKILDVEI----IFNERGSKG 70
Query: 486 -GLVEFLQKNQAKAAFNSL 503
G V F A A L
Sbjct: 71 FGFVTFENSADADRAREKL 89
>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 = 76.9 bits (190), Expect = 2e-17
Identities = 21/89 (23%), Positives = 40/89 (44%), Gaps = 5/89 (5%)
Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
++ + + + +NLS+ +TED+L ++FE E+ + + K+KG A + F
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFEDAL---EIR--LVSQDGKSKGIAYIEFKSEA 64
Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
A + + G GR + L K
Sbjct: 65 DAEKNLEEKQGAEIDGRSVSLYYTGEKGG 93
Score = 71.9 bits (177), Expect = 1e-15
Identities = 18/97 (18%), Positives = 47/97 (48%), Gaps = 7/97 (7%)
Query: 670 ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 729
+ ++ ++ + +L +N+ F + E++E+F+ E++ V G +G
Sbjct: 1 SHMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS------QDGKSKG 54
Query: 730 FGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
++EF ++ +A++ ++ Q + GR + L + E
Sbjct: 55 IAYIEFKSEADAEKNLEEK-QGAEIDGRSVSLYYTGE 90
Score = 64.2 bits (157), Expect = 6e-13
Identities = 22/98 (22%), Positives = 40/98 (40%), Gaps = 11/98 (11%)
Query: 567 ENVEEDEEREPEPD-TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
+E+ + TL KNL+FN TED ++ F+ I V+ K
Sbjct: 2 HMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGK---------- 51
Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSN 663
S G +++F + + L+ Q + +D + L +
Sbjct: 52 SKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 89
Score = 44.6 bits (106), Expect = 6e-06
Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 4/66 (6%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ IT+++LK FE+ + V + +GK + A+I + E A+ L+ +
Sbjct: 26 FNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGR 81
Query: 87 RIKVEK 92
+ +
Sbjct: 82 SVSLYY 87
Score = 39.2 bits (92), Expect = 4e-04
Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 11/67 (16%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFG------DLGRVLVPPYGITGLVEFLQKNQA 496
+ R+ R +L KNL + +LK +FE G+ GI +EF + A
Sbjct: 12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGK----SKGI-AYIEFKSEADA 66
Query: 497 KAAFNSL 503
+
Sbjct: 67 EKNLEEK 73
Score = 33.0 bits (76), Expect = 0.057
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 222 RQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTT--FLGMAYIGFKDEKNCNKAL-NK 277
R T++ KNL + + +LK F+ + V G+AYI FK E + K L K
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 278 NKSFWKGKQLNI 289
+ G+ +++
Sbjct: 74 QGAEIDGRSVSL 85
>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 = 78.6 bits (194), Expect = 2e-17
Identities = 29/123 (23%), Positives = 48/123 (39%)
Query: 304 ADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPL 363
D + + + Q + + V + TV E L +LFE+YGP+
Sbjct: 10 YDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI 69
Query: 364 AEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVD 423
V + D+ET +++G+ V F A QA L+G L + L + +
Sbjct: 70 ESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIA 129
Query: 424 GKV 426
G V
Sbjct: 130 GAV 132
Score = 66.7 bits (163), Expect = 3e-13
Identities = 22/123 (17%), Positives = 53/123 (43%), Gaps = 5/123 (4%)
Query: 661 RSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK 720
+ + + + + N ++V IP + ++ +LF+ +G ++ V++
Sbjct: 18 QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77
Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA---EEADNVEDIRKRT 777
+ RG+GFV+F + + A++A+ L ++ +RL + A + +
Sbjct: 78 RE-TRQSRGYGFVKFQSGSSAQQAIAGL-NGFNILNKRLKVALAASGHQRPGIAGAVGDG 135
Query: 778 NRY 780
N Y
Sbjct: 136 NGY 138
Score = 55.5 bits (134), Expect = 3e-09
Identities = 27/102 (26%), Positives = 46/102 (45%), Gaps = 11/102 (10%)
Query: 552 NTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVT 611
++ QQ +P + N EP+ L + + E +R+ F++ GPI SV
Sbjct: 20 QQLQQQQQQHIPPTQMN------PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVK 73
Query: 612 VARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLD 653
+ ++ Q S GYGFV+F + S QA+ L ++
Sbjct: 74 IVCDRE---TRQ--SRGYGFVKFQSGSSAQQAIAGLNGFNIL 110
Score = 46.7 bits (111), Expect = 2e-06
Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 5/67 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+ + QL+ FE G + V++ + T + R + F+ + AQ A+ N +
Sbjct: 52 TTVDEVQLRQLFERYGPIESVKIVCDRET--RQSRGYGFVKFQSGSSAQQAIAGLNGFNI 109
Query: 84 FSSRIKV 90
+ R+KV
Sbjct: 110 LNKRLKV 116
Score = 35.9 bits (83), Expect = 0.012
Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 6/60 (10%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 503
++V +P L+ LFE +G + V + T V+F + A+ A L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 79.5 bits (196), Expect = 2e-17
Identities = 20/95 (21%), Positives = 42/95 (44%), Gaps = 1/95 (1%)
Query: 324 EDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
+ E + ++ V NL + V++ D+ +LF ++G L + + D + ++ G A V
Sbjct: 76 DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADV 134
Query: 384 TFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
F A +A + G GR + + + +
Sbjct: 135 HFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 169
Score = 70.6 bits (173), Expect = 3e-14
Identities = 26/107 (24%), Positives = 44/107 (41%), Gaps = 3/107 (2%)
Query: 660 KRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPK 719
+ + +TG+K+LV N+ F ++++ELF FG LK +
Sbjct: 63 PKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDY 122
Query: 720 KMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
SG G V F + +A +AMK + L GR + ++
Sbjct: 123 D--RSGRSLGTADVHFERRADALKAMKQY-KGVPLDGRPMDIQLVAS 166
Score = 63.7 bits (155), Expect = 8e-12
Identities = 20/96 (20%), Positives = 39/96 (40%), Gaps = 6/96 (6%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
E L + NL+F ++ I+ F + G + V + G+ S+G V F
Sbjct: 83 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS----GR--SLGTADVHF 136
Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEA 670
R +A+K + LD ++++ ++ E
Sbjct: 137 ERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEH 172
Score = 58.3 bits (141), Expect = 5e-10
Identities = 10/65 (15%), Positives = 26/65 (40%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ ++ ++ F E GT+ + Y G+ A + + R A A+ + +
Sbjct: 98 FGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGR 157
Query: 87 RIKVE 91
+ ++
Sbjct: 158 PMDIQ 162
Score = 46.4 bits (110), Expect = 7e-06
Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 5/76 (6%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSLA 504
+LV NL + D++ LF FG L + V G T V F ++ A A
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 505 YTKFKEVPLYLEWAPE 520
P+ ++
Sbjct: 151 GVPLDGRPMDIQLVAS 166
Score = 40.2 bits (94), Expect = 8e-04
Identities = 17/98 (17%), Positives = 30/98 (30%), Gaps = 8/98 (8%)
Query: 200 KSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF- 257
K ++V NL GV D++ F L +
Sbjct: 64 KPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD 123
Query: 258 -----LGMAYIGFKDEKNCNKALNK-NKSFWKGKQLNI 289
LG A + F+ + KA+ + G+ ++I
Sbjct: 124 RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI 161
>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 = 76.9 bits (190), Expect = 3e-17
Identities = 30/87 (34%), Positives = 40/87 (45%), Gaps = 1/87 (1%)
Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
S S F +FV NL V E+ L +LF + GPL +V + D+E K K F
Sbjct: 2 SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFG 60
Query: 382 LVTFLMPEHATQAYQHLDGTVFLGRML 408
V F PE + A L+G GR +
Sbjct: 61 FVCFKHPESVSYAIALLNGIRLYGRPI 87
Score = 69.2 bits (170), Expect = 1e-14
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
+ E D T+++ NL E+ + F + GP+ VT+ + ++ K +GFV
Sbjct: 10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGK------PKSFGFVC 63
Query: 634 FYTRESLNQALKVLQNSSLD 653
F ES++ A+ +L L
Sbjct: 64 FKHPESVSYAIALLNGIRLY 83
Score = 64.2 bits (157), Expect = 7e-13
Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 3/83 (3%)
Query: 682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
++ + V N+ + ++ + ELF G L V + K G + FGFV F
Sbjct: 13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD--REGKPKSFGFVCFKHPESV 70
Query: 742 KRAMKALCQSTHLYGRRLVLEWA 764
A+ L LYGR + +
Sbjct: 71 SYAIALL-NGIRLYGRPINVSGP 92
Score = 56.1 bits (136), Expect = 4e-10
Identities = 16/69 (23%), Positives = 30/69 (43%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
++ +E L F + G +T V + EGK + F F+ + + A+ N ++
Sbjct: 26 ARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGR 85
Query: 87 RIKVEKCSN 95
I V S+
Sbjct: 86 PINVSGPSS 94
Score = 42.6 bits (101), Expect = 3e-05
Identities = 19/85 (22%), Positives = 27/85 (31%), Gaps = 7/85 (8%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP------PYGITGLVEFLQKNQA 496
+ + R + V NL R L LF G L +V + P G V F
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSF-GFVCFKHPESV 70
Query: 497 KAAFNSLAYTKFKEVPLYLEWAPEG 521
A L + P+ + G
Sbjct: 71 SYAIALLNGIRLYGRPINVSGPSSG 95
>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 = 81.8 bits (201), Expect = 3e-17
Identities = 46/329 (13%), Positives = 87/329 (26%), Gaps = 64/329 (19%)
Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTK----LFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+ + I++ NL+ + +D+L K +F ++G + ++++ + K +G A V F
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIF 59
Query: 386 LMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEAR 445
AT A + + G F + + + K S+ VE
Sbjct: 60 KEVSSATNALRSMQGFPFYDKPMRIQYAKTD--------------SDIIAKMKGTFVERD 105
Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY 505
KR K P K + G V + G+ Q +
Sbjct: 106 RKR---EKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMP---- 158
Query: 506 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEV 565
G+
Sbjct: 159 --------------------------GQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMP 192
Query: 566 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
+ E P+ L++ NL + E + F + V + +
Sbjct: 193 GQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH-------- 244
Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDE 654
FV+F A LQ + +
Sbjct: 245 --DIAFVEFDNEVQAGAARDALQGFKITQ 271
Score = 66.1 bits (160), Expect = 7e-12
Identities = 50/329 (15%), Positives = 88/329 (26%), Gaps = 60/329 (18%)
Query: 443 EARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQ 495
E R I + NL + +LK A+F FG + +LV V F + +
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 496 AKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAE 555
A A S+ F + P+ +++A + K K E + E+ K ++
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYA------KTDSDIIAKMKGTFVERDRKREKRKPKSQET 118
Query: 556 EDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK 615
++ V +++ P+
Sbjct: 119 PATKKAVQ-----------------------GGGATPVVGAVQGPVPGMPPMTQAPRIMH 155
Query: 616 KDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKR 675
P P G + Q +
Sbjct: 156 HMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMP------------------P 197
Query: 676 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
+ + N+P + + + LF F K VRL FVEF
Sbjct: 198 AQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG------RHDIAFVEF 251
Query: 736 ITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
+ +A A AL + + +A
Sbjct: 252 DNEVQAGAARDALQGFKITQNNAMKISFA 280
Score = 60.7 bits (146), Expect = 4e-10
Identities = 38/279 (13%), Positives = 88/279 (31%), Gaps = 27/279 (9%)
Query: 27 YKITQEQLK----AKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY 82
KI +++LK A F + G + D+ + + K R AF+ + A AL
Sbjct: 19 EKIKKDELKKSLYAIFSQFGQILDILVSRS--LKMRGQAFVIFKEVSSATNALRSMQGFP 76
Query: 83 VFSSRIKVEKCSNLGDTTKPKSWSKYAPDSSA--YQKLHNIAPKQDLKPEHTKDSKPGKK 140
+ ++++ ++K D A K++ + ++++ KK
Sbjct: 77 FYDKPMRIQ-------------YAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKK 123
Query: 141 SKNDPTFSDFLQLHGKDVSKLLPLSNKDGEEKEEENEDESNNQIAHADISDMEYLKLKTK 200
+ + + V + P++ + + ++
Sbjct: 124 AVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPG 183
Query: 201 SKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLP---LASVRTTF 257
+ P P ++ H + + NLP + L F P +
Sbjct: 184 AMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR 243
Query: 258 LGMAYIGFKDEKNCNKALNK--NKSFWKGKQLNIYKYSK 294
+A++ F +E A + + + I ++K
Sbjct: 244 HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKI-SFAK 281
Score = 57.6 bits (138), Expect = 4e-09
Identities = 18/87 (20%), Positives = 44/87 (50%), Gaps = 9/87 (10%)
Query: 688 ILVRNIPFQAKQSEVEE----LFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
I + N+ + K+ E+++ +F FG++ + + + S RG FV F + A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR----SLKMRGQAFVIFKEVSSATN 67
Query: 744 AMKALCQSTHLYGRRLVLEWAEEADNV 770
A++++ Q Y + + +++A+ ++
Sbjct: 68 ALRSM-QGFPFYDKPMRIQYAKTDSDI 93
Score = 54.9 bits (131), Expect = 3e-08
Identities = 53/324 (16%), Positives = 88/324 (27%), Gaps = 57/324 (17%)
Query: 207 SDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-----PLASVRT----TF 257
+ P P HTI + NL +KK +LK + + +
Sbjct: 2 AVPETRPN----------HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM 51
Query: 258 LGMAYIGFKDEKNCNKALNK-NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIK 316
G A++ FK+ + AL + K + I +Y+K +S + + K
Sbjct: 52 RGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI-QYAKTDSDIIAKMKGTFVERDRKREK 110
Query: 317 AKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDK 376
K + + + A + G V
Sbjct: 111 RKPKSQETPATKKA--------------------------VQGGGATPVVGAVQGPVPGM 144
Query: 377 TKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLD 436
+ Y G + + P + L
Sbjct: 145 PPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAP--GQIPPGAMPPQQLMPGQMPPAQPLS 202
Query: 437 AFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDL-GRVLVPPYGITGLVEFLQKNQ 495
I+ + NLP T L LF F LVP VEF + Q
Sbjct: 203 ENPP------NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQ 256
Query: 496 AKAAFNSLAYTKF-KEVPLYLEWA 518
A AA ++L K + + + +A
Sbjct: 257 AGAARDALQGFKITQNNAMKISFA 280
>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 = 75.8 bits (187), Expect = 5e-17
Identities = 19/76 (25%), Positives = 31/76 (40%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
I V+N+ +TV+ D++ F Y + + E G A+V F + AT A
Sbjct: 14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 395 YQHLDGTVFLGRMLHL 410
L+ R + L
Sbjct: 74 VIDLNDRPIGSRKVKL 89
Score = 65.4 bits (160), Expect = 3e-13
Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 4/89 (4%)
Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEF 735
S+ K + I V+N+PF E+ + F + + V L G+ G V F
Sbjct: 7 GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN--EKGMPTGEAMVAF 64
Query: 736 ITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
+++EA A+ L + R++ L
Sbjct: 65 ESRDEATAAVIDL-NDRPIGSRKVKLSGP 92
Score = 63.9 bits (156), Expect = 9e-13
Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 5/87 (5%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
T + ++N+ F + D I F I V K + K G G V F +
Sbjct: 12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGS-VCLKYNEK--GM--PTGEAMVAFES 66
Query: 637 RESLNQALKVLQNSSLDEHQIELKRSN 663
R+ A+ L + + +++L +
Sbjct: 67 RDEATAAVIDLNDRPIGSRKVKLSGPS 93
Score = 51.5 bits (124), Expect = 2e-08
Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ ++ +++ F + V LKY +G A + + D+A AA+ N+ + S
Sbjct: 25 FTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS 84
Query: 86 SRIKVEKCS 94
++K+ S
Sbjct: 85 RKVKLSGPS 93
Score = 41.5 bits (98), Expect = 7e-05
Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 6/82 (7%)
Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAA 499
+I V+N+P+ ++ F + + + Y G +V F +++A AA
Sbjct: 14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 500 FNSLAYTKFKEVPLYLEWAPEG 521
L + L G
Sbjct: 74 VIDLNDRPIGSRKVKLSGPSSG 95
Score = 41.1 bits (97), Expect = 8e-05
Identities = 12/79 (15%), Positives = 25/79 (31%), Gaps = 9/79 (11%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL--------GMAYIGFKDEKNCNKALN 276
I V+N+P V ++ +F + G A + F+ A+
Sbjct: 16 TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75
Query: 277 K-NKSFWKGKQLNIYKYSK 294
N +++ + S
Sbjct: 76 DLNDRPIGSRKVKLSGPSS 94
>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 = 75.8 bits (187), Expect = 6e-17
Identities = 26/90 (28%), Positives = 46/90 (51%), Gaps = 8/90 (8%)
Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
+ +A+ +FVRNL+ TVTE+ L K F ++G L V K K +A + F +
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERV--------KKLKDYAFIHFDERD 56
Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
A +A + ++G G + ++ KP + +
Sbjct: 57 GAVKAMEEMNGKDLEGENIEIVFAKPPDQK 86
Score = 61.9 bits (151), Expect = 5e-12
Identities = 17/109 (15%), Positives = 40/109 (36%), Gaps = 13/109 (11%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
L+++NL TE+ + + F + G + V + Y F+ F
Sbjct: 8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK-------------DYAFIHFDE 54
Query: 637 RESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTG 685
R+ +A++ + L+ IE+ + + ++ + +G
Sbjct: 55 RDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSSG 103
Score = 60.8 bits (148), Expect = 1e-11
Identities = 22/103 (21%), Positives = 43/103 (41%), Gaps = 10/103 (9%)
Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
S + + VRN+ + +E+ F FG+L+ V+ K + F+ F
Sbjct: 3 SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK---------DYAFIHFD 53
Query: 737 TKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
++ A +AM+ + L G + + +A+ D RK +
Sbjct: 54 ERDGAVKAMEEM-NGKDLEGENIEIVFAKPPDQKRKERKAQRQ 95
Score = 47.3 bits (113), Expect = 8e-07
Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 7/65 (10%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+T+E L+ F + G + V+ K + +AFI + D A A++ N +
Sbjct: 21 NTVTEEILEKAFSQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMNGKDLEGE 73
Query: 87 RIKVE 91
I++
Sbjct: 74 NIEIV 78
Score = 43.4 bits (103), Expect = 2e-05
Identities = 18/99 (18%), Positives = 38/99 (38%), Gaps = 12/99 (12%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-PYGITGLVEFLQKNQAKAAFNSLAYT 506
+++ V+NL L+ F FG L RV Y + F +++ A A +
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY---AFIHFDERDGAVKAMEEMNGK 68
Query: 507 KFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEG 545
+ + + + AK + +++ K + + G
Sbjct: 69 DLEGENIEIVF--------AKPPDQKRKERKAQRQAASG 99
Score = 30.3 bits (69), Expect = 0.65
Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 3/69 (4%)
Query: 223 QYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTFLGMAYIGFKDEKNCNKALNK-NKS 280
+ + V+NL V ++ L+ F L V+ A+I F + KA+ + N
Sbjct: 10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVK-KLKDYAFIHFDERDGAVKAMEEMNGK 68
Query: 281 FWKGKQLNI 289
+G+ + I
Sbjct: 69 DLEGENIEI 77
>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 = 75.4 bits (186), Expect = 7e-17
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 7/81 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++++ NLS VT DDL +LF LP+ + G+A V + A +A +
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63
Query: 398 LDGTV-FLGRMLHLIPGKPKE 417
L G V G+++ + K+
Sbjct: 64 LSGKVELHGKIMEVDYSVSKK 84
Score = 71.5 bits (176), Expect = 1e-15
Identities = 15/79 (18%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+K+ + N+ ++ +LF ++ L G+ FV++ +N A RA+
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-------LLKSGYAFVDYPDQNWAIRAI 61
Query: 746 KALCQSTHLYGRRLVLEWA 764
+ L L+G+ + ++++
Sbjct: 62 ETLSGKVELHGKIMEVDYS 80
Score = 53.4 bits (129), Expect = 4e-09
Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 11/71 (15%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
LYI NL+ T D +R+ F + V K GY FV +
Sbjct: 5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS-----------GYAFVDYPD 53
Query: 637 RESLNQALKVL 647
+ +A++ L
Sbjct: 54 QNWAIRAIETL 64
Score = 47.6 bits (114), Expect = 4e-07
Identities = 10/67 (14%), Positives = 27/67 (40%), Gaps = 6/67 (8%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+T + L+ F ++ Q+ +AF+ Y ++ A A++ +
Sbjct: 18 PAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETLSGKVELHG 72
Query: 87 R-IKVEK 92
+ ++V+
Sbjct: 73 KIMEVDY 79
Score = 36.8 bits (86), Expect = 0.003
Identities = 13/69 (18%), Positives = 27/69 (39%), Gaps = 3/69 (4%)
Query: 452 VKNLPYRTLPTDLKALFEPFGD-LGRVLVPPYGITGLVEFLQKNQAKAAFNSL-AYTKFK 509
+ NL DL+ LF L ++ G V++ +N A A +L +
Sbjct: 13 IGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGY-AFVDYPDQNWAIRAIETLSGKVELH 71
Query: 510 EVPLYLEWA 518
+ ++++
Sbjct: 72 GKIMEVDYS 80
Score = 33.4 bits (77), Expect = 0.045
Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 5/83 (6%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKP--LPLASVRTTFLGMAYIGFKDEKNCNKALNK--NKS 280
+ + + NL V DL+ F LPLA G A++ + D+ +A+ K
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKV 68
Query: 281 FWKGKQLNIYKYSKDNSAKYSGA 303
GK + + YS + SG
Sbjct: 69 ELHGKIMEV-DYSVSKKLRSSGP 90
>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 = 75.3 bits (186), Expect = 7e-17
Identities = 20/75 (26%), Positives = 34/75 (45%)
Query: 332 DIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
+ +FV +LS +T + F +G +++ + D T K+KG+ V+F A
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61
Query: 392 TQAYQHLDGTVFLGR 406
A Q + G GR
Sbjct: 62 ENAIQQMGGQWLGGR 76
Score = 55.6 bits (135), Expect = 6e-10
Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 2/83 (2%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
+ + V ++ + + + F FG + R+ K M +G +G+GFV F K +A+
Sbjct: 5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMA-TGKSKGYGFVSFFNKWDAEN 63
Query: 744 AMKALCQSTHLYGRRLVLEWAEE 766
A++ + L GR++ WA
Sbjct: 64 AIQQM-GGQWLGGRQIRTNWATR 85
Score = 55.3 bits (134), Expect = 8e-10
Identities = 21/88 (23%), Positives = 37/88 (42%), Gaps = 5/88 (5%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
+++ +L+ T +I F G I+ V + D + G+ S GYGFV F+
Sbjct: 3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVK--DMAT-GK--SKGYGFVSFFN 57
Query: 637 RESLNQALKVLQNSSLDEHQIELKRSNR 664
+ A++ + L QI + R
Sbjct: 58 KWDAENAIQQMGGQWLGGRQIRTNWATR 85
Score = 41.8 bits (99), Expect = 5e-05
Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 6/85 (7%)
Query: 7 GPVVPRNHISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGY 65
GP+ H+ + DL +IT + A F G ++D ++ GK + + F+ +
Sbjct: 1 GPLGSHFHVFVGDLS-----PEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSF 55
Query: 66 HREDQAQAALDYFNNTYVFSSRIKV 90
+ A+ A+ ++ +I+
Sbjct: 56 FNKWDAENAIQQMGGQWLGGRQIRT 80
Score = 32.5 bits (75), Expect = 0.071
Identities = 17/75 (22%), Positives = 24/75 (32%), Gaps = 6/75 (8%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
+ V +L + A F PFG + V T G V F K A+ A +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 504 AYTKFKEVPLYLEWA 518
+ WA
Sbjct: 69 GGQWLGGRQIRTNWA 83
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 75.4 bits (186), Expect = 8e-17
Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+++V NL + +L + F YGPL V + + GFA V F P A A +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56
Query: 398 LDGTVFLGRML 408
LDG V G +
Sbjct: 57 LDGKVICGSRV 67
Score = 68.9 bits (169), Expect = 2e-14
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 7/80 (8%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V N+ A + E+E F +G L+ V + + GF FVEF +A+ A++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP------PGFAFVEFEDPRDAEDAVR 55
Query: 747 ALCQSTHLYGRRLVLEWAEE 766
L + G R+ +E +
Sbjct: 56 GL-DGKVICGSRVRVELSTG 74
Score = 55.4 bits (134), Expect = 9e-10
Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 10/71 (14%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+Y+ NL + + + R F GP+ +V + ++P G+ FV+F
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWI--ARNPP--------GFAFVEFEDPRDAED 52
Query: 643 ALKVLQNSSLD 653
A++ L +
Sbjct: 53 AVRGLDGKVIC 63
Score = 48.8 bits (117), Expect = 2e-07
Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 4/65 (6%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ +L+ F G + V + G FAF+ + A+ A+ + + S
Sbjct: 10 TGAGKGELERAFSYYGPLRTVWIARNPPG----FAFVEFEDPRDAEDAVRGLDGKVICGS 65
Query: 87 RIKVE 91
R++VE
Sbjct: 66 RVRVE 70
Score = 40.7 bits (96), Expect = 1e-04
Identities = 17/69 (24%), Positives = 25/69 (36%), Gaps = 3/69 (4%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGITGLVEFLQKNQAKAAFNSLAYTKFK 509
V NL +L+ F +G L V + P G VEF A+ A L
Sbjct: 5 VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGF-AFVEFEDPRDAEDAVRGLDGKVIC 63
Query: 510 EVPLYLEWA 518
+ +E +
Sbjct: 64 GSRVRVELS 72
Score = 27.3 bits (61), Expect = 8.2
Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 4/65 (6%)
Query: 227 IVVKNLPAGVKKKDLKAYFK---PLPLASVRTTFLGMAYIGFKDEKNCNKALNK-NKSFW 282
+ V NL G K +L+ F PL + G A++ F+D ++ A+ +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 283 KGKQL 287
G ++
Sbjct: 63 CGSRV 67
>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 = 79.0 bits (194), Expect = 1e-16
Identities = 24/145 (16%), Positives = 53/145 (36%), Gaps = 3/145 (2%)
Query: 275 LNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNA-SMENIKAKHWKSQEDSVQFAEDI 333
N+ + Q+++Y SA A +D + ++
Sbjct: 6 FNQEAEYGGHDQIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYT 65
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGP--LAEVILPIDKETDKTKGFALVTFLMPEHA 391
+ +++ NL++ T++DLT+ G + E+ ++ ++KGFALV +
Sbjct: 66 GKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASS 125
Query: 392 TQAYQHLDGTVFLGRMLHLIPGKPK 416
+ L G+ + P +
Sbjct: 126 KKLMDLLPKRELHGQNPVVTPVNKQ 150
Score = 62.0 bits (150), Expect = 7e-11
Identities = 22/145 (15%), Positives = 47/145 (32%), Gaps = 3/145 (2%)
Query: 541 EGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRH 600
E ++ G + LYI NL + +T++ +
Sbjct: 29 ANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEA 88
Query: 601 FKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELK 660
G + + ++ + GQ S G+ V + S + + +L L +
Sbjct: 89 VHSLGVNDILEIKFFENRAN-GQ--SKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVT 145
Query: 661 RSNRNLESEATTVKRKSSNVAKQTG 685
N+ S+ RK++ + +G
Sbjct: 146 PVNKQFLSQFEMQSRKTTQSGQMSG 170
Score = 56.6 bits (136), Expect = 4e-09
Identities = 18/128 (14%), Positives = 45/128 (35%), Gaps = 9/128 (7%)
Query: 646 VLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGS-----KILVRNIPFQAKQS 700
V+ S+ + E + L K + + + N+ +
Sbjct: 24 VISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDE 83
Query: 701 EVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR 758
++ E + G ++ ++ + +G +GF V ++ +K+ M L L+G+
Sbjct: 84 DLTEAVHSLGVNDILEIKFFENRA-NGQSKGFALVGVGSEASSKKLMDLL-PKRELHGQN 141
Query: 759 LVLEWAEE 766
V+ +
Sbjct: 142 PVVTPVNK 149
Score = 40.9 bits (95), Expect = 7e-04
Identities = 12/71 (16%), Positives = 25/71 (35%), Gaps = 3/71 (4%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE---GKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+ T E L G +++K+ G+ + FA +G E ++ +D +
Sbjct: 78 WWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKREL 137
Query: 84 FSSRIKVEKCS 94
V +
Sbjct: 138 HGQNPVVTPVN 148
Score = 38.9 bits (90), Expect = 0.003
Identities = 21/164 (12%), Positives = 51/164 (31%), Gaps = 16/164 (9%)
Query: 166 NKDGEEKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQY- 224
N++ E + D ++ I+ ++ + + + P+ AP Y
Sbjct: 7 NQEAEYGGHDQIDLYDDVIS-PSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYT 65
Query: 225 ---HTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL----------GMAYIGFKDEKNC 271
+ + NL +DL L + + G A +G E +
Sbjct: 66 GKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASS 125
Query: 272 NKALNK-NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMEN 314
K ++ K G+ + +K +++ + + +
Sbjct: 126 KKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMS 169
Score = 31.2 bits (70), Expect = 0.97
Identities = 13/91 (14%), Positives = 29/91 (31%), Gaps = 8/91 (8%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFG--DLGRVLVPPYGITG------LVEFLQKNQAKAAFN 501
+ + NL + T DL G D+ + G LV + +K +
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 502 SLAYTKFKEVPLYLEWAPEGVFAEAKEKSKG 532
L + + + ++ + +S+
Sbjct: 131 LLPKRELHGQNPVVTPVNKQFLSQFEMQSRK 161
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 74.7 bits (184), Expect = 1e-16
Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 2/69 (2%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYG--PLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
I +RN++ D + Y + + L DK+T + +GFA V A+
Sbjct: 8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDAS 67
Query: 393 QAYQHLDGT 401
Q Q L
Sbjct: 68 QLLQILQSL 76
Score = 67.7 bits (166), Expect = 4e-14
Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 7/93 (7%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
T+ ++N+ ++ DSI +A + KD ++ + G+ FVQ
Sbjct: 5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQ---QNRGFAFVQLS 61
Query: 636 TRESLNQALKVLQNS----SLDEHQIELKRSNR 664
+ +Q L++LQ+ +D I + +
Sbjct: 62 SAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94
Score = 67.3 bits (165), Expect = 5e-14
Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKF--VRLPKKMVGSGLHRGFGFVEFITKNEAK 742
I++RNI + + L +RL K + +RGF FV+ + +A
Sbjct: 9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQ-TQQNRGFAFVQLSSAMDAS 67
Query: 743 RAMKAL---CQSTHLYGRRLVLEWAEEA 767
+ ++ L + G+ + +++A+ A
Sbjct: 68 QLLQILQSLHPPLKIDGKTIGVDFAKSA 95
Score = 40.0 bits (94), Expect = 2e-04
Identities = 12/76 (15%), Positives = 23/76 (30%), Gaps = 11/76 (14%)
Query: 27 YKITQEQLKAKFEEKGT--VTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNT 81
+ + + V +++L K T + R FAF+ A L +
Sbjct: 19 PHTVVDSIMTALSPYASLAVNNIRLIKDKQT--QQNRGFAFVQLSSAMDASQLLQILQSL 76
Query: 82 YVFSS----RIKVEKC 93
+ I V+
Sbjct: 77 HPPLKIDGKTIGVDFA 92
Score = 36.1 bits (84), Expect = 0.005
Identities = 9/62 (14%), Positives = 19/62 (30%), Gaps = 8/62 (12%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLG--RVLVPPYGITGL------VEFLQKNQAKAAFN 501
I+++N+ T+ + P+ L + + T V+ A
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
Query: 502 SL 503
L
Sbjct: 72 IL 73
Score = 29.6 bits (67), Expect = 0.88
Identities = 13/91 (14%), Positives = 28/91 (30%), Gaps = 16/91 (17%)
Query: 220 HKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL----------GMAYIGFKDEK 269
H TI+++N+ + P +V L G A++
Sbjct: 5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64
Query: 270 NCNKALNK-NKSFWK----GKQLNIYKYSKD 295
+ ++ L GK + + ++K
Sbjct: 65 DASQLLQILQSLHPPLKIDGKTIGV-DFAKS 94
>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 = 74.2 bits (183), Expect = 2e-16
Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 8/84 (9%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
+ +IFV N+S T +L LFE+ G + E + K +A V A
Sbjct: 7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKA 58
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKE 417
A L+G G+ +++ +
Sbjct: 59 AIAQLNGKEVKGKRINVELSTKGQ 82
Score = 66.1 bits (162), Expect = 1e-13
Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 10/89 (11%)
Query: 678 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT 737
S+ + KI V N+ E+ LF+ G + + + + FV
Sbjct: 2 SSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECD---------VVKDYAFVHMEK 52
Query: 738 KNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
+ +AK A+ L + G+R+ +E + +
Sbjct: 53 EADAKAAIAQL-NGKEVKGKRINVELSTK 80
Score = 55.3 bits (134), Expect = 9e-10
Identities = 12/84 (14%), Positives = 25/84 (29%), Gaps = 13/84 (15%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
+++ N++ T +R F++ G + V + Y FV
Sbjct: 4 GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK-------------DYAFVHM 50
Query: 635 YTRESLNQALKVLQNSSLDEHQIE 658
A+ L + +I
Sbjct: 51 EKEADAKAAIAQLNGKEVKGKRIN 74
Score = 49.5 bits (119), Expect = 7e-08
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 7/78 (8%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
T ++L++ FE +G V + + + +AF+ +E A+AA+ N V
Sbjct: 19 AACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQLNGKEVKGK 71
Query: 87 RIKVEKCSNLGDTTKPKS 104
RI VE + + P S
Sbjct: 72 RINVELSTKGQKKSGPSS 89
Score = 38.0 bits (89), Expect = 0.001
Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 4/70 (5%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYTKF 508
I V N+ +L++LFE G + +V Y V ++ AKAA L +
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKDY---AFVHMEKEADAKAAIAQLNGKEV 68
Query: 509 KEVPLYLEWA 518
K + +E +
Sbjct: 69 KGKRINVELS 78
>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 = 74.4 bits (183), Expect = 3e-16
Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 2/92 (2%)
Query: 683 QTGSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
++ + IP K+ E+ E E + V + +RGF FVE+ + A
Sbjct: 6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65
Query: 742 KRAMKALCQSTH-LYGRRLVLEWAEEADNVED 772
A + L L+G ++ ++WAE +V++
Sbjct: 66 AMARRKLMPGRIQLWGHQIAVDWAEPEIDVDE 97
Score = 60.2 bits (146), Expect = 3e-11
Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 4/78 (5%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGP-LAEVILPID-KETDKTKGFALVTFLMPEHAT 392
+ R+F+ + +++ + K + +VI+ + K +GFA V + A
Sbjct: 7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66
Query: 393 QAYQHL--DGTVFLGRML 408
A + L G +
Sbjct: 67 MARRKLMPGRIQLWGHQI 84
Score = 58.7 bits (142), Expect = 8e-11
Identities = 16/104 (15%), Positives = 36/104 (34%), Gaps = 7/104 (6%)
Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGP-IASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
+ L+I + + I K + V V + + G+ FV++ +
Sbjct: 6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIV--YASAADKMK--NRGFAFVEYES 61
Query: 637 RESLNQALKVLQNSS--LDEHQIELKRSNRNLESEATTVKRKSS 678
+ A + L L HQI + + ++ + ++ S
Sbjct: 62 HRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSG 105
Score = 39.4 bits (92), Expect = 4e-04
Identities = 14/70 (20%), Positives = 26/70 (37%), Gaps = 5/70 (7%)
Query: 27 YKITQEQLKAKFEEKGT-VTDVQLKY--TTEGKFRRFAFIGYHREDQAQAALDYFNN--T 81
+E++ + + V DV + + K R FAF+ Y A A
Sbjct: 18 KMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRI 77
Query: 82 YVFSSRIKVE 91
++ +I V+
Sbjct: 78 QLWGHQIAVD 87
Score = 38.2 bits (89), Expect = 0.001
Identities = 9/88 (10%), Positives = 24/88 (27%), Gaps = 10/88 (11%)
Query: 441 VVEARSKRIILVKNLPYRTLPTDLKALFEPFGD--LGRVLVPPYGITG------LVEFLQ 492
+ + + +P ++ + L ++ VE+
Sbjct: 2 SSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES 61
Query: 493 KNQAKAAFNSLAYTKFK--EVPLYLEWA 518
A A L + + + ++WA
Sbjct: 62 HRAAAMARRKLMPGRIQLWGHQIAVDWA 89
Score = 31.3 bits (71), Expect = 0.30
Identities = 9/78 (11%), Positives = 26/78 (33%), Gaps = 13/78 (16%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKP----------LPLASVRTTFLGMAYIGFKDEKNCNKA 274
+ + +P K++++ A+ + G A++ ++ + A
Sbjct: 9 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68
Query: 275 ---LNKNKSFWKGKQLNI 289
L + G Q+ +
Sbjct: 69 RRKLMPGRIQLWGHQIAV 86
>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 = 73.9 bits (182), Expect = 4e-16
Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 6/81 (7%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++ ++ +T+ + + F +G + E+ + + KG++ V F E A A
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS 80
Query: 398 LDGTVFLGRMLHLIPGKPKEN 418
++GT G ++ GK +
Sbjct: 81 VNGTTIEGHVVKCYWGKESPD 101
Score = 68.9 bits (169), Expect = 2e-14
Identities = 20/100 (20%), Positives = 40/100 (40%), Gaps = 11/100 (11%)
Query: 558 NQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 617
+ + E+ + + T+Y + T+ +R+ F G I + V +K
Sbjct: 3 SGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK- 61
Query: 618 PKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI 657
GY FV+F T ES A+ + ++++ H +
Sbjct: 62 ----------GYSFVRFSTHESAAHAIVSVNGTTIEGHVV 91
Score = 64.7 bits (158), Expect = 6e-13
Identities = 20/100 (20%), Positives = 38/100 (38%), Gaps = 11/100 (11%)
Query: 668 SEATTVKRKSSNVAKQTGSK---ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS 724
S T + + +V Q+ K + I + + F FG++ +R+
Sbjct: 5 SSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP----- 59
Query: 725 GLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
+G+ FV F T A A+ ++ T + G + W
Sbjct: 60 --EKGYSFVRFSTHESAAHAIVSV-NGTTIEGHVVKCYWG 96
Score = 45.0 bits (107), Expect = 5e-06
Identities = 13/88 (14%), Positives = 34/88 (38%), Gaps = 18/88 (20%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+T + ++ F G + ++++ + ++F+ + + A A+ N T +
Sbjct: 35 SGLTDQLMRQTFSPFGQIMEIRVF-----PEKGYSFVRFSTHESAAHAIVSVNGTTIEGH 89
Query: 87 RIKVEKCSNLGDTTKPKSWSKYAPDSSA 114
+K W K +PD ++
Sbjct: 90 VVKC-------------YWGKESPDMTS 104
Score = 44.2 bits (105), Expect = 1e-05
Identities = 14/69 (20%), Positives = 22/69 (31%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEV 511
+ ++ F PFG + + V P V F A A S+ T +
Sbjct: 30 CGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGH 89
Query: 512 PLYLEWAPE 520
+ W E
Sbjct: 90 VVKCYWGKE 98
Score = 30.4 bits (69), Expect = 0.59
Identities = 16/107 (14%), Positives = 44/107 (41%), Gaps = 7/107 (6%)
Query: 204 TAPSDPSVPPVSKAPVHKR---QYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF-L 258
++ S + + V + + T+ + +G+ + ++ F P + +R
Sbjct: 2 SSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK 61
Query: 259 GMAYIGFKDEKNCNKALNK-NKSFWKGKQLNIYKYSKDNSAKYSGAA 304
G +++ F ++ A+ N + +G + Y + K++ SG +
Sbjct: 62 GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY-WGKESPDMTSGPS 107
>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 = 73.0 bits (180), Expect = 4e-16
Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 8/80 (10%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++F+ NL TE ++ LFE+YG + E + K + V A A ++
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61
Query: 398 LDGTVFLGRMLHLIPGKPKE 417
L G +++ K K
Sbjct: 62 LHHYKLHGVNINVEASKNKS 81
Score = 67.6 bits (166), Expect = 4e-14
Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 10/81 (12%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
K+ + N+P +A + E+ LF+ +G++ + K +GFV K A+ A+
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK---------NYGFVHIEDKTAAEDAI 59
Query: 746 KALCQSTHLYGRRLVLEWAEE 766
+ L L+G + +E ++
Sbjct: 60 RNL-HHYKLHGVNINVEASKN 79
Score = 53.0 bits (128), Expect = 5e-09
Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 13/77 (16%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
L+I NL +TE IR F++ G + + + YGFV + +
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK-------------NYGFVHIEDKTAA 55
Query: 641 NQALKVLQNSSLDEHQI 657
A++ L + L I
Sbjct: 56 EDAIRNLHHYKLHGVNI 72
Score = 48.3 bits (116), Expect = 2e-07
Identities = 11/66 (16%), Positives = 30/66 (45%), Gaps = 7/66 (10%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ T++++++ FE+ G V + + + + F+ + A+ A+ ++ +
Sbjct: 18 REATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGV 70
Query: 87 RIKVEK 92
I VE
Sbjct: 71 NINVEA 76
Score = 39.1 bits (92), Expect = 4e-04
Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 4/76 (5%)
Query: 444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNS 502
+ + + NLP ++++LFE +G + ++ Y G V K A+ A +
Sbjct: 5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNY---GFVHIEDKTAAEDAIRN 61
Query: 503 LAYTKFKEVPLYLEWA 518
L + K V + +E +
Sbjct: 62 LHHYKLHGVNINVEAS 77
>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 = 73.4 bits (181), Expect = 4e-16
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 2/77 (2%)
Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
ED + ++V NLS VTE + +LF + GP + + ++ + V F
Sbjct: 9 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHR 66
Query: 390 HATQAYQHLDGTVFLGR 406
A A ++G LG+
Sbjct: 67 DAAAALAAMNGRKILGK 83
Score = 61.9 bits (151), Expect = 5e-12
Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 4/81 (4%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
+ V N+ + + +LF G K ++ + + + FVEF +A
Sbjct: 14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS---NDPYCFVEFYEHRDAAA 70
Query: 744 AMKALCQSTHLYGRRLVLEWA 764
A+ A+ + G+ + + WA
Sbjct: 71 ALAAM-NGRKILGKEVKVNWA 90
Score = 60.7 bits (148), Expect = 1e-11
Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 7/82 (8%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
+ TLY+ NL+ + TE I + F + GP S + + P Y FV+FY
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-------YCFVEFY 63
Query: 636 TRESLNQALKVLQNSSLDEHQI 657
AL + + ++
Sbjct: 64 EHRDAAAALAAMNGRKILGKEV 85
Score = 46.5 bits (111), Expect = 1e-06
Identities = 16/84 (19%), Positives = 27/84 (32%), Gaps = 4/84 (4%)
Query: 439 NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL----VEFLQKN 494
+ + R + V NL + LF G + + VEF +
Sbjct: 7 GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR 66
Query: 495 QAKAAFNSLAYTKFKEVPLYLEWA 518
A AA ++ K + + WA
Sbjct: 67 DAAAALAAMNGRKILGKEVKVNWA 90
Score = 45.3 bits (108), Expect = 3e-06
Identities = 11/64 (17%), Positives = 23/64 (35%), Gaps = 1/64 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+T+ + F + G ++ + F+ ++ A AAL N +
Sbjct: 25 RDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAAMNGRKILGK 83
Query: 87 RIKV 90
+KV
Sbjct: 84 EVKV 87
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 75.0 bits (184), Expect = 6e-16
Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 2/75 (2%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGP--LAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
++V + S+ T+ L ++ G + E+ ++ ++KG+A V +
Sbjct: 55 RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHK 114
Query: 394 AYQHLDGTVFLGRML 408
+ L G V G +
Sbjct: 115 LLELLPGKVLNGEKV 129
Score = 57.6 bits (139), Expect = 7e-10
Identities = 14/111 (12%), Positives = 42/111 (37%), Gaps = 6/111 (5%)
Query: 659 LKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLP 718
+++ + T + + + + + V + + ++ ++ ++ G V L
Sbjct: 29 VRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVEL- 87
Query: 719 KKMV---GSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
K +G +G+ V ++N + ++ L L G ++ + A
Sbjct: 88 -KFAENRANGQSKGYAEVVVASENSVHKLLELL-PGKVLNGEKVDVRPATR 136
Score = 53.4 bits (128), Expect = 2e-08
Identities = 17/131 (12%), Positives = 46/131 (35%), Gaps = 13/131 (9%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLY 584
+ + E ++E + + +N+ + +Y
Sbjct: 6 HHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTP------AILYTYSGLRNRRAAVY 59
Query: 585 IKNLNFNSTEDSIRRHFKKCGP--IASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+ + ++ +T+ + + + G + + A + GQ S GY V + S+++
Sbjct: 60 VGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA---NGQ--SKGYAEVVVASENSVHK 114
Query: 643 ALKVLQNSSLD 653
L++L L+
Sbjct: 115 LLELLPGKVLN 125
Score = 38.7 bits (90), Expect = 0.002
Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 3/71 (4%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE---GKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+ T +QL G V+LK+ G+ + +A + E+ L+ +
Sbjct: 65 WWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVL 124
Query: 84 FSSRIKVEKCS 94
++ V +
Sbjct: 125 NGEKVDVRPAT 135
Score = 33.0 bits (75), Expect = 0.15
Identities = 22/148 (14%), Positives = 49/148 (33%), Gaps = 21/148 (14%)
Query: 181 NNQIAHADISDMEYLKLKTKSKDTAPS---DPSVPPVSKAPVHKRQY-------HTIVVK 230
++ H+ D+ L +S + P +PS P +K P Y + V
Sbjct: 2 HHHHHHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVG 61
Query: 231 NLPAGVKKKDLKAYFKPLPLASVRTTFL----------GMAYIGFKDEKNCNKALNK-NK 279
+ + L + + + V G A + E + +K L
Sbjct: 62 SFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPG 121
Query: 280 SFWKGKQLNIYKYSKDNSAKYSGAADDN 307
G+++++ ++ N +++ A
Sbjct: 122 KVLNGEKVDVRPATRQNLSQFEAQARKR 149
Score = 31.0 bits (70), Expect = 0.65
Identities = 9/62 (14%), Positives = 16/62 (25%), Gaps = 8/62 (12%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFG--DLGRVLVPPYGITG------LVEFLQKNQAKAAFN 501
+ V + + T L + G D+ + G V +N
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 502 SL 503
L
Sbjct: 118 LL 119
>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 = 73.1 bits (180), Expect = 7e-16
Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 4/91 (4%)
Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
S K+ V + Q + +V LF+ FG + + + G +G FV+F
Sbjct: 7 GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG--PDGSSKGCAFVKFS 64
Query: 737 TKNEAKRAMKALCQSTHLYG--RRLVLEWAE 765
+ EA+ A+ AL S + G LV+++A+
Sbjct: 65 SHTEAQAAIHALHGSQTMPGASSSLVVKFAD 95
Score = 66.9 bits (164), Expect = 1e-13
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
++FV L+ +E+D+ +LF+ +G + E + +KG A V F A
Sbjct: 13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQA 71
Query: 394 AYQHLDGTVFL 404
A L G+ +
Sbjct: 72 AIHALHGSQTM 82
Score = 65.4 bits (160), Expect = 3e-13
Identities = 22/83 (26%), Positives = 31/83 (37%), Gaps = 6/83 (7%)
Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
E D L++ LN +E+ + R F+ G I TV R D S G F
Sbjct: 7 GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSK------GCAF 60
Query: 632 VQFYTRESLNQALKVLQNSSLDE 654
V+F + A+ L S
Sbjct: 61 VKFSSHTEAQAAIHALHGSQTMP 83
Score = 46.1 bits (110), Expect = 2e-06
Identities = 13/67 (19%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF-- 84
+ ++E + F+ G + + + +G + AF+ + +AQAA+ + +
Sbjct: 25 KQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPG 84
Query: 85 -SSRIKV 90
SS + V
Sbjct: 85 ASSSLVV 91
Score = 41.5 bits (98), Expect = 9e-05
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 8/75 (10%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLG--RVLVPPYGIT---GLVEFLQKNQAKAAFNSLAYT 506
V L + D+ LF+PFG + VL P G + V+F +A+AA ++L +
Sbjct: 20 VGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGS 79
Query: 507 KFKE---VPLYLEWA 518
+ L +++A
Sbjct: 80 QTMPGASSSLVVKFA 94
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 72.7 bits (179), Expect = 7e-16
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 2/86 (2%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
+V NL + + D+ +F+ + V L DK+TDK KGF V F + +A
Sbjct: 15 PYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73
Query: 396 QHLDGTVFLGRMLHLIPGKPKENEGN 421
DG + R L + + ++ + +
Sbjct: 74 T-YDGALLGDRSLRVDIAEGRKQDKS 98
Score = 58.4 bits (142), Expect = 9e-11
Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 7/80 (8%)
Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
EP T Y+ NL FN+ + I FK I SV + R KD G+ +V+F
Sbjct: 13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKF-----KGFCYVEFDEV 66
Query: 638 ESLNQALKVLQNSSLDEHQI 657
+SL +AL + L + +
Sbjct: 67 DSLKEALT-YDGALLGDRSL 85
Score = 54.2 bits (131), Expect = 3e-09
Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 4/83 (4%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
V N+PF Q +++ +FK ++ VRL + + +GF +VEF + K A+
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDK-DTDKFKGFCYVEFDEVDSLKEALT 74
Query: 747 ALCQSTHLYGRRLVLEWAEEADN 769
L R L ++ AE
Sbjct: 75 Y--DGALLGDRSLRVDIAEGRKQ 95
Score = 35.7 bits (83), Expect = 0.008
Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 7/82 (8%)
Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVR-------TTFLGMAYIGFKD 267
S + +T V NLP + D+ A FK L + SVR F G Y+ F +
Sbjct: 6 SGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDE 65
Query: 268 EKNCNKALNKNKSFWKGKQLNI 289
+ +AL + + + L +
Sbjct: 66 VDSLKEALTYDGALLGDRSLRV 87
Score = 34.9 bits (81), Expect = 0.014
Identities = 12/65 (18%), Positives = 29/65 (44%), Gaps = 3/65 (4%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ Q + A F++ + V+L + KF+ F ++ + D + AL ++ +
Sbjct: 25 FNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGD 82
Query: 86 SRIKV 90
++V
Sbjct: 83 RSLRV 87
Score = 28.0 bits (63), Expect = 3.4
Identities = 15/64 (23%), Positives = 23/64 (35%), Gaps = 15/64 (23%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFG----------DLGRVLVPPYGITGLVEFLQKNQAK 497
V NLP+ T+ D+ A+F+ D + G VEF + + K
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDK----FKGF-CYVEFDEVDSLK 70
Query: 498 AAFN 501
A
Sbjct: 71 EALT 74
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 72.5 bits (178), Expect = 8e-16
Identities = 20/71 (28%), Positives = 30/71 (42%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
+G + + V + LT LF K G + + PID+ T KTKGF V A +
Sbjct: 12 NGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKII 71
Query: 396 QHLDGTVFLGR 406
+ G +
Sbjct: 72 KSFHGKRLDLK 82
Score = 47.8 bits (114), Expect = 5e-07
Identities = 17/70 (24%), Positives = 30/70 (42%), Gaps = 7/70 (10%)
Query: 685 GSKILVRNIP------FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 738
I+V P + + LF G++ + P +G +GF FVE +
Sbjct: 6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEA-TGKTKGFLFVECGSM 64
Query: 739 NEAKRAMKAL 748
N+AK+ +K+
Sbjct: 65 NDAKKIIKSF 74
Score = 46.3 bits (110), Expect = 2e-06
Identities = 11/70 (15%), Positives = 24/70 (34%), Gaps = 5/70 (7%)
Query: 584 YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQA 643
I + + ++ F K G + ++ P + G+ FV+ + +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEF-----PIDEATGKTKGFLFVECGSMNDAKKI 70
Query: 644 LKVLQNSSLD 653
+K LD
Sbjct: 71 IKSFHGKRLD 80
Score = 41.3 bits (97), Expect = 8e-05
Identities = 10/56 (17%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNT 81
+ ++ L + F + G V +++ GK + F F+ + A+ + F+
Sbjct: 22 VPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77
Score = 33.2 bits (76), Expect = 0.059
Identities = 17/68 (25%), Positives = 22/68 (32%), Gaps = 12/68 (17%)
Query: 448 RIILVKNLPY------RTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQ 495
+ I+V P L L +LF G + + P TG VE N
Sbjct: 7 QYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMND 66
Query: 496 AKAAFNSL 503
AK S
Sbjct: 67 AKKIIKSF 74
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 72.3 bits (178), Expect = 9e-16
Identities = 21/96 (21%), Positives = 33/96 (34%), Gaps = 12/96 (12%)
Query: 563 PEVEENVEEDEEREPEPD-TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 621
P+V + R P TT YI N+ +TE + F+ G I +K
Sbjct: 9 PQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK----- 63
Query: 622 GQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI 657
G F+++ T E + L N +
Sbjct: 64 ------GCCFIKYDTHEQAAVCIVALANFPFQGRNL 93
Score = 71.2 bits (175), Expect = 3e-15
Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 6/79 (7%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++ N+ + TE DL LF+ +G + + + KG + + E A
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVA 82
Query: 398 LDGTVFLGRMLHLIPGKPK 416
L F GR L GK +
Sbjct: 83 LANFPFQGRNLRTGWGKER 101
Score = 68.5 bits (168), Expect = 2e-14
Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 8/88 (9%)
Query: 679 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 738
A + + NIP A ++++ LF+ FG + + +G F+++ T
Sbjct: 21 RSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-------EKGCCFIKYDTH 73
Query: 739 NEAKRAMKALCQSTHLYGRRLVLEWAEE 766
+A + AL + GR L W +E
Sbjct: 74 EQAAVCIVAL-ANFPFQGRNLRTGWGKE 100
Score = 47.7 bits (114), Expect = 5e-07
Identities = 11/64 (17%), Positives = 21/64 (32%), Gaps = 5/64 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ T+ L F+ G + D + + FI Y +QA + N
Sbjct: 37 HFATEADLIPLFQNFGFILDFKH-----YPEKGCCFIKYDTHEQAAVCIVALANFPFQGR 91
Query: 87 RIKV 90
++
Sbjct: 92 NLRT 95
Score = 45.4 bits (108), Expect = 3e-06
Identities = 16/67 (23%), Positives = 26/67 (38%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEV 511
+ N+P+ DL LF+ FG + P +++ QA +LA F+
Sbjct: 32 IGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGR 91
Query: 512 PLYLEWA 518
L W
Sbjct: 92 NLRTGWG 98
Score = 30.4 bits (69), Expect = 0.51
Identities = 14/92 (15%), Positives = 31/92 (33%), Gaps = 6/92 (6%)
Query: 204 TAPSDPSVPPVSKAPVHKR---QYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF-L 258
T P V P + + + + T + N+P + DL F+ + +
Sbjct: 4 TIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK 63
Query: 259 GMAYIGFKDEKNCNKALNK-NKSFWKGKQLNI 289
G +I + + + ++G+ L
Sbjct: 64 GCCFIKYDTHEQAAVCIVALANFPFQGRNLRT 95
>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 = 72.4 bits (178), Expect = 1e-15
Identities = 19/66 (28%), Positives = 35/66 (53%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
++ ++F+ + + E DL LFE++G + E+ + D+ T KG A +T+ E A +A
Sbjct: 12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Query: 395 YQHLDG 400
L
Sbjct: 72 QSALHE 77
Score = 62.7 bits (153), Expect = 3e-12
Identities = 22/92 (23%), Positives = 46/92 (50%), Gaps = 3/92 (3%)
Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
SS + K+ + IP + +++ LF+ FG++ + + K +G+H+G F+ +
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF-TGMHKGCAFLTYC 63
Query: 737 TKNEAKRAMKALCQSTHLYG--RRLVLEWAEE 766
+ A +A AL + L G R + ++ A+
Sbjct: 64 ERESALKAQSALHEQKTLPGMNRPIQVKPADS 95
Score = 58.1 bits (141), Expect = 1e-10
Identities = 25/107 (23%), Positives = 43/107 (40%), Gaps = 12/107 (11%)
Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
+ L+I + N E ++ F++ G I +TV + D + G G F+
Sbjct: 6 SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLK--DRFT-GM--HKGCAFL 60
Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLE-SEATTVKRKSS 678
+ RES +A +L E + L NR ++ A + R S
Sbjct: 61 TYCERESALKAQS-----ALHEQKT-LPGMNRPIQVKPADSESRGGS 101
Score = 46.2 bits (110), Expect = 2e-06
Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 8/70 (11%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+ ++ LK FEE G + ++ + ++T G + AF+ Y + A A +
Sbjct: 23 RNLDEKDLKPLFEEFGKIYELTVLKDRFT--GMHKGCAFLTYCERESALKAQSALHEQKT 80
Query: 84 F---SSRIKV 90
+ I+V
Sbjct: 81 LPGMNRPIQV 90
Score = 34.2 bits (79), Expect = 0.031
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 503
+ +P DLK LFE FG + + V TG+ + + ++ A A ++L
Sbjct: 18 IGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
>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 = 71.9 bits (177), Expect = 1e-15
Identities = 19/91 (20%), Positives = 43/91 (47%), Gaps = 7/91 (7%)
Query: 332 DIAESGRIFVRNLSYTVTEDDLTK----LFEKYGPLAEVILPIDKETDKTKGFALVTFLM 387
+ + I++ NL+ + +D+L K +F ++G + ++++ + K +G A V F
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS---RSLKMRGQAFVIFKE 60
Query: 388 PEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
AT A + + G F + + + K +
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYAKTDSD 91
Score = 61.1 bits (149), Expect = 9e-12
Identities = 17/79 (21%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 690 VRNIPFQAKQSEVEE----LFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ N+ + K+ E+++ +F FG++ + + + S RG FV F + A A+
Sbjct: 13 INNLNEKIKKDELKKSLHAIFSRFGQILDILVSR----SLKMRGQAFVIFKEVSSATNAL 68
Query: 746 KALCQSTHLYGRRLVLEWA 764
+++ Q Y + + +++A
Sbjct: 69 RSM-QGFPFYDKPMRIQYA 86
Score = 58.4 bits (142), Expect = 8e-11
Identities = 27/111 (24%), Positives = 44/111 (39%), Gaps = 23/111 (20%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRH----FKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
E P+ T+YI NLN +D +++ F + G I + V + K GQ F
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV--SRSLKMRGQ------AF 55
Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAK 682
V F S AL+ +Q + + ++ + K S +AK
Sbjct: 56 VIFKEVSSATNALRSMQGFPFYDKPMRIQYA-----------KTDSDIIAK 95
Score = 45.7 bits (109), Expect = 3e-06
Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 6/69 (8%)
Query: 27 YKITQEQLK----AKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY 82
KI +++LK A F G + D+ + + K R AF+ + A AL
Sbjct: 18 EKIKKDELKKSLHAIFSRFGQILDILVSRS--LKMRGQAFVIFKEVSSATNALRSMQGFP 75
Query: 83 VFSSRIKVE 91
+ ++++
Sbjct: 76 FYDKPMRIQ 84
Score = 43.8 bits (104), Expect = 1e-05
Identities = 25/102 (24%), Positives = 39/102 (38%), Gaps = 15/102 (14%)
Query: 443 EARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQ 495
E R I + NL + +LK A+F FG + +LV V F + +
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 496 AKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEK 537
A A S+ F + P+ +++ AK S K K
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQY--------AKTDSDIIAKMK 97
Score = 33.0 bits (76), Expect = 0.072
Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 11/83 (13%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKPL-----PLASVRTT----FLGMAYIGFKDEKNCNKAL 275
HTI + NL +KK +LK + + + + G A++ FK+ + AL
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 276 NK-NKSFWKGKQLNIYKYSKDNS 297
+ K + I +Y+K +S
Sbjct: 69 RSMQGFPFYDKPMRI-QYAKTDS 90
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 71.3 bits (175), Expect = 2e-15
Identities = 16/75 (21%), Positives = 27/75 (36%), Gaps = 3/75 (4%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
++ +RN+ + + L L +YG + TD VT+ + A QA
Sbjct: 14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQ---VNTDSETAVVNVTYSSKDQARQA 70
Query: 395 YQHLDGTVFLGRMLH 409
L+G L
Sbjct: 71 LDKLNGFQLENFTLK 85
Score = 59.0 bits (143), Expect = 5e-11
Identities = 17/100 (17%), Positives = 39/100 (39%), Gaps = 5/100 (5%)
Query: 672 TVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFG 731
+ S +Q K+ +RNIP + ++ L +G ++ V +
Sbjct: 2 SSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQ----VNTDSETAVV 57
Query: 732 FVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVE 771
V + +K++A++A+ L L L + + + +
Sbjct: 58 NVTYSSKDQARQALDKL-NGFQLENFTLKVAYIPDEMAAQ 96
Score = 50.9 bits (122), Expect = 3e-08
Identities = 11/83 (13%), Positives = 27/83 (32%), Gaps = 8/83 (9%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
+ + L I+N+ + + + + G + S V +
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET--------AVVNVTYS 62
Query: 636 TRESLNQALKVLQNSSLDEHQIE 658
+++ QAL L L+ ++
Sbjct: 63 SKDQARQALDKLNGFQLENFTLK 85
Score = 49.0 bits (117), Expect = 2e-07
Identities = 17/92 (18%), Positives = 38/92 (41%), Gaps = 3/92 (3%)
Query: 437 AFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFG---DLGRVLVPPYGITGLVEFLQK 493
+ V + + R + ++N+P L +L +G +V V + K
Sbjct: 5 SSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSK 64
Query: 494 NQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAE 525
+QA+ A + L + + L + + P+ + A+
Sbjct: 65 DQARQALDKLNGFQLENFTLKVAYIPDEMAAQ 96
Score = 47.4 bits (113), Expect = 5e-07
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 2/65 (3%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ E L + + G V + T + Y +DQA+ ALD N + +
Sbjct: 25 PHLQWEVLDSLLVQYGVVESCEQVNTDSET--AVVNVTYSSKDQARQALDKLNGFQLENF 82
Query: 87 RIKVE 91
+KV
Sbjct: 83 TLKVA 87
Score = 32.0 bits (73), Expect = 0.15
Identities = 17/103 (16%), Positives = 39/103 (37%), Gaps = 18/103 (17%)
Query: 204 TAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASV------RTT 256
++ S SVP +++ + ++N+P ++ + L + + S T
Sbjct: 2 SSGSSGSVPK-------RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET 54
Query: 257 FLGMAYIGFKDEKNCNKALNK-NKSFWKGKQLNIYKYSKDNSA 298
+ + + + +AL+K N + L + Y D A
Sbjct: 55 --AVVNVTYSSKDQARQALDKLNGFQLENFTLKV-AYIPDEMA 94
>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 = 70.8 bits (174), Expect = 4e-15
Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 3/85 (3%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDK-ETDKTKGFALVTFLMPEHATQAYQ 396
F+ NL Y VTE+ + + F + V LP + ++ KGF F + A
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLNI-SAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75
Query: 397 HLDGTVFLGRMLHLIPGKPKENEGN 421
L+ + + + +++ +
Sbjct: 76 -LNEESLGNKRIRVDVADQAQDKDS 99
Score = 68.1 bits (167), Expect = 3e-14
Identities = 20/95 (21%), Positives = 41/95 (43%), Gaps = 3/95 (3%)
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
S + K + N+P+ + ++E F+ VRLP++ +GFG+ E
Sbjct: 5 SSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYAE 63
Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
F + A+ L +R+ ++ A++A +
Sbjct: 64 FEDLDSLLSALS--LNEESLGNKRIRVDVADQAQD 96
Score = 64.6 bits (158), Expect = 7e-13
Identities = 27/93 (29%), Positives = 48/93 (51%), Gaps = 7/93 (7%)
Query: 572 DEEREP-EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYG 630
R P P T ++ NL ++ TE+SI+ F+ I++V + R +P +P + G+G
Sbjct: 6 SGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPR--EPSNPERLK--GFG 60
Query: 631 FVQFYTRESLNQALKVLQNSSLDEHQIELKRSN 663
+ +F +SL AL L SL +I + ++
Sbjct: 61 YAEFEDLDSLLSALS-LNEESLGNKRIRVDVAD 92
Score = 39.6 bits (93), Expect = 3e-04
Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 13/93 (13%)
Query: 205 APSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVR------TT-- 256
S S + K+P + T + NLP V ++ +K +F+ L +++VR
Sbjct: 1 GSSGSSGSRLPKSPPY-----TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPER 55
Query: 257 FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNI 289
G Y F+D + AL+ N+ K++ +
Sbjct: 56 LKGFGYAEFEDLDSLLSALSLNEESLGNKRIRV 88
Score = 38.8 bits (91), Expect = 6e-04
Identities = 15/67 (22%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL--KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF 84
Y +T+E +K F ++ V+L + + + + F + + D +AL N +
Sbjct: 25 YDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLG 82
Query: 85 SSRIKVE 91
+ RI+V+
Sbjct: 83 NKRIRVD 89
Score = 31.8 bits (73), Expect = 0.18
Identities = 12/79 (15%), Positives = 21/79 (26%), Gaps = 7/79 (8%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFN 501
+ NLPY +K F L EF + +A +
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75
Query: 502 SLAYTKFKEVPLYLEWAPE 520
L + ++ A +
Sbjct: 76 -LNEESLGNKRIRVDVADQ 93
>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 = 71.2 bits (175), Expect = 4e-15
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 1/84 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+FV NL Y V L ++F G + + DK+ K++G VTF A QA
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAISM 75
Query: 398 LDGTVFLGRMLHLIPGKPKENEGN 421
+G + R +H+ + +G+
Sbjct: 76 FNGQLLFDRPMHVKMDERALPKGD 99
Score = 63.9 bits (156), Expect = 1e-12
Identities = 20/111 (18%), Positives = 39/111 (35%), Gaps = 6/111 (5%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
+ +T+++ NL++ ++ F G + + KD G+ S G G V F
Sbjct: 10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD----GK--SRGIGTVTF 63
Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTG 685
QA+ + L + + +K R L + +G
Sbjct: 64 EQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSSG 114
Score = 63.5 bits (155), Expect = 2e-12
Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 3/88 (3%)
Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
A + GS + V N+ ++ +++E+F G + + + G RG G V F E
Sbjct: 11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED--KDGKSRGIGTVTFEQSIE 68
Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEAD 768
A +A+ L+ R + ++ E A
Sbjct: 69 AVQAISMF-NGQLLFDRPMHVKMDERAL 95
Score = 54.2 bits (131), Expect = 3e-09
Identities = 16/64 (25%), Positives = 28/64 (43%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
YK+ ++LK F G V + +GK R + + + +A A+ FN +F
Sbjct: 25 YKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDR 84
Query: 87 RIKV 90
+ V
Sbjct: 85 PMHV 88
Score = 38.8 bits (91), Expect = 7e-04
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 5/59 (8%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSL 503
+ V NL Y+ LK +F G + R + G G V F Q +A A +
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
>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 = 72.2 bits (177), Expect = 5e-15
Identities = 25/141 (17%), Positives = 49/141 (34%), Gaps = 9/141 (6%)
Query: 628 GYGFVQFYTRESLNQALKVLQNSSLDE--HQIELKRSNRNLESEATTVKRKSSNVAKQTG 685
G + + + K N + + + + + +
Sbjct: 14 GETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLD 73
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
K+ V N+ ++E+E F +G L+ V + + GF FVEF +A A+
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN------PPGFAFVEFEDPRDAADAV 127
Query: 746 KALCQSTHLYGRRLVLEWAEE 766
+ L L G R+ +E +
Sbjct: 128 REL-DGRTLCGCRVRVELSNG 147
Score = 71.8 bits (176), Expect = 6e-15
Identities = 28/115 (24%), Positives = 40/115 (34%), Gaps = 9/115 (7%)
Query: 292 YSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTED 351
Y+ DN DD + H + +++V NL +
Sbjct: 33 YANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHR----DSCPLDCKVYVGNLGNNGNKT 88
Query: 352 DLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGR 406
+L + F YGPL V + + GFA V F P A A + LDG G
Sbjct: 89 ELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVRELDGRTLCGC 138
Score = 61.0 bits (148), Expect = 4e-11
Identities = 29/138 (21%), Positives = 50/138 (36%), Gaps = 12/138 (8%)
Query: 528 EKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE--REPEPDTTLYI 585
E EK ++ E T ++ + + D +Y+
Sbjct: 19 EAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYV 78
Query: 586 KNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALK 645
NL N + + R F GP+ SV VAR +P G+ FV+F A++
Sbjct: 79 GNLGNNGNKTELERAFGYYGPLRSVWVAR--NPP--------GFAFVEFEDPRDAADAVR 128
Query: 646 VLQNSSLDEHQIELKRSN 663
L +L ++ ++ SN
Sbjct: 129 ELDGRTLCGCRVRVELSN 146
Score = 44.5 bits (105), Expect = 2e-05
Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 4/66 (6%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ +L+ F G + V + G FAF+ + A A+ + +
Sbjct: 83 NNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRELDGRTLCGC 138
Query: 87 RIKVEK 92
R++VE
Sbjct: 139 RVRVEL 144
Score = 39.1 bits (91), Expect = 0.001
Identities = 19/71 (26%), Positives = 26/71 (36%), Gaps = 3/71 (4%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGITGLVEFLQKNQAKAAFNSLAYTK 507
+ V NL T+L+ F +G L V V P G VEF A A L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGF-AFVEFEDPRDAADAVRELDGRT 134
Query: 508 FKEVPLYLEWA 518
+ +E +
Sbjct: 135 LCGCRVRVELS 145
Score = 27.9 bits (62), Expect = 6.8
Identities = 20/118 (16%), Positives = 35/118 (29%), Gaps = 3/118 (2%)
Query: 162 LPLSNKDGEEKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHK 221
E + ++ Q A+ + D E+ T
Sbjct: 11 TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSC 70
Query: 222 RQYHTIVVKNLPAGVKKKDLKAYFK---PLPLASVRTTFLGMAYIGFKDEKNCNKALN 276
+ V NL K +L+ F PL V G A++ F+D ++ A+
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVR 128
>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 = 70.3 bits (173), Expect = 5e-15
Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 3/82 (3%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKET-DKTKGFALVTFLMPEHATQAYQ 396
F+ NL Y VTE+ + + F + V LP + ++ KGF F + A
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLNI-SAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79
Query: 397 HLDGTVFLGRMLHLIPGKPKEN 418
L+ R + + ++
Sbjct: 80 -LNEESLGNRRIRVDVADQAQD 100
Score = 65.0 bits (159), Expect = 4e-13
Identities = 21/96 (21%), Positives = 41/96 (42%), Gaps = 3/96 (3%)
Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 733
S + K + N+P+ + ++E F+ VRLP++ +GFG+
Sbjct: 8 HHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYA 66
Query: 734 EFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
EF + A+ L RR+ ++ A++A +
Sbjct: 67 EFEDLDSLLSALS--LNEESLGNRRIRVDVADQAQD 100
Score = 63.8 bits (156), Expect = 1e-12
Identities = 26/91 (28%), Positives = 45/91 (49%), Gaps = 9/91 (9%)
Query: 570 EEDEEREPEPDT---TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLS 626
R P + T ++ NL ++ TE+SI+ F+ I++V + R +P +P +
Sbjct: 6 HHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPR--EPSNPERL-- 60
Query: 627 MGYGFVQFYTRESLNQALKVLQNSSLDEHQI 657
G+G+ +F +SL AL L SL +I
Sbjct: 61 KGFGYAEFEDLDSLLSALS-LNEESLGNRRI 90
Score = 41.1 bits (97), Expect = 1e-04
Identities = 15/67 (22%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL--KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF 84
Y +T+E +K F ++ V+L + + + + F + + D +AL N +
Sbjct: 29 YDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLG 86
Query: 85 SSRIKVE 91
+ RI+V+
Sbjct: 87 NRRIRVD 93
Score = 38.4 bits (90), Expect = 8e-04
Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASVR------TT--FLGMAYIGFKDEKNCNKALNK 277
T + NLP V ++ +K +F+ L +++VR G Y F+D + AL+
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 80
Query: 278 NKSFWKGKQLNI 289
N+ +++ +
Sbjct: 81 NEESLGNRRIRV 92
Score = 29.9 bits (68), Expect = 0.83
Identities = 12/79 (15%), Positives = 21/79 (26%), Gaps = 7/79 (8%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFN 501
+ NLPY +K F L EF + +A +
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79
Query: 502 SLAYTKFKEVPLYLEWAPE 520
L + ++ A +
Sbjct: 80 -LNEESLGNRRIRVDVADQ 97
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 69.9 bits (172), Expect = 6e-15
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 2/82 (2%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
+ +IFVRNL + T L F + G + I E K+KG +V F PE A +A
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYAD--IKMENGKSKGCGVVKFESPEVAERAC 65
Query: 396 QHLDGTVFLGRMLHLIPGKPKE 417
+ ++G GR + + +
Sbjct: 66 RMMNGMKLSGREIDVRIDRNAS 87
Score = 65.7 bits (161), Expect = 2e-13
Identities = 17/89 (19%), Positives = 39/89 (43%), Gaps = 7/89 (7%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
++++NL F+ T ++ F +CG + + + G+ S G G V+F +
Sbjct: 5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-----GK--SKGCGVVKFES 57
Query: 637 RESLNQALKVLQNSSLDEHQIELKRSNRN 665
E +A +++ L +I+++
Sbjct: 58 PEVAERACRMMNGMKLSGREIDVRIDRNA 86
Score = 61.1 bits (149), Expect = 9e-12
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 4/88 (4%)
Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
+I VRN+PF +++ F G + + + + +G +G G V+F +
Sbjct: 4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI---KMENGKSKGCGVVKFESPEV 60
Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEAD 768
A+RA + + L GR + + A
Sbjct: 61 AERACRMM-NGMKLSGREIDVRIDRNAS 87
Score = 46.0 bits (110), Expect = 2e-06
Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 1/64 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ T + LK KF E G V +K GK + + + + A+ A N +
Sbjct: 18 FDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEVAERACRMMNGMKLSGR 76
Query: 87 RIKV 90
I V
Sbjct: 77 EIDV 80
Score = 35.6 bits (83), Expect = 0.007
Identities = 14/61 (22%), Positives = 22/61 (36%), Gaps = 10/61 (16%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-------YGITGLVEFLQKNQAKAAFNS 502
I V+NLP+ LK F G + + G+ V+F A+ A
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGV---VKFESPEVAERACRM 67
Query: 503 L 503
+
Sbjct: 68 M 68
Score = 28.3 bits (64), Expect = 2.9
Identities = 17/93 (18%), Positives = 31/93 (33%), Gaps = 8/93 (8%)
Query: 217 APVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF-----LGMAYIGFKDEKN 270
I V+NLP K LK F + G + F+ +
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEV 60
Query: 271 CNKALNK-NKSFWKGKQLNIYKYSKDNSAKYSG 302
+A N G+++++ + ++ S SG
Sbjct: 61 AERACRMMNGMKLSGREIDV-RIDRNASGPSSG 92
>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 = 70.0 bits (172), Expect = 7e-15
Identities = 19/102 (18%), Positives = 36/102 (35%), Gaps = 9/102 (8%)
Query: 317 AKHWKSQEDSVQFAEDIAESGRIFVRNLSY-TVTEDDLTKLFEKYGPLAEVILPIDKETD 375
+ H S R+F+ NL V+++DL ++F YG + ++ +
Sbjct: 3 SSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------ 56
Query: 376 KTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
F + F P+ A + + G+ L L
Sbjct: 57 --NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA 96
Score = 65.0 bits (159), Expect = 3e-13
Identities = 14/83 (16%), Positives = 37/83 (44%), Gaps = 11/83 (13%)
Query: 685 GSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
S++ + N+P + + ++ +F +G + + + FGF++F +
Sbjct: 22 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---------KNAFGFIQFDNPQSVRD 72
Query: 744 AMKALCQSTHLYGRRLVLEWAEE 766
A++ +G++L+LE +
Sbjct: 73 AIEXE-SQEMNFGKKLILEVSSS 94
Score = 55.4 bits (134), Expect = 1e-09
Identities = 17/90 (18%), Positives = 36/90 (40%), Gaps = 14/90 (15%)
Query: 575 REPEPDTTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
R + L+I NL + +++ + R F G I + + +GF+Q
Sbjct: 17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------------AFGFIQ 63
Query: 634 FYTRESLNQALKVLQNSSLDEHQIELKRSN 663
F +S+ A++ ++ L+ S+
Sbjct: 64 FDNPQSVRDAIEXESQEMNFGKKLILEVSS 93
Score = 45.0 bits (107), Expect = 3e-06
Identities = 11/64 (17%), Positives = 25/64 (39%), Gaps = 7/64 (10%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
+++E L F G + + +K F FI + + A++ + F +
Sbjct: 34 NVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFGKK 86
Query: 88 IKVE 91
+ +E
Sbjct: 87 LILE 90
Score = 37.3 bits (87), Expect = 0.002
Identities = 14/71 (19%), Positives = 30/71 (42%), Gaps = 5/71 (7%)
Query: 450 ILVKNLPYRTL-PTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
+ + NLP + + DL +F P+G + ++ + + G ++F + A +
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAF---GFIQFDNPQSVRDAIEXESQEM 81
Query: 508 FKEVPLYLEWA 518
L LE +
Sbjct: 82 NFGKKLILEVS 92
>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 = 70.0 bits (172), Expect = 1e-14
Identities = 20/80 (25%), Positives = 40/80 (50%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+F+ +L + DL ++F +G + + IDK+T+ +K F V++ P A A Q +
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 399 DGTVFLGRMLHLIPGKPKEN 418
+G + L + + K +
Sbjct: 88 NGFQIGMKRLKVQLKRSKND 107
Score = 55.4 bits (134), Expect = 1e-09
Identities = 16/110 (14%), Positives = 48/110 (43%), Gaps = 6/110 (5%)
Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM 721
S+ + ++ S G+ + + ++P + ++ ++F FG + ++
Sbjct: 2 SSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKV---F 58
Query: 722 V--GSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
+ + L + FGFV + A+ A++++ + +RL ++ ++
Sbjct: 59 IDKQTNLSKCFGFVSYDNPVSAQAAIQSM-NGFQIGMKRLKVQLKRSKND 107
Score = 54.6 bits (132), Expect = 3e-09
Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 10/90 (11%)
Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
++E L+I +L + + + F G + S V D ++ S +GF
Sbjct: 17 GSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFI--DKQT-NL--SKCFGF 71
Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKR 661
V + S A++ S++ QI +KR
Sbjct: 72 VSYDNPVSAQAAIQ-----SMNGFQIGMKR 96
Score = 39.6 bits (93), Expect = 4e-04
Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 5/67 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+ + L F G V ++ K T + F F+ Y AQAA+ N +
Sbjct: 35 QEFGDQDLLQMFMPFGNVVSAKVFIDKQT--NLSKCFGFVSYDNPVSAQAAIQSMNGFQI 92
Query: 84 FSSRIKV 90
R+KV
Sbjct: 93 GMKRLKV 99
Score = 33.4 bits (77), Expect = 0.061
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 503
+ + +LP DL +F PFG++ V T L V + A+AA S+
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 68.6 bits (168), Expect = 1e-14
Identities = 20/73 (27%), Positives = 26/73 (35%), Gaps = 7/73 (9%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
S I V+NL ++ L + Y D+ K A VT L E A A
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAI 57
Query: 396 QHLDGTVFLGRML 408
Q F G+ L
Sbjct: 58 QMFHQYSFRGKDL 70
Score = 67.8 bits (166), Expect = 3e-14
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 9/80 (11%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
S ILV+N+P + EV +L K + K ++ FV + +A+ A+
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD--------LKYCYVDRNKRTAFVTLLNGEQAQNAI 57
Query: 746 KALCQSTHLYGRRLVLEWAE 765
+ Q G+ L+++
Sbjct: 58 QMFHQ-YSFRGKDLIVQLQP 76
Score = 54.7 bits (132), Expect = 1e-09
Identities = 19/76 (25%), Positives = 29/76 (38%), Gaps = 1/76 (1%)
Query: 444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL 503
+ ILVKNLP + ++ L + + L V T V L QA+ A
Sbjct: 2 SSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60
Query: 504 AYTKFKEVPLYLEWAP 519
F+ L ++ P
Sbjct: 61 HQYSFRGKDLIVQLQP 76
Score = 47.8 bits (114), Expect = 4e-07
Identities = 13/82 (15%), Positives = 25/82 (30%), Gaps = 12/82 (14%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
+ + +KNL +S + K + V R K FV E
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNK-----------RTAFVTLLNGEQA 53
Query: 641 NQALKVLQNSSLDEHQIELKRS 662
A+++ S + ++
Sbjct: 54 QNAIQMFHQYSFRGKDLIVQLQ 75
Score = 43.6 bits (103), Expect = 9e-06
Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 3/79 (3%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL-GMAYIGFKDEKNCNKALNK-NKSFWK 283
I+VKNLP +++ K L A++ + + A+ ++ ++
Sbjct: 7 GILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFR 66
Query: 284 GKQLNIYKYSKDNSAKYSG 302
GK L + + ++ SG
Sbjct: 67 GKDLIV-QLQPTDALLCSG 84
Score = 42.0 bits (99), Expect = 3e-05
Identities = 12/65 (18%), Positives = 25/65 (38%), Gaps = 6/65 (9%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+++ ++ LKY + +R AF+ +QAQ A+ F+
Sbjct: 15 QDSNCQEVHDLLKDYD------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGK 68
Query: 87 RIKVE 91
+ V+
Sbjct: 69 DLIVQ 73
>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 = 69.4 bits (170), Expect = 2e-14
Identities = 13/85 (15%), Positives = 31/85 (36%), Gaps = 1/85 (1%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+ N+ +++T+ D+ + E + + + G ALV F + A ++
Sbjct: 14 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKS 73
Query: 395 YQHLDGTVFLGRMLHLIPGKPKENE 419
+ L GR + ++
Sbjct: 74 -ERLHRKKLNGREAFVHVVTLEDMR 97
Score = 64.8 bits (158), Expect = 6e-13
Identities = 16/107 (14%), Positives = 35/107 (32%), Gaps = 5/107 (4%)
Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFGF 732
+ NIPF + +V + + + V + +G G
Sbjct: 4 GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD--NNGQGLGQAL 61
Query: 733 VEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
V+F +++A+++ + L GR + D E + +
Sbjct: 62 VQFKNEDDARKSER--LHRKKLNGREAFVHVVTLEDMREIEKNPPAQ 106
Score = 62.1 bits (151), Expect = 6e-12
Identities = 13/94 (13%), Positives = 31/94 (32%), Gaps = 8/94 (8%)
Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPGQFLSMGYGF 631
E +I N+ F+ T+ + + + +V V + + +G
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQ------GLGQAL 61
Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKRSNRN 665
VQF + ++ + L L+ + +
Sbjct: 62 VQFKNEDDARKSER-LHRKKLNGREAFVHVVTLE 94
Score = 58.2 bits (141), Expect = 2e-10
Identities = 14/108 (12%), Positives = 37/108 (34%), Gaps = 8/108 (7%)
Query: 212 PPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL--------GMAYI 263
S + N+P + K D+ + + +P+ L G A +
Sbjct: 3 SGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALV 62
Query: 264 GFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNAS 311
FK+E + K+ ++ G++ ++ + ++ + +
Sbjct: 63 QFKNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSG 110
Score = 45.5 bits (108), Expect = 3e-06
Identities = 16/91 (17%), Positives = 30/91 (32%), Gaps = 7/91 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALD----YFNNT 81
+ IT+ + E + V + G+ A + + ED A+ + N
Sbjct: 25 FSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGR 84
Query: 82 YVFSSRIKVEKCSNLGDTTKPKSWSKYAPDS 112
F + +E + P + K P S
Sbjct: 85 EAFVHVVTLEDMREIEK--NPPAQGKSGPSS 113
Score = 39.7 bits (93), Expect = 4e-04
Identities = 10/61 (16%), Positives = 21/61 (34%), Gaps = 6/61 (9%)
Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKA 498
+K + N+P+ D+ E + G LV+F ++ A+
Sbjct: 13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 72
Query: 499 A 499
+
Sbjct: 73 S 73
>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 = 69.5 bits (170), Expect = 2e-14
Identities = 23/107 (21%), Positives = 44/107 (41%), Gaps = 5/107 (4%)
Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGF 732
KR S + G + ++ +PF+A+ V + FK ++ + + G G GF
Sbjct: 14 KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK--ATGEGF 71
Query: 733 VEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
VEF + + K A+ ++ R + + + +E I R
Sbjct: 72 VEFRNEADYKAALC--RHKQYMGNRFIQVHPITKKGMLEKIDMIRKR 116
Score = 69.5 bits (170), Expect = 2e-14
Identities = 13/89 (14%), Positives = 25/89 (28%), Gaps = 1/89 (1%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
++++ L + + F+K + + I K G V F A
Sbjct: 24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA 83
Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGNVD 423
R + + P K +D
Sbjct: 84 LC-RHKQYMGNRFIQVHPITKKGMLEKID 111
Score = 66.0 bits (161), Expect = 4e-13
Identities = 24/119 (20%), Positives = 41/119 (34%), Gaps = 9/119 (7%)
Query: 563 PEVEENVEEDEEREP-EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKS 620
+ + R P E +Y+K L F + + FKK + S+ +A + K
Sbjct: 7 GKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK- 65
Query: 621 PGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSN 679
+ G GFV+F AL + I++ + E + RK
Sbjct: 66 -----ATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQ 118
Score = 59.9 bits (145), Expect = 5e-11
Identities = 18/104 (17%), Positives = 41/104 (39%), Gaps = 8/104 (7%)
Query: 201 SKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL-- 258
S ++ PS S++ + +K LP + K + +FK L +
Sbjct: 2 SSGSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG 61
Query: 259 ------GMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDN 296
G ++ F++E + AL ++K + + + ++ +K
Sbjct: 62 PNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKKG 105
Score = 45.2 bits (107), Expect = 6e-06
Identities = 17/90 (18%), Positives = 35/90 (38%), Gaps = 5/90 (5%)
Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
++ + + F++ V D + + Y GK F+ + E +AAL + Y+ +
Sbjct: 35 FEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR-HKQYMGN 93
Query: 86 SRIKVEKCSN---LGDTTKPKSWSKYAPDS 112
I+V + L + + P S
Sbjct: 94 RFIQVHPITKKGMLEKIDMIRKRLQSGPSS 123
Score = 36.7 bits (85), Expect = 0.006
Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 6/63 (9%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQA 496
+ + +K LP+ + F+ + + YG G VEF +
Sbjct: 21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADY 80
Query: 497 KAA 499
KAA
Sbjct: 81 KAA 83
>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 = 69.0 bits (169), Expect = 2e-14
Identities = 16/95 (16%), Positives = 34/95 (35%), Gaps = 1/95 (1%)
Query: 323 QEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFAL 382
S + D A G + +R L + +++++ + F + + ++ G A
Sbjct: 2 SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61
Query: 383 VTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
V F E A +A + R + + E
Sbjct: 62 VQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAE 95
Score = 62.8 bits (153), Expect = 2e-12
Identities = 20/96 (20%), Positives = 39/96 (40%), Gaps = 8/96 (8%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPGQFLSMG 628
+ D + ++ L F +++ I + F + +T+ + S G
Sbjct: 5 SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR------STG 58
Query: 629 YGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
FVQF ++E +ALK + IE+ +S+R
Sbjct: 59 EAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSR 93
Score = 57.4 bits (139), Expect = 2e-10
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 4/75 (5%)
Query: 674 KRKSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFG 731
S N + +R +PF + E+ + F + + LP G G
Sbjct: 3 SGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR--STGEA 60
Query: 732 FVEFITKNEAKRAMK 746
FV+F ++ A++A+K
Sbjct: 61 FVQFASQEIAEKALK 75
Score = 51.7 bits (124), Expect = 2e-08
Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 11/94 (11%)
Query: 220 HKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL--------GMAYIGFKDEKNC 271
+ ++ LP G K+++ +F L + T G A++ F ++
Sbjct: 11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70
Query: 272 NKALNKNKSFWKGKQLNIYKYSKD---NSAKYSG 302
KAL K+K + + I+K S+ S SG
Sbjct: 71 EKALKKHKERIGHRYIEIFKSSRAEVRTSGPSSG 104
Score = 42.4 bits (100), Expect = 3e-05
Identities = 13/69 (18%), Positives = 31/69 (44%), Gaps = 2/69 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ ++E++ F V + + L +G+ AF+ + ++ A+ AL + +
Sbjct: 25 FGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGH 83
Query: 86 SRIKVEKCS 94
I++ K S
Sbjct: 84 RYIEIFKSS 92
Score = 37.0 bits (86), Expect = 0.003
Identities = 9/63 (14%), Positives = 22/63 (34%), Gaps = 6/63 (9%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQA 496
+ + + ++ LP+ ++ F + + P G V+F + A
Sbjct: 11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70
Query: 497 KAA 499
+ A
Sbjct: 71 EKA 73
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 68.6 bits (168), Expect = 3e-14
Identities = 20/70 (28%), Positives = 35/70 (50%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+F+ +L T+ DL F +G + + IDK+T +K F V+F P+ A A + +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 399 DGTVFLGRML 408
+G + L
Sbjct: 103 NGFQVGTKRL 112
Score = 57.0 bits (138), Expect = 4e-10
Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 5/85 (5%)
Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
++ E L+I +L T+ + F G + S V D ++ S +GFV
Sbjct: 33 KQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFI--DKQT-SL--SKCFGFV 87
Query: 633 QFYTRESLNQALKVLQNSSLDEHQI 657
F +S A+K + + ++
Sbjct: 88 SFDNPDSAQVAIKAMNGFQVGTKRL 112
Score = 56.6 bits (137), Expect = 6e-10
Identities = 17/92 (18%), Positives = 41/92 (44%), Gaps = 6/92 (6%)
Query: 676 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFV 733
+ G + + ++P + +++ F FG + ++ + + L + FGFV
Sbjct: 31 AGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKV---FIDKQTSLSKCFGFV 87
Query: 734 EFITKNEAKRAMKALCQSTHLYGRRLVLEWAE 765
F + A+ A+KA+ + +RL ++ +
Sbjct: 88 SFDNPDSAQVAIKAM-NGFQVGTKRLKVQLKK 118
Score = 40.8 bits (96), Expect = 2e-04
Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 5/67 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+ T L + F G V ++ K T + F F+ + D AQ A+ N V
Sbjct: 50 QEFTDTDLASTFLPFGNVISAKVFIDKQT--SLSKCFGFVSFDNPDSAQVAIKAMNGFQV 107
Query: 84 FSSRIKV 90
+ R+KV
Sbjct: 108 GTKRLKV 114
Score = 33.1 bits (76), Expect = 0.093
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 503
+ + +LP TDL + F PFG++ V T L V F + A+ A ++
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
>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 = 68.6 bits (168), Expect = 3e-14
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 9/85 (10%)
Query: 336 SGRIFVRNLSY-TVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+ R+F+ NL+ V + D+ +F KYG +A + KG+A V + HA A
Sbjct: 27 NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAA 78
Query: 395 YQHLDGTVFLGRMLHLIPGKPKENE 419
+G V G+ L + + +
Sbjct: 79 VLGENGRVLAGQTLDINMAGEPKPD 103
Score = 67.8 bits (166), Expect = 6e-14
Identities = 26/121 (21%), Positives = 51/121 (42%), Gaps = 21/121 (17%)
Query: 668 SEATTVKRKSSNVAKQT-----GSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKM 721
S ++K ++SNV + S++ + N+ K+S+VE +F +G + +
Sbjct: 5 SSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---- 60
Query: 722 VGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYF 781
H+G+ FV++ + A+ A+ L G+ L + A E R+
Sbjct: 61 -----HKGYAFVQYSNERHARAAVLGE-NGRVLAGQTLDINMAGEPK-----PDRSGPSS 109
Query: 782 G 782
G
Sbjct: 110 G 110
Score = 57.0 bits (138), Expect = 3e-10
Identities = 18/110 (16%), Positives = 36/110 (32%), Gaps = 17/110 (15%)
Query: 560 QGVPEVEENVEEDEEREPEPD-TTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVARKKD 617
G+ + + +P+ + ++I NLN + + F K G +A +V +
Sbjct: 6 SGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--- 62
Query: 618 PKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI--ELKRSNRN 665
GY FVQ+ A+ L + + +
Sbjct: 63 ----------GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKP 102
Score = 45.4 bits (108), Expect = 3e-06
Identities = 11/64 (17%), Positives = 25/64 (39%), Gaps = 7/64 (10%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
+ + ++ F + G V + + +AF+ Y E A+AA+ N +
Sbjct: 39 LVKKSDVETIFSKYGRVAGCSVH-------KGYAFVQYSNERHARAAVLGENGRVLAGQT 91
Query: 88 IKVE 91
+ +
Sbjct: 92 LDIN 95
Score = 33.9 bits (78), Expect = 0.042
Identities = 13/69 (18%), Positives = 25/69 (36%), Gaps = 5/69 (7%)
Query: 452 VKNLPY-RTLPTDLKALFEPFGDLGRVLVPP-YGITGLVEFLQKNQAKAAFNSLAYTKFK 509
+ NL +D++ +F +G + V Y V++ + A+AA
Sbjct: 32 IGNLNTALVKKSDVETIFSKYGRVAGCSVHKGY---AFVQYSNERHARAAVLGENGRVLA 88
Query: 510 EVPLYLEWA 518
L + A
Sbjct: 89 GQTLDINMA 97
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 67.6 bits (166), Expect = 4e-14
Identities = 20/95 (21%), Positives = 41/95 (43%), Gaps = 13/95 (13%)
Query: 332 DIAESGRIFVRNLSY-TVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
+I R+F+ NL V+++DL ++F YG + ++ + F + F P+
Sbjct: 6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQS 57
Query: 391 ATQAYQHLDGTVFLGRMLHL----IPGKPKENEGN 421
A + + G+ L L +P+ + G+
Sbjct: 58 VRDAIECESQEMNFGKKLILEVSSSNARPQFDHGD 92
Score = 66.5 bits (163), Expect = 1e-13
Identities = 16/99 (16%), Positives = 39/99 (39%), Gaps = 18/99 (18%)
Query: 685 GSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
S++ + N+P + + ++ +F +G + + + FGF++F +
Sbjct: 10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---------KNAFGFIQFDNPQSVRD 60
Query: 744 AMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFG 782
A++ +G++L+LE + R G
Sbjct: 61 AIECE-SQEMNFGKKLILEVSSS-------NARPQFDHG 91
Score = 57.6 bits (140), Expect = 1e-10
Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 14/88 (15%)
Query: 579 PDTTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
P + L+I NL + +++ + R F G I + + +GF+QF
Sbjct: 9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------------AFGFIQFDNP 55
Query: 638 ESLNQALKVLQNSSLDEHQIELKRSNRN 665
+S+ A++ ++ L+ S+ N
Sbjct: 56 QSVRDAIECESQEMNFGKKLILEVSSSN 83
Score = 46.8 bits (112), Expect = 8e-07
Identities = 11/65 (16%), Positives = 25/65 (38%), Gaps = 7/65 (10%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+++E L F G + + +K F FI + + A++ + F
Sbjct: 21 KNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGK 73
Query: 87 RIKVE 91
++ +E
Sbjct: 74 KLILE 78
Score = 32.6 bits (75), Expect = 0.097
Identities = 14/71 (19%), Positives = 30/71 (42%), Gaps = 5/71 (7%)
Query: 450 ILVKNLPYRTL-PTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
+ + NLP + + DL +F P+G + ++ + + G ++F + A +
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAF---GFIQFDNPQSVRDAIECESQEM 69
Query: 508 FKEVPLYLEWA 518
L LE +
Sbjct: 70 NFGKKLILEVS 80
>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 = 67.1 bits (164), Expect = 5e-14
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP-----IDKETDKTKGFALVTFLMPEHAT 392
R++V N+ + +TE+ + F L + + + ++ K FA + F + T
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 393 QAYQHLDGTVFLGRML 408
QA DG +F G+ L
Sbjct: 68 QAMA-FDGIIFQGQSL 82
Score = 51.7 bits (124), Expect = 1e-08
Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 6/77 (7%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRL----PKKMVGSGLHRGFGFVEFITKNEAK 742
++ V NIPF + + + F A L + P V + F F+EF + +E
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 743 RAMKALCQSTHLYGRRL 759
+AM A G+ L
Sbjct: 68 QAM-AF-DGIIFQGQSL 82
Score = 51.3 bits (123), Expect = 2e-08
Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 1/79 (1%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+ N+ F TE+++ F + +T A + + F++F + + Q
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 643 ALKVLQNSSLDEHQIELKR 661
A+ ++++R
Sbjct: 69 AMA-FDGIIFQGQSLKIRR 86
Score = 33.6 bits (77), Expect = 0.030
Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 13/81 (16%)
Query: 222 RQYHTIVVKNLPAGVKKKDLKAYFKPL------------PLASVRTTF-LGMAYIGFKDE 268
+ V N+P G+ ++ + +F P+ +V+ A++ F+
Sbjct: 4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63
Query: 269 KNCNKALNKNKSFWKGKQLNI 289
+A+ + ++G+ L I
Sbjct: 64 DETTQAMAFDGIIFQGQSLKI 84
Score = 32.4 bits (74), Expect = 0.096
Identities = 11/70 (15%), Positives = 26/70 (37%), Gaps = 7/70 (10%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE------GKFRRFAFIGYHREDQAQAALDYFNN 80
+ IT+E + F + + + + + FAF+ + D+ A+ F+
Sbjct: 16 FGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDG 74
Query: 81 TYVFSSRIKV 90
+K+
Sbjct: 75 IIFQGQSLKI 84
Score = 31.6 bits (72), Expect = 0.17
Identities = 12/68 (17%), Positives = 20/68 (29%), Gaps = 11/68 (16%)
Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT-----------GLVEFLQK 493
S R + V N+P+ + F LG + P +EF
Sbjct: 4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63
Query: 494 NQAKAAFN 501
++ A
Sbjct: 64 DETTQAMA 71
>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 = 67.3 bits (165), Expect = 7e-14
Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 6/68 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R++V L + L + F+++G + + FA + + + A A
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72
Query: 398 LDGTVFLG 405
+ G G
Sbjct: 73 MRGFPLGG 80
Score = 64.6 bits (158), Expect = 4e-13
Identities = 12/77 (15%), Positives = 31/77 (40%), Gaps = 11/77 (14%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
P T L++ L N++ ++ R F + G I ++ + + ++Q+ +
Sbjct: 14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD-----------SFAYIQYES 62
Query: 637 RESLNQALKVLQNSSLD 653
++ A ++ L
Sbjct: 63 LDAAQAACAKMRGFPLG 79
Score = 53.0 bits (128), Expect = 5e-09
Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 10/77 (12%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC 749
V + + + F FG ++ + K F ++++ + + A+ A +
Sbjct: 22 VGGLGPNTSLAALAREFDRFGSIRTIDHVK-------GDSFAYIQYESLDAAQAACAKM- 73
Query: 750 QSTHLYG--RRLVLEWA 764
+ L G RRL +++A
Sbjct: 74 RGFPLGGPDRRLRVDFA 90
Score = 40.7 bits (96), Expect = 1e-04
Identities = 10/52 (19%), Positives = 19/52 (36%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL 503
V L T L F+ FG + + +++ + A+AA +
Sbjct: 22 VGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKM 73
Score = 40.7 bits (96), Expect = 1e-04
Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 7/67 (10%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ L +F+ G++ + K FA+I Y D AQAA +
Sbjct: 27 PNTSLAALAREFDRFGSIRTIDHV-----KGDSFAYIQYESLDAAQAACAKMRGFPLGGP 81
Query: 87 --RIKVE 91
R++V+
Sbjct: 82 DRRLRVD 88
Score = 28.0 bits (63), Expect = 3.2
Identities = 9/55 (16%), Positives = 15/55 (27%), Gaps = 2/55 (3%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKPL-PLASVRT-TFLGMAYIGFKDEKNCNKALNK 277
+ V L L F + ++ AYI ++ A K
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAK 72
>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 = 66.9 bits (164), Expect = 8e-14
Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 3/88 (3%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
E +FV + + E ++ F +YG + EV + D+ T +KG+ V+F
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVD 62
Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
+ + F G+ L L P K+N
Sbjct: 63 VQKIVE--SQINFHGKKLKLGPAIRKQN 88
Score = 57.2 bits (139), Expect = 2e-10
Identities = 18/91 (19%), Positives = 36/91 (39%), Gaps = 10/91 (10%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T+++ ++ E IR F + G + V + + S GYGFV FY
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGV------SKGYGFVSFYNDVD- 62
Query: 641 NQALKVLQNS-SLDEHQIELKRSNRNLESEA 670
K++++ + +++L + R
Sbjct: 63 --VQKIVESQINFHGKKLKLGPAIRKQNLST 91
Score = 52.6 bits (127), Expect = 8e-09
Identities = 19/96 (19%), Positives = 44/96 (45%), Gaps = 5/96 (5%)
Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
K + + V I + ++E+ F +G +K V++ +G+ +G+GFV F +
Sbjct: 5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD--RTGVSKGYGFVSFYNDVD 62
Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKR 776
++ ++ + +G++L L A N+ +
Sbjct: 63 VQKIVE---SQINFHGKKLKLGPAIRKQNLSTYHVQ 95
Score = 42.2 bits (100), Expect = 4e-05
Identities = 7/50 (14%), Positives = 26/50 (52%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALD 76
++ + ++++ F G+V +V++ G + + F+ ++ + Q ++
Sbjct: 19 VRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68
Score = 29.5 bits (67), Expect = 1.3
Identities = 5/24 (20%), Positives = 12/24 (50%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGD 473
+ V + R T++++ F +G
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGS 35
>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 = 68.3 bits (167), Expect = 9e-14
Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 5/88 (5%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPL----AEVILPI-DKETDKTKGFALVTFLMPEH 390
+ RI+V+NL+ V E DL +F +Y ++ I + + KG A + +
Sbjct: 45 NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104
Query: 391 ATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
A +A + +G V G+ + + +
Sbjct: 105 AAKALKEANGYVLFGKPMVVQFARSARP 132
Score = 62.5 bits (152), Expect = 9e-12
Identities = 22/133 (16%), Positives = 47/133 (35%), Gaps = 1/133 (0%)
Query: 539 EEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREP-EPDTTLYIKNLNFNSTEDSI 597
+ + + E + + E E + EP EP+ +Y+KNL + E +
Sbjct: 3 LGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDL 62
Query: 598 RRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQI 657
+ F + +S T D + + G F+ ++ +ALK L +
Sbjct: 63 KYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM 122
Query: 658 ELKRSNRNLESEA 670
++ + +
Sbjct: 123 VVQFARSARPKQD 135
Score = 56.4 bits (136), Expect = 1e-09
Identities = 19/139 (13%), Positives = 56/139 (40%), Gaps = 8/139 (5%)
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
+ + + ++E R +R + + I V+N+ ++
Sbjct: 4 GSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCR---IYVKNLAKHVQEK 60
Query: 701 EVEELFKAFGEL----KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG 756
+++ +F + + + + +++ G +G F+ + A +A+K L+G
Sbjct: 61 DLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEA-NGYVLFG 119
Query: 757 RRLVLEWAEEADNVEDIRK 775
+ +V+++A A +D ++
Sbjct: 120 KPMVVQFARSARPKQDPKE 138
Score = 41.0 bits (96), Expect = 3e-04
Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 6/71 (8%)
Query: 27 YKITQEQLKAKFEEKGTVTD------VQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
+ ++ LK F + ++ EG+ + AFIG E A AL N
Sbjct: 55 KHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANG 114
Query: 81 TYVFSSRIKVE 91
+F + V+
Sbjct: 115 YVLFGKPMVVQ 125
Score = 39.4 bits (92), Expect = 8e-04
Identities = 20/116 (17%), Positives = 32/116 (27%), Gaps = 13/116 (11%)
Query: 431 SERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGIT---- 485
L F I VKNL DLK +F + D + I
Sbjct: 29 EMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKE 88
Query: 486 ------GLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEK 535
+ + A A P+ +++A ++ +GK K
Sbjct: 89 GRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSA--RPKQDPKEGKRK 142
Score = 32.1 bits (73), Expect = 0.29
Identities = 26/89 (29%), Positives = 38/89 (42%), Gaps = 15/89 (16%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL-------------GMAYIGFKDEKNC 271
I VKNL V++KDLK F S T + G A+IG +EK
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105
Query: 272 NKALNK-NKSFWKGKQLNIYKYSKDNSAK 299
KAL + N GK + + ++++ K
Sbjct: 106 AKALKEANGYVLFGKPMVV-QFARSARPK 133
>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 = 66.4 bits (163), Expect = 1e-13
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
++S +IFV + + E +L + F+K+G + EV++ D E + +GF +TF + Q
Sbjct: 8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQ 67
Query: 394 A----YQHLDG 400
A + + G
Sbjct: 68 AVNMHFHDIMG 78
Score = 51.8 bits (125), Expect = 1e-08
Identities = 19/86 (22%), Positives = 40/86 (46%), Gaps = 6/86 (6%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
+++ + N E +R +FKK G + V + D + + G+GF+ F
Sbjct: 6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVM--IYDAEK-QR--PRGFGFITFE 60
Query: 636 TRESLNQALKVLQNSSLDEHQIELKR 661
+S++QA+ + + ++E+KR
Sbjct: 61 DEQSVDQAVN-MHFHDIMGKKVEVKR 85
Score = 47.2 bits (113), Expect = 7e-07
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
SS + +KI V IP ++E+ E FK FG + V + RGFGF+ F
Sbjct: 2 SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDA-EKQRPRGFGFITFE 60
Query: 737 TKNEAKRAMKA 747
+ +A+
Sbjct: 61 DEQSVDQAVNM 71
Score = 36.4 bits (85), Expect = 0.004
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAAL 75
+ + +L+ F++ G VT+V + Y E + R F FI + E A+
Sbjct: 20 HNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>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 = 66.1 bits (162), Expect = 1e-13
Identities = 20/87 (22%), Positives = 41/87 (47%), Gaps = 1/87 (1%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVI-LPIDKETDKTKGFALVTFLMPEHATQA 394
S IF+ NL + E L F +G + + + D +T +KG+A + F + + A
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGN 421
+ ++G R + + K+++G+
Sbjct: 65 IEAMNGQYLCNRPITVSYAFKKDSKGS 91
Score = 57.2 bits (139), Expect = 2e-10
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 6/80 (7%)
Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVT-VARKKDPKSPGQFLSMGYGFVQFYTR 637
+ ++I NL+ E + F G I + R DP + G S GY F+ F +
Sbjct: 4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMR--DPDT-GN--SKGYAFINFASF 58
Query: 638 ESLNQALKVLQNSSLDEHQI 657
++ + A++ + L I
Sbjct: 59 DASDAAIEAMNGQYLCNRPI 78
Score = 48.7 bits (117), Expect = 2e-07
Identities = 20/86 (23%), Positives = 45/86 (52%), Gaps = 5/86 (5%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKR 743
S I + N+ + + + + F AFG + ++ PK M +G +G+ F+ F + + +
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVI--LQTPKIMRDPDTGNSKGYAFINFASFDASDA 63
Query: 744 AMKALCQSTHLYGRRLVLEWAEEADN 769
A++A+ +L R + + +A + D+
Sbjct: 64 AIEAM-NGQYLCNRPITVSYAFKKDS 88
Score = 34.5 bits (80), Expect = 0.016
Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQ--LKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF 84
+I ++ L F G + ++ G + +AFI + D + AA++ N Y+
Sbjct: 15 PEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLC 74
Query: 85 SSRIKV 90
+ I V
Sbjct: 75 NRPITV 80
>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 = 67.2 bits (164), Expect = 1e-13
Identities = 19/112 (16%), Positives = 42/112 (37%), Gaps = 8/112 (7%)
Query: 554 AEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI-ASVTV 612
+ + ++ + D + ++ L F T++ I + F + +T+
Sbjct: 16 PRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITL 75
Query: 613 ARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
+ K G FVQF ++E +AL + IE+ +S++
Sbjct: 76 PVDPEGK------ITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKSSQ 120
Score = 66.4 bits (162), Expect = 2e-13
Identities = 19/96 (19%), Positives = 33/96 (34%), Gaps = 1/96 (1%)
Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
Q + D A G + +R L + T++++ + F + I K G A
Sbjct: 28 QQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEA 87
Query: 382 LVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
V F E A +A R + + +E
Sbjct: 88 FVQFASQELAEKALG-KHKERIGHRYIEVFKSSQEE 122
Score = 59.5 bits (144), Expect = 7e-11
Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 3/86 (3%)
Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKK 720
S+ + + R S++ + +R +PF + E+ + F + + LP
Sbjct: 19 SHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVD 78
Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMK 746
G G FV+F ++ A++A+
Sbjct: 79 PEGK--ITGEAFVQFASQELAEKALG 102
Score = 51.8 bits (124), Expect = 3e-08
Identities = 18/105 (17%), Positives = 39/105 (37%), Gaps = 8/105 (7%)
Query: 199 TKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL 258
S + + + ++ LP G K+++ +F L + T
Sbjct: 17 RGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLP 76
Query: 259 --------GMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKD 295
G A++ F ++ KAL K+K + + ++K S++
Sbjct: 77 VDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQE 121
Score = 43.7 bits (103), Expect = 2e-05
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 2/69 (2%)
Query: 27 YKITQEQLKAKFEEKGTV-TDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ T+E++ F V + L EGK AF+ + ++ A+ AL + +
Sbjct: 52 FGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGH 110
Query: 86 SRIKVEKCS 94
I+V K S
Sbjct: 111 RYIEVFKSS 119
Score = 37.6 bits (87), Expect = 0.003
Identities = 9/63 (14%), Positives = 23/63 (36%), Gaps = 6/63 (9%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQA 496
++ + + ++ LP+ ++ F + + P G V+F + A
Sbjct: 38 DSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELA 97
Query: 497 KAA 499
+ A
Sbjct: 98 EKA 100
>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 = 72.6 bits (177), Expect = 2e-13
Identities = 28/140 (20%), Positives = 56/140 (40%), Gaps = 10/140 (7%)
Query: 533 KEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVE-----EDEEREPEPDTTLYIKN 587
++ E EE+ E E ++ EVE ++ D + + TL++
Sbjct: 50 DPRDAPPPTRAETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVAR 109
Query: 588 LNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVL 647
+N+++TE +RR F+ GPI + + K P GY F+++ ++ A K
Sbjct: 110 VNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKP-----RGYAFIEYEHERDMHSAYKHA 164
Query: 648 QNSSLDEHQIELKRSNRNLE 667
+D ++ +
Sbjct: 165 DGKKIDGRRVLVDVERGRTV 184
Score = 64.9 bits (157), Expect = 4e-11
Identities = 22/73 (30%), Positives = 37/73 (50%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV ++Y TE L + FE YGP+ + + K + K +G+A + + AY+H
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 399 DGTVFLGRMLHLI 411
DG GR + +
Sbjct: 165 DGKKIDGRRVLVD 177
Score = 41.8 bits (97), Expect = 8e-04
Identities = 16/79 (20%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V + + +S++ F+ +G +K + + SG RG+ F+E+ + + A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVY-SKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 748 LCQSTHLYGRRLVLEWAEE 766
+ GRR++++
Sbjct: 164 A-DGKKIDGRRVLVDVERG 181
Score = 33.7 bits (76), Expect = 0.22
Identities = 21/168 (12%), Positives = 48/168 (28%), Gaps = 15/168 (8%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFN 501
+ + V + Y T + L+ FE +G + R+ + +G +E+ + +A+
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 502 SLAYTKFKEVPLYLE---------WAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKEN 552
K + ++ W P + +G G + E
Sbjct: 163 HADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDER 222
Query: 553 TAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRH 600
+ + E E ++ + + S R
Sbjct: 223 PGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRD 270
>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 = 65.8 bits (161), Expect = 2e-13
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 11/74 (14%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
TTLY+ L TE +R HF + G I ++TV +++ F+QF TR++
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ-----------QCAFIQFATRQAA 61
Query: 641 NQALKVLQNSSLDE 654
A + N +
Sbjct: 62 EVAAEKSFNKLIVN 75
Score = 61.5 bits (150), Expect = 4e-12
Identities = 15/75 (20%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC 749
V + ++++ F FGE++ + + ++ + F++F T+ A+ A +
Sbjct: 17 VGGLGDTITETDLRNHFYQFGEIRTITVVQR-------QQCAFIQFATRQAAEVAAEKSF 69
Query: 750 QSTHLYGRRLVLEWA 764
+ GRRL ++W
Sbjct: 70 NKLIVNGRRLNVKWG 84
Score = 58.8 bits (143), Expect = 4e-11
Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 7/73 (9%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH- 397
++V L T+TE DL F ++G + + + + A + F + A A +
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68
Query: 398 LDGTVFLGRMLHL 410
+ + GR L++
Sbjct: 69 FNKLIVNGRRLNV 81
Score = 39.9 bits (94), Expect = 2e-04
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 1/75 (1%)
Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQA-KAAFNSL 503
++ + V L TDL+ F FG++ + V ++F + A AA S
Sbjct: 10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSF 69
Query: 504 AYTKFKEVPLYLEWA 518
L ++W
Sbjct: 70 NKLIVNGRRLNVKWG 84
Score = 38.4 bits (90), Expect = 7e-04
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 6/65 (9%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGY-HREDQAQAALDYFNNTYVFS 85
IT+ L+ F + G + + + ++ AFI + R+ AA FN V
Sbjct: 22 DTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNG 76
Query: 86 SRIKV 90
R+ V
Sbjct: 77 RRLNV 81
Score = 31.5 bits (72), Expect = 0.17
Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 4/72 (5%)
Query: 222 RQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVR-TTFLGMAYIGFKDEKNCNKALNK-- 277
+ T+ V L + + DL+ +F + ++ A+I F + A K
Sbjct: 10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSF 69
Query: 278 NKSFWKGKQLNI 289
NK G++LN+
Sbjct: 70 NKLIVNGRRLNV 81
>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 = 66.3 bits (162), Expect = 2e-13
Identities = 20/105 (19%), Positives = 36/105 (34%), Gaps = 8/105 (7%)
Query: 321 KSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGF 380
+ DS + ++V +T L F +G + ++ + +
Sbjct: 24 FRRSDSFPERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NC 75
Query: 381 ALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGK 425
A VT+ E A QA L+GT L + + + GK
Sbjct: 76 AFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDAATGK 120
Score = 64.0 bits (156), Expect = 2e-12
Identities = 21/105 (20%), Positives = 41/105 (39%), Gaps = 13/105 (12%)
Query: 568 NVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 627
+ E R P TLY+ + T +R F G I +++ +
Sbjct: 27 SDSFPERRAPRKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDPPR----------- 73
Query: 628 GYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATT 672
FV + ES +QA+ L + ++ Q+++ + + +A T
Sbjct: 74 NCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDAAT 118
Score = 58.2 bits (141), Expect = 2e-10
Identities = 15/92 (16%), Positives = 32/92 (34%), Gaps = 10/92 (10%)
Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
A + G+ + V + + F FG + + + R FV +
Sbjct: 35 APRKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDP-------PRNCAFVTYEKMES 85
Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEADNVED 772
A +A+ L T + +L + A + ++
Sbjct: 86 ADQAVAEL-NGTQVESVQLKVNIARKQPMLDA 116
Score = 45.1 bits (107), Expect = 6e-06
Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 5/64 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+T L+ F G + D+ + R AF+ Y + + A A+ N T V S
Sbjct: 47 EDMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVESV 101
Query: 87 RIKV 90
++KV
Sbjct: 102 QLKV 105
Score = 37.0 bits (86), Expect = 0.004
Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 2/86 (2%)
Query: 433 RKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQ 492
R+ D+F + R + V PT L+ F PFG++ + + P V + +
Sbjct: 25 RRSDSFPERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEK 82
Query: 493 KNQAKAAFNSLAYTKFKEVPLYLEWA 518
A A L T+ + V L + A
Sbjct: 83 MESADQAVAELNGTQVESVQLKVNIA 108
>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 = 65.7 bits (161), Expect = 2e-13
Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 6/85 (7%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPL--AEVILPIDKETDKTKGFALVTFLMPEHAT 392
+ ++V+NL + ++ L K F +G + A+V+ E ++KGF V F PE AT
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVM----MEGGRSKGFGFVCFSSPEEAT 69
Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKE 417
+A ++G + + L++ + KE
Sbjct: 70 KAVTEMNGRIVATKPLYVALAQRKE 94
Score = 57.2 bits (139), Expect = 2e-10
Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 4/93 (4%)
Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 733
+ + + V+N+ + + F FG + ++ M+ G +GFGFV
Sbjct: 4 GSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKV---MMEGGRSKGFGFV 60
Query: 734 EFITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
F + EA +A+ + + + L + A+
Sbjct: 61 CFSSPEEATKAVTEM-NGRIVATKPLYVALAQR 92
Score = 54.5 bits (132), Expect = 2e-09
Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 7/85 (8%)
Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
+ LY+KNL+ ++ +R+ F G I S V + G+ S G+GFV
Sbjct: 8 DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-----GR--SKGFGFV 60
Query: 633 QFYTRESLNQALKVLQNSSLDEHQI 657
F + E +A+ + + +
Sbjct: 61 CFSSPEEATKAVTEMNGRIVATKPL 85
Score = 43.0 bits (102), Expect = 2e-05
Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
I E+L+ F GT+T ++ G+ + F F+ + ++A A+ N V +
Sbjct: 25 DGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEMNGRIVATK 83
Query: 87 RIKV 90
+ V
Sbjct: 84 PLYV 87
Score = 32.6 bits (75), Expect = 0.100
Identities = 19/75 (25%), Positives = 25/75 (33%), Gaps = 12/75 (16%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------GLVEFLQKNQAKAAFNSL 503
VKNL L+ F PFG + V + G V F +A A +
Sbjct: 20 VKNLDDGIDDERLRKAFSPFGTITSAKV----MMEGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 504 AYTKFKEVPLYLEWA 518
PLY+ A
Sbjct: 76 NGRIVATKPLYVALA 90
>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 = 65.8 bits (161), Expect = 3e-13
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 4/83 (4%)
Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
S + ++ +IFV L Y T+ L K FE +G + E ++ D++T K++G+
Sbjct: 3 SGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYG 62
Query: 382 LVTFLMPEHATQA----YQHLDG 400
VT A +A +DG
Sbjct: 63 FVTMADRAAAERACKDPNPIIDG 85
Score = 57.7 bits (140), Expect = 2e-10
Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 6/87 (6%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
++ T +++ L +++T+ S+R++F+ G I V D ++ G+ S GYGFV
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVV--ITDRQT-GK--SRGYGFVTM 66
Query: 635 YTRESLNQALKVLQNSSLDEHQIELKR 661
R + +A K N +D + +
Sbjct: 67 ADRAAAERACKDP-NPIIDGRKANVNL 92
Score = 43.1 bits (102), Expect = 3e-05
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKR 743
+KI V +P+ + + + F+ FG+++ + + +G RG+GFV + A+R
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVV---ITDRQTGKSRGYGFVTMADRAAAER 74
Query: 744 AMKA 747
A K
Sbjct: 75 ACKD 78
Score = 35.0 bits (81), Expect = 0.021
Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 1/51 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALD 76
Y T L+ FE G + + + + GK R + F+ A+ A
Sbjct: 27 YHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Score = 27.3 bits (61), Expect = 9.3
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLV 479
I V LPY T L+ FE FGD+ +V
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVV 49
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 66.5 bits (162), Expect = 3e-13
Identities = 17/101 (16%), Positives = 35/101 (34%), Gaps = 7/101 (6%)
Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTK----LFEKYGPLAEVILPIDKETDKT 377
D S + + N++ V ++ L L G + ++++ +D
Sbjct: 15 DSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVV---DLSDDN 71
Query: 378 KGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKEN 418
G A + F E A + G F G L + + ++
Sbjct: 72 SGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS 112
Score = 58.0 bits (140), Expect = 3e-10
Identities = 23/138 (16%), Positives = 44/138 (31%), Gaps = 26/138 (18%)
Query: 550 KENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRH----FKKCG 605
KE A + +Q + + EP + I N+N ++ ++ G
Sbjct: 2 KETAAAKFERQHMDSPDLGSTPPH---TEPSQVVLITNINPEVPKEKLQALLYALASSQG 58
Query: 606 PIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRN 665
I + V D G ++ F T+ES ++ Q + + + S
Sbjct: 59 DILDIVVDLSDDNS--------GKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS--- 107
Query: 666 LESEATTVKRKSSNVAKQ 683
+ S VA+
Sbjct: 108 --------ETPQSQVAED 117
Score = 57.6 bits (139), Expect = 3e-10
Identities = 17/115 (14%), Positives = 44/115 (38%), Gaps = 9/115 (7%)
Query: 660 KRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE----VEELFKAFGELKFV 715
+ + + S+ + +L+ NI + + + + L + G++ +
Sbjct: 4 TAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDI 63
Query: 716 RLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNV 770
+ S + G ++ F T+ A+ ++A Q G LV+ ++E +
Sbjct: 64 VVDL----SDDNSGKAYIVFATQESAQAFVEAF-QGYPFQGNPLVITFSETPQSQ 113
Score = 48.0 bits (114), Expect = 8e-07
Identities = 16/119 (13%), Positives = 38/119 (31%), Gaps = 15/119 (12%)
Query: 433 RKLDAFNQVVEARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLV---PPYGIT 485
D + +++L+ N+ L+ AL GD+ ++V
Sbjct: 15 DSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGK 74
Query: 486 GLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEE 544
+ F + A+A + F+ PL + + ++ ++ + E
Sbjct: 75 AYIVFATQESAQAFVEAFQGYPFQGNPLVITF--------SETPQSQVAEDGSLEHHHH 125
Score = 42.6 bits (100), Expect = 5e-05
Identities = 11/69 (15%), Positives = 30/69 (43%), Gaps = 6/69 (8%)
Query: 27 YKITQEQLK----AKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY 82
++ +E+L+ A +G + D+ + + A+I + ++ AQA ++ F
Sbjct: 39 PEVPKEKLQALLYALASSQGDILDIVVDLS--DDNSGKAYIVFATQESAQAFVEAFQGYP 96
Query: 83 VFSSRIKVE 91
+ + +
Sbjct: 97 FQGNPLVIT 105
Score = 39.1 bits (91), Expect = 0.001
Identities = 19/109 (17%), Positives = 37/109 (33%), Gaps = 11/109 (10%)
Query: 199 TKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-----PLASV 253
T + P + P H +++ N+ V K+ L+A L + +
Sbjct: 4 TAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDI 63
Query: 254 R----TTFLGMAYIGFKDEKNCNKALNK-NKSFWKGKQLNIYKYSKDNS 297
G AYI F +++ + ++G L I +S+
Sbjct: 64 VVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI-TFSETPQ 111
>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 = 65.1 bits (159), Expect = 4e-13
Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 3/72 (4%)
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
S+ TG + +R +P++A ++++ F ++ V + G G VE
Sbjct: 5 SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGP--DGRVTGEADVE 61
Query: 735 FITKNEAKRAMK 746
F T +A AM
Sbjct: 62 FATHEDAVAAMA 73
Score = 61.3 bits (149), Expect = 9e-12
Identities = 16/95 (16%), Positives = 35/95 (36%), Gaps = 8/95 (8%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
+ ++++ L + +TE+ I F P+ V + D + G
Sbjct: 5 SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGR------VTGE 57
Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
V+F T E A+ +++ +EL ++
Sbjct: 58 ADVEFATHEDAVAAMA-KDKANMQHRYVELFLNST 91
Score = 59.3 bits (144), Expect = 4e-11
Identities = 21/82 (25%), Positives = 29/82 (35%), Gaps = 3/82 (3%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ +R L Y TE+D+ F P V + I + + G A V F E A A
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDG-RVTGEADVEFATHEDAVAAMA-K 74
Query: 399 DGTVFLGRMLHLIPGKPKENEG 420
D R + L G
Sbjct: 75 DKANMQHRYVELFLNSTAGTSG 96
Score = 52.0 bits (125), Expect = 1e-08
Identities = 19/97 (19%), Positives = 37/97 (38%), Gaps = 9/97 (9%)
Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVR------TTFLGMAYIGFKDE 268
S + H + ++ LP + D+ +F PL V G A + F
Sbjct: 6 SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATH 65
Query: 269 KNCNKALNKNKSFWKGKQLNIYKYSK---DNSAKYSG 302
++ A+ K+K+ + + + ++ S S SG
Sbjct: 66 EDAVAAMAKDKANMQHRYVELFLNSTAGTSGSGPSSG 102
Score = 38.5 bits (90), Expect = 7e-04
Identities = 10/69 (14%), Positives = 26/69 (37%), Gaps = 2/69 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
Y+ T+ + F V ++ +G+ A + + + A AA+ + +
Sbjct: 25 YRATENDIYNFFSP-LNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHR 82
Query: 87 RIKVEKCSN 95
+++ S
Sbjct: 83 YVELFLNST 91
Score = 35.8 bits (83), Expect = 0.006
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 4/65 (6%)
Query: 439 NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLG-RVLVPPYG---ITGLVEFLQKN 494
++ + + ++ LPYR D+ F P + + + P G VEF
Sbjct: 7 GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHE 66
Query: 495 QAKAA 499
A AA
Sbjct: 67 DAVAA 71
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 64.5 bits (157), Expect = 5e-13
Identities = 15/90 (16%), Positives = 30/90 (33%), Gaps = 5/90 (5%)
Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
E + ++V NL DL + + G + P+ + A + +
Sbjct: 13 GEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSA 67
Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
A QA L G L + + + ++
Sbjct: 68 AAQQAVSCLQGLRLGTDTLRVALARQQRDK 97
Score = 60.6 bits (147), Expect = 1e-11
Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 7/86 (8%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
+ + V N+P A+ S+++ + G + P ++ G R F+ + A++
Sbjct: 18 LAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQG-PRRRAFLHYPDSAAAQQ 71
Query: 744 AMKALCQSTHLYGRRLVLEWAEEADN 769
A+ L Q L L + A + +
Sbjct: 72 AVSCL-QGLRLGTDTLRVALARQQRD 96
Score = 54.1 bits (130), Expect = 3e-09
Identities = 15/95 (15%), Positives = 32/95 (33%), Gaps = 12/95 (12%)
Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
+Y+ NL ++ ++R ++ G + + P+ F+
Sbjct: 12 PGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQG--PR--------RRAFL 61
Query: 633 QFYTRESLNQALKVLQNSSLDEHQI--ELKRSNRN 665
+ + QA+ LQ L + L R R+
Sbjct: 62 HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD 96
Score = 38.3 bits (89), Expect = 9e-04
Identities = 20/89 (22%), Positives = 32/89 (35%), Gaps = 8/89 (8%)
Query: 203 DTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL---G 259
+ S P PP AP + V NLP + DLK + L +R T+
Sbjct: 2 SSGSSGPGSPPGEGAP----LAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRR 57
Query: 260 MAYIGFKDEKNCNKALNK-NKSFWKGKQL 287
A++ + D +A++ L
Sbjct: 58 RAFLHYPDSAAAQQAVSCLQGLRLGTDTL 86
Score = 37.5 bits (87), Expect = 0.002
Identities = 16/78 (20%), Positives = 25/78 (32%), Gaps = 3/78 (3%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLV--PPYGITGLVEFLQKNQAKAAF 500
A + V NLP +DLK G + L P + + A+ A
Sbjct: 15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRR-AFLHYPDSAAAQQAV 73
Query: 501 NSLAYTKFKEVPLYLEWA 518
+ L + L + A
Sbjct: 74 SCLQGLRLGTDTLRVALA 91
Score = 37.1 bits (86), Expect = 0.002
Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 4/65 (6%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
LK E G+V L+ T +G RR AF+ Y AQ A+ + +
Sbjct: 29 RDARVSDLKRALRELGSVP---LRLTWQGP-RRRAFLHYPDSAAAQQAVSCLQGLRLGTD 84
Query: 87 RIKVE 91
++V
Sbjct: 85 TLRVA 89
>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 = 63.9 bits (156), Expect = 7e-13
Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 3/82 (3%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ +R + VTE ++ + P + + + G+ V F E QA +
Sbjct: 13 VKLRGAPFNVTEKNVMEFLAPLKP-VAIRIVRNAHG-NKTGYIFVDFSNEEEVKQALK-C 69
Query: 399 DGTVFLGRMLHLIPGKPKENEG 420
+ GR + + K + G
Sbjct: 70 NREYMGGRYIEVFREKSGPSSG 91
Score = 63.5 bits (155), Expect = 1e-12
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
SS + T + +R PF + V E + +R+ + G+ G+ FV+F
Sbjct: 2 SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVA-IRIVRNAHGN--KTGYIFVDFS 58
Query: 737 TKNEAKRAMK 746
+ E K+A+K
Sbjct: 59 NEEEVKQALK 68
Score = 63.1 bits (154), Expect = 2e-12
Identities = 20/89 (22%), Positives = 32/89 (35%), Gaps = 8/89 (8%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
T+ ++ FN TE ++ P+ ++ + R GY FV F
Sbjct: 6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAHGN------KTGYIFVDFS 58
Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSNR 664
E + QALK + IE+ R
Sbjct: 59 NEEEVKQALK-CNREYMGGRYIEVFREKS 86
Score = 56.5 bits (137), Expect = 3e-10
Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 9/84 (10%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKPLPLASVR------TTFLGMAYIGFKDEKNCNKALNKN 278
HT+ ++ P V +K++ + PL ++R G ++ F +E+ +AL N
Sbjct: 11 HTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCN 70
Query: 279 KSFWKGKQLNIYKYSKDNSAKYSG 302
+ + G+ + ++ ++ S SG
Sbjct: 71 REYMGGRYIEVF---REKSGPSSG 91
Score = 41.1 bits (97), Expect = 7e-05
Identities = 10/69 (14%), Positives = 28/69 (40%), Gaps = 2/69 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ +T++ + +++ G + F+ + E++ + AL N Y+
Sbjct: 20 FNVTEKNVMEFLAP-LKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGR 77
Query: 87 RIKVEKCSN 95
I+V + +
Sbjct: 78 YIEVFREKS 86
Score = 34.2 bits (79), Expect = 0.024
Identities = 8/61 (13%), Positives = 22/61 (36%), Gaps = 4/61 (6%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLG-RVLVPPYGIT---GLVEFLQKNQAKA 498
+ + ++ P+ ++ P + R++ +G V+F + + K
Sbjct: 6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQ 65
Query: 499 A 499
A
Sbjct: 66 A 66
>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 = 64.5 bits (157), Expect = 9e-13
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 339 IFVRNLSYTVTEDDLTK---LFEKYGPLAEVILPIDKETDKTK---GFALVTFLMPEHAT 392
+FV LS + + ++ K F K+G + +V++ ++ A VT++ E A
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 393 QAYQHLDGTVFLGRML 408
+A Q ++ V GR L
Sbjct: 78 RAIQCVNNVVVDGRTL 93
Score = 53.7 bits (129), Expect = 6e-09
Identities = 11/79 (13%), Positives = 28/79 (35%), Gaps = 5/79 (6%)
Query: 582 TLYIKNLNFNSTEDSIRR---HFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
+++ L+ + + + +F K G I V + +V + E
Sbjct: 17 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQG--PSASAYVTYIRSE 74
Query: 639 SLNQALKVLQNSSLDEHQI 657
+A++ + N +D +
Sbjct: 75 DALRAIQCVNNVVVDGRTL 93
Score = 49.9 bits (119), Expect = 1e-07
Identities = 18/80 (22%), Positives = 31/80 (38%), Gaps = 6/80 (7%)
Query: 690 VRNIPFQAKQSEV---EELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKRA 744
V + + EV E F FG++ V + GS +V +I +A RA
Sbjct: 20 VVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRA 79
Query: 745 MKALCQSTHLYGRRLVLEWA 764
++ + + + GR L
Sbjct: 80 IQCV-NNVVVDGRTLKASLG 98
Score = 41.8 bits (98), Expect = 7e-05
Identities = 26/111 (23%), Positives = 46/111 (41%), Gaps = 19/111 (17%)
Query: 9 VVPRNHISLLDLDEVEFIYKITQEQL---KAKFEEKGTVTDVQLKYTTEGKFRR----FA 61
VV +N + ++ L ++ ++ F + G + V + +T + A
Sbjct: 12 VVQKNLVFVVGLS-----QRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASA 66
Query: 62 FIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSNLGDTTKPKSWSKYAPDS 112
++ Y R + A A+ NN V +K +LG TTK S+S P S
Sbjct: 67 YVTYIRSEDALRAIQCVNNVVVDGRTLKA----SLG-TTKYCSYS--GPSS 110
Score = 27.1 bits (60), Expect = 9.6
Identities = 11/70 (15%), Positives = 23/70 (32%), Gaps = 12/70 (17%)
Query: 446 SKRIILVKNLPYRTLPTDL---KALFEPFGDLGRVLVPPYGITGL---------VEFLQK 493
K ++ V L R ++ F FG + +V++ V +++
Sbjct: 14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73
Query: 494 NQAKAAFNSL 503
A A +
Sbjct: 74 EDALRAIQCV 83
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 62.9 bits (154), Expect = 1e-12
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA--- 394
+IFV LS T +D+ FE++G + + +L DK T++ +GF VTF + +
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 395 -YQHLDG 400
+ ++
Sbjct: 61 HFHEINN 67
Score = 50.5 bits (122), Expect = 3e-08
Identities = 13/79 (16%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ L+ N+T + ++ +F++ G + + D + + G+GFV F + + + +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAML--MFDKTT-NR--HRGFGFVTFESEDIVEK 56
Query: 643 ALKVLQNSSLDEHQIELKR 661
++ ++ +E K+
Sbjct: 57 VCEI-HFHEINNKMVECKK 74
Score = 40.1 bits (95), Expect = 1e-04
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 5/63 (7%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKRA 744
KI V + +V+ F+ FG++ L M + HRGFGFV F +++ ++
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAML---MFDKTTNRHRGFGFVTFESEDIVEKV 57
Query: 745 MKA 747
+
Sbjct: 58 CEI 60
Score = 34.4 bits (80), Expect = 0.014
Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAAL 75
T E +K FE+ G V D L + + R F F+ + ED +
Sbjct: 12 TVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC 58
>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure
genomics, RRM domain, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 63.8 bits (156), Expect = 2e-12
Identities = 15/98 (15%), Positives = 34/98 (34%), Gaps = 2/98 (2%)
Query: 321 KSQEDSVQFAEDIAESG-RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKG 379
K+ Q A+ + +++ NL ++ E +L + + +G + + D + ++G
Sbjct: 9 KASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRG 67
Query: 380 FALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
E H +G P +P
Sbjct: 68 VGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLL 105
Score = 58.0 bits (141), Expect = 1e-10
Identities = 20/105 (19%), Positives = 44/105 (41%), Gaps = 5/105 (4%)
Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM 721
S+ + +A+ V+ + + +Q + + + N+P + E+E + K FG++ R+ +
Sbjct: 2 SSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRI---L 58
Query: 722 V-GSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE 765
SG RG GF + + + + + V E
Sbjct: 59 RDSSGTSRGVGFARMESTEKCEAVIGHF-NGKFIKTPPGVSAPTE 102
Score = 55.7 bits (135), Expect = 1e-09
Identities = 17/85 (20%), Positives = 29/85 (34%), Gaps = 6/85 (7%)
Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
+++ + T LYI NL + E + K G + S + R G S G GF
Sbjct: 18 AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS----GT--SRGVGFA 71
Query: 633 QFYTRESLNQALKVLQNSSLDEHQI 657
+ + E + +
Sbjct: 72 RMESTEKCEAVIGHFNGKFIKTPPG 96
Score = 45.3 bits (108), Expect = 5e-06
Identities = 9/64 (14%), Positives = 26/64 (40%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ +++L+ + G V ++ + G R F ++ +A + +FN ++ +
Sbjct: 35 LSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTP 94
Query: 87 RIKV 90
Sbjct: 95 PGVS 98
Score = 37.2 bits (87), Expect = 0.003
Identities = 17/96 (17%), Positives = 31/96 (32%), Gaps = 12/96 (12%)
Query: 431 SERKLDAFNQVVEARSKRI-------ILVKNLPYRTLPTDLKALFEPFGDLG--RVLVPP 481
S V+A+ + + + NLP +L+ + +PFG + R+L
Sbjct: 2 SSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS 61
Query: 482 YGIT---GLVEFLQKNQAKAAFNSLAYTKFKEVPLY 514
G + G + +A K P
Sbjct: 62 SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGV 97
>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 = 63.6 bits (155), Expect = 2e-12
Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 3/93 (3%)
Query: 325 DSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVT 384
S + + + V + ++ E+D+ F V L D + G LV
Sbjct: 5 SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRV-DAVHLLKDHVG-RNNGNGLVK 62
Query: 385 FLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
FL P+ +A + + + + R + + P ++
Sbjct: 63 FLSPQDTFEALK-RNRMLMIQRYVEVSPATERQ 94
Score = 62.8 bits (153), Expect = 3e-12
Identities = 21/91 (23%), Positives = 38/91 (41%), Gaps = 5/91 (5%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V +PF A +++V + F + V L K G + G G V+F++ + A+K
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH--VGRNNGNGLVKFLSPQDTFEALK- 74
Query: 748 LCQSTHLYGRRLVLEWAEEADNVEDIRKRTN 778
+ R + + A E V T+
Sbjct: 75 -RNRMLMIQRYVEVSPATERQWVAAGGHITS 104
Score = 60.5 bits (147), Expect = 2e-11
Identities = 14/90 (15%), Positives = 36/90 (40%), Gaps = 8/90 (8%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
D + + + F++ E+ +R F + +V + + + + G G V+F
Sbjct: 12 INPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGR------NNGNGLVKFL 64
Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSNRN 665
+ + +ALK + + +E+ +
Sbjct: 65 SPQDTFEALK-RNRMLMIQRYVEVSPATER 93
Score = 55.9 bits (135), Expect = 7e-10
Identities = 16/102 (15%), Positives = 36/102 (35%), Gaps = 10/102 (9%)
Query: 207 SDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVR------TTFLGM 260
S S P+ P + V +P + D++ +F L + +V G
Sbjct: 3 SGSSGKPLPINPDD----LYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGN 58
Query: 261 AYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSG 302
+ F ++ +AL +N+ + + + ++ G
Sbjct: 59 GLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATERQWVAAGG 100
Score = 41.3 bits (97), Expect = 1e-04
Identities = 9/68 (13%), Positives = 20/68 (29%), Gaps = 2/68 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ + ++ F V V L G+ + + AL N +
Sbjct: 26 FSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK-RNRMLMIQR 83
Query: 87 RIKVEKCS 94
++V +
Sbjct: 84 YVEVSPAT 91
Score = 32.0 bits (73), Expect = 0.19
Identities = 12/58 (20%), Positives = 20/58 (34%), Gaps = 4/58 (6%)
Query: 446 SKRIILVKNLPYRTLPTDLKALFEPFGDLG-RVLVPPYGI---TGLVEFLQKNQAKAA 499
+ V +P+ + D++ F +L G GLV+FL A
Sbjct: 15 DDLYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEA 72
>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 = 64.1 bits (156), Expect = 3e-12
Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 3/73 (4%)
Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 733
V TG + +R +P++A ++++ F ++ V + G G V
Sbjct: 35 GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR-VHIEIGP--DGRVTGEADV 91
Query: 734 EFITKNEAKRAMK 746
EF T EA AM
Sbjct: 92 EFATHEEAVAAMS 104
Score = 62.9 bits (153), Expect = 5e-12
Identities = 17/95 (17%), Positives = 37/95 (38%), Gaps = 8/95 (8%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
+ + + ++++ L + +TE+ I F P+ V + D + G
Sbjct: 36 DSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPDGR------VTGE 88
Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
V+F T E A+ +++ IEL ++
Sbjct: 89 ADVEFATHEEAVAAMS-KDRANMQHRYIELFLNST 122
Score = 58.7 bits (142), Expect = 2e-10
Identities = 20/84 (23%), Positives = 29/84 (34%), Gaps = 3/84 (3%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
+ +R L Y TE+D+ F P+ V + I + + G A V F E A
Sbjct: 44 TTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPD-GRVTGEADVEFATHEEAVA 101
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKE 417
A D R + L
Sbjct: 102 AMS-KDRANMQHRYIELFLNSTTG 124
Score = 52.9 bits (127), Expect = 2e-08
Identities = 17/100 (17%), Positives = 36/100 (36%), Gaps = 6/100 (6%)
Query: 201 SKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTT---- 256
S S+ V H + ++ LP + D+ +F PL V
Sbjct: 23 SMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPD 82
Query: 257 --FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSK 294
G A + F + A++K+++ + + + ++ S
Sbjct: 83 GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNST 122
Score = 38.3 bits (89), Expect = 0.002
Identities = 12/69 (17%), Positives = 27/69 (39%), Gaps = 2/69 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
YK T+ + F V ++ +G+ A + + ++A AA+ + +
Sbjct: 56 YKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSK-DRANMQHR 113
Query: 87 RIKVEKCSN 95
I++ S
Sbjct: 114 YIELFLNST 122
Score = 36.7 bits (85), Expect = 0.008
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLG-RVLVPPYG-ITG--LVEFLQKNQAKA 498
++ + + ++ LPY+ D+ F P + + + P G +TG VEF +A A
Sbjct: 42 QSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVA 101
Query: 499 A 499
A
Sbjct: 102 A 102
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 63.4 bits (154), Expect = 3e-12
Identities = 22/99 (22%), Positives = 34/99 (34%), Gaps = 11/99 (11%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI----ASVTVARKKDPKSPGQFL 625
E + E + ++ L F +T + + F + PI + D +
Sbjct: 13 EVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR------ 66
Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
G FV F E AL+ L + IEL RS
Sbjct: 67 PTGDAFVLFACEEYAQNALR-KHKDLLGKRYIELFRSTA 104
Score = 61.8 bits (150), Expect = 1e-11
Identities = 21/117 (17%), Positives = 43/117 (36%), Gaps = 8/117 (6%)
Query: 667 ESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGEL----KFVRLPKKMV 722
S T + ++K+ + +R +PF A EV F + + +
Sbjct: 5 SSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD 64
Query: 723 GSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
G G FV F + A+ A++ L R + L + A+ + + + ++
Sbjct: 65 GR--PTGDAFVLFACEEYAQNALR--KHKDLLGKRYIELFRSTAAEVQQVLNRFSSA 117
Score = 60.3 bits (146), Expect = 3e-11
Identities = 19/88 (21%), Positives = 35/88 (39%), Gaps = 4/88 (4%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLA---EVILPIDKETDKTKGFALVTFLMPEHA 391
+ +R L +T T +++ F ++ P+ E IL + + G A V F E+A
Sbjct: 22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYA 81
Query: 392 TQAYQHLDGTVFLGRMLHLIPGKPKENE 419
A + + R + L E +
Sbjct: 82 QNALR-KHKDLLGKRYIELFRSTAAEVQ 108
Score = 50.3 bits (120), Expect = 1e-07
Identities = 14/102 (13%), Positives = 33/102 (32%), Gaps = 11/102 (10%)
Query: 205 APSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-----PLASVRTT--- 256
S + K + ++ LP +++ A+F +
Sbjct: 4 GSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP 63
Query: 257 ---FLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKD 295
G A++ F E+ AL K+K + + +++ +
Sbjct: 64 DGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAA 105
Score = 38.7 bits (90), Expect = 0.001
Identities = 17/91 (18%), Positives = 34/91 (37%), Gaps = 6/91 (6%)
Query: 27 YKITQEQLKAKFEE----KGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY 82
+ T E++ A F + G + +G+ AF+ + E+ AQ AL +
Sbjct: 33 FTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDL 91
Query: 83 VFSSRIKVEKCSNLG-DTTKPKSWSKYAPDS 112
+ I++ + + + S P S
Sbjct: 92 LGKRYIELFRSTAAEVQQVLNRFSSASGPSS 122
Score = 31.8 bits (72), Expect = 0.31
Identities = 12/69 (17%), Positives = 25/69 (36%), Gaps = 9/69 (13%)
Query: 440 QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLG------RVLVPPYGI---TGLVEF 490
Q + ++ I+ ++ LP+ ++ A F + + P G V F
Sbjct: 16 QFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLF 75
Query: 491 LQKNQAKAA 499
+ A+ A
Sbjct: 76 ACEEYAQNA 84
>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 = 62.7 bits (153), Expect = 4e-12
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 2/83 (2%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
SG IF++NL ++ L F +G + + D + +KG+ V F E A +A
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAI 62
Query: 396 QHLDGTVFLGRMLHLIPGKPKEN 418
+ ++G + R + + K ++
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKE 85
Score = 58.4 bits (142), Expect = 1e-10
Identities = 27/106 (25%), Positives = 49/106 (46%), Gaps = 9/106 (8%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
P ++IKNL+ + ++ F G I S V D S GYGFV F T
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENG-----SKGYGFVHFET 54
Query: 637 RESLNQALKVLQNSSLDEHQI--ELKRSNRNLESEATTVKRKSSNV 680
+E+ +A++ + L++ ++ +S + E+E ++ +NV
Sbjct: 55 QEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNV 100
Score = 53.0 bits (128), Expect = 9e-09
Identities = 23/102 (22%), Positives = 44/102 (43%), Gaps = 9/102 (8%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
I ++N+ + + F AFG + K + +G+GFV F T+ A+RA+
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGN---ILSCKVVCDENGSKGYGFVHFETQEAAERAI 62
Query: 746 KALCQSTHLYGRRLVLEWAE-----EADNVEDIRKRTNRYFG 782
+ + L R++ + + EA+ ++ TN Y
Sbjct: 63 EKM-NGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIK 103
Score = 38.4 bits (90), Expect = 0.001
Identities = 10/66 (15%), Positives = 27/66 (40%), Gaps = 1/66 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
I + L F G + ++ E + + F+ + ++ A+ A++ N +
Sbjct: 15 KSIDNKALYDTFSAFGNILSCKV-VCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 73
Query: 87 RIKVEK 92
++ V +
Sbjct: 74 KVFVGR 79
Score = 34.9 bits (81), Expect = 0.021
Identities = 27/155 (17%), Positives = 42/155 (27%), Gaps = 57/155 (36%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------GLVEFLQKNQAKAAFN 501
I +KNL L F FG++ V + G V F + A+ A
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKV----VCDENGSKGYGFVHFETQEAAERAIE 63
Query: 502 SLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQG 561
+ + +++ K + E E E G K+
Sbjct: 64 KMNGMLLNDRKVFVGRF----------------KSRKEREAELGARAKE----------- 96
Query: 562 VPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDS 596
T +YIKN ST +
Sbjct: 97 ------------------FTNVYIKNFGPGSTRAA 113
Score = 31.8 bits (73), Expect = 0.21
Identities = 20/134 (14%), Positives = 42/134 (31%), Gaps = 38/134 (28%)
Query: 227 IVVKNLPAGVKKKDLKAYFKPL-PLASVR-----TTFLGMAYIGFKDEKNCNKALNK-NK 279
I +KNL + K L F + S + G ++ F+ ++ +A+ K N
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 280 SFWKGKQL--NIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESG 337
+++ +K K+ A+ A + N
Sbjct: 68 MLLNDRKVFVGRFKSRKEREAELGARAKEFTN---------------------------- 99
Query: 338 RIFVRNLSYTVTED 351
++++N T
Sbjct: 100 -VYIKNFGPGSTRA 112
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 61.4 bits (150), Expect = 4e-12
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA--- 394
+IFV LS E+ + + F +G + + LP+D +T+K +GF +TF E +
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 395 -YQHLDG 400
Y ++
Sbjct: 61 KYHNVGL 67
Score = 46.0 bits (110), Expect = 1e-06
Identities = 15/79 (18%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ L+ ++ E+ IR +F G + S+ + D K+ + G+ F+ F E + +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIEL--PMDNKT-NK--RRGFCFITFKEEEPVKK 56
Query: 643 ALKVLQNSSLDEHQIELKR 661
++ + ++ + E+K
Sbjct: 57 IMEK-KYHNVGLSKCEIKV 74
Score = 41.7 bits (99), Expect = 3e-05
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
KI V + + ++ E F FGE++ + LP + RGF F+ F + K+ M+
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMD-NKTNKRRGFCFITFKEEEPVKKIME 59
Query: 747 A 747
Sbjct: 60 K 60
Score = 35.2 bits (82), Expect = 0.008
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAAL 75
+E+++ F G V ++L + K R F FI + E+ + +
Sbjct: 9 PDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58
>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 = 61.9 bits (151), Expect = 4e-12
Identities = 22/98 (22%), Positives = 38/98 (38%), Gaps = 15/98 (15%)
Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
E R P TLY+ + T +R F G I +++ + FV
Sbjct: 8 ERRAPRKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDPPR-----------NCAFV 54
Query: 633 QFYTRESLNQALKVLQNSSLDEHQI--ELKRSNRNLES 668
+ ES +QA+ L + ++ Q+ + R L+S
Sbjct: 55 TYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDS 92
Score = 61.5 bits (150), Expect = 6e-12
Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 8/80 (10%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V +T L F +G + ++ + + A VT+ E A QA L
Sbjct: 18 LYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAEL 69
Query: 399 DGTVFLGRMLHLIPGKPKEN 418
+GT L + + +
Sbjct: 70 NGTQVESVQLKVNIARKQPM 89
Score = 53.8 bits (130), Expect = 3e-09
Identities = 12/66 (18%), Positives = 23/66 (34%), Gaps = 8/66 (12%)
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV 760
+ F FG + + + R FV + A +A+ L T + +L
Sbjct: 29 LLRGAFSPFGNIIDLSMDP-------PRNCAFVTYEKMESADQAVAEL-NGTQVESVQLK 80
Query: 761 LEWAEE 766
+ A +
Sbjct: 81 VNIARK 86
Score = 45.7 bits (109), Expect = 2e-06
Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 12/86 (13%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+T L+ F G + D+ + R AF+ Y + + A A+ N T V S
Sbjct: 23 EDMTPTLLRGAFSPFGNIIDLSM-----DPPRNCAFVTYEKMESADQAVAELNGTQVESV 77
Query: 87 RIKVEKCSNLGDTTKPKSWSKYAPDS 112
++KV N+ + + P S
Sbjct: 78 QLKV----NIA---RKQPMLDSGPSS 96
Score = 33.0 bits (76), Expect = 0.066
Identities = 15/57 (26%), Positives = 25/57 (43%)
Query: 462 TDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 518
T L+ F PFG++ + + P V + + A A L T+ + V L + A
Sbjct: 28 TLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA 84
>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 = 61.7 bits (150), Expect = 6e-12
Identities = 12/92 (13%), Positives = 37/92 (40%), Gaps = 9/92 (9%)
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
++++ ++++V +P ++++ + G++ + + + G G VE
Sbjct: 5 SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--------GTGVVE 56
Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEE 766
F+ K + A++ L +T +
Sbjct: 57 FVRKEDMTYAVRKL-DNTKFRSHEGETAYIRV 87
Score = 59.8 bits (145), Expect = 3e-11
Identities = 17/80 (21%), Positives = 27/80 (33%), Gaps = 7/80 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+ V L + + DL + G + + G +V F+ E T A +
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKEDMTYAVRK 69
Query: 398 LDGTVFLGRMLHLIPGKPKE 417
LD T F + K
Sbjct: 70 LDNTKFRSHEGETAYIRVKV 89
Score = 55.2 bits (133), Expect = 2e-09
Identities = 15/85 (17%), Positives = 32/85 (37%), Gaps = 12/85 (14%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
+ + + L + + ++ H ++ G + V R G G V+F
Sbjct: 10 PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------------GTGVVEF 57
Query: 635 YTRESLNQALKVLQNSSLDEHQIEL 659
+E + A++ L N+ H+ E
Sbjct: 58 VRKEDMTYAVRKLDNTKFRSHEGET 82
Score = 45.9 bits (109), Expect = 3e-06
Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 1/74 (1%)
Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 504
RS+ ++V LP DLK GD+ V G TG+VEF++K A L
Sbjct: 13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFVRKEDMTYAVRKLD 71
Query: 505 YTKFKEVPLYLEWA 518
TKF+ +
Sbjct: 72 NTKFRSHEGETAYI 85
Score = 38.6 bits (90), Expect = 0.001
Identities = 10/66 (15%), Positives = 20/66 (30%), Gaps = 6/66 (9%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ + LK E G V + + + R++ A+ +NT S
Sbjct: 25 PSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKLDNTKFRSH 78
Query: 87 RIKVEK 92
+
Sbjct: 79 EGETAY 84
Score = 37.1 bits (86), Expect = 0.003
Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 2/75 (2%)
Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTFLGMAYIGFKDEKNCNK 273
S P +R + +VV LP +DLK + + + G + F +++
Sbjct: 6 SGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTY 65
Query: 274 ALNK-NKSFWKGKQL 287
A+ K + + ++ +
Sbjct: 66 AVRKLDNTKFRSHEG 80
>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 = 61.4 bits (149), Expect = 1e-11
Identities = 21/97 (21%), Positives = 33/97 (34%), Gaps = 8/97 (8%)
Query: 323 QEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFAL 382
S ++ S + VR L +V E DL + EK+G + V++ K AL
Sbjct: 2 SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM------PFKRQAL 55
Query: 383 VTFLMPEHATQAYQHLDGTVFL--GRMLHLIPGKPKE 417
V F + A + G+ K
Sbjct: 56 VEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR 92
Score = 55.6 bits (134), Expect = 1e-09
Identities = 15/91 (16%), Positives = 35/91 (38%), Gaps = 9/91 (9%)
Query: 677 SSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
S + K + S ++ VR + ++++ E + FG + +V + + VEF
Sbjct: 6 SGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-------FKRQALVEF 58
Query: 736 ITKNEAKRAMKALCQSTHLY-GRRLVLEWAE 765
+ AK + G++ ++
Sbjct: 59 ENIDSAKECVTFAADVPVYIAGQQAFFNYST 89
Score = 53.6 bits (129), Expect = 4e-09
Identities = 12/92 (13%), Positives = 27/92 (29%), Gaps = 13/92 (14%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
+ ++++ L + E + +K G I V + K V+F
Sbjct: 11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK-----------RQALVEFE 59
Query: 636 TRESLNQALKVLQNS--SLDEHQIELKRSNRN 665
+S + + + + Q S
Sbjct: 60 NIDSAKECVTFAADVPVYIAGQQAFFNYSTSK 91
Score = 52.1 bits (125), Expect = 2e-08
Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 2/73 (2%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
++ V+ L + DL E FG + V++ P+ LVEF + AK A
Sbjct: 16 PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVP 75
Query: 508 F--KEVPLYLEWA 518
+ ++
Sbjct: 76 VYIAGQQAFFNYS 88
Score = 38.6 bits (90), Expect = 7e-04
Identities = 11/67 (16%), Positives = 25/67 (37%), Gaps = 7/67 (10%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT--YVF 84
+ + L E+ GT+ V + F+R A + + D A+ + + + Y+
Sbjct: 25 ESVVEADLVEALEKFGTICYVMMM-----PFKRQALVEFENIDSAKECVTFAADVPVYIA 79
Query: 85 SSRIKVE 91
+
Sbjct: 80 GQQAFFN 86
Score = 35.5 bits (82), Expect = 0.009
Identities = 15/109 (13%), Positives = 32/109 (29%), Gaps = 15/109 (13%)
Query: 205 APSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTFL-GMAY 262
+ VS + V+ L V + DL + + V A
Sbjct: 5 SSGSHHKVSVSP---------VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQAL 55
Query: 263 IGFKDEKNCNKAL---NKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNN 308
+ F++ + + + + G+Q YS G + ++
Sbjct: 56 VEFENIDSAKECVTFAADVPVYIAGQQAFF-NYSTSKRITRPGNSGPSS 103
>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 = 60.8 bits (148), Expect = 1e-11
Identities = 12/69 (17%), Positives = 29/69 (42%), Gaps = 1/69 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYG-PLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+++ +L + E+ +++ F G + V + ++ T G+ V F A +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 398 LDGTVFLGR 406
++G G
Sbjct: 72 INGKPLPGA 80
Score = 51.9 bits (125), Expect = 1e-08
Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 6/79 (7%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCG-PIASVTVARKKDPKSPGQFLSMGYGFVQF 634
+L++ +L E+ I R F G + SV + R + GY FV+F
Sbjct: 5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGI-----PAGYCFVEF 59
Query: 635 YTRESLNQALKVLQNSSLD 653
+ + L + L
Sbjct: 60 ADLATAEKCLHKINGKPLP 78
Score = 46.2 bits (110), Expect = 2e-06
Identities = 12/72 (16%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 678 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFI 736
S+ + + + + ++ ++ + F GE + V++ + + +G+ G+ FVEF
Sbjct: 2 SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRL-TGIPAGYCFVEFA 60
Query: 737 TKNEAKRAMKAL 748
A++ + +
Sbjct: 61 DLATAEKCLHKI 72
Score = 34.2 bits (79), Expect = 0.028
Identities = 18/104 (17%), Positives = 36/104 (34%), Gaps = 28/104 (26%)
Query: 19 DLDEVEFIYKITQEQLKAKFEEKG-TVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAA 74
DL+ + + + F G TV V++ + T G + F+ + A+
Sbjct: 16 DLE-----PYMDENFISRAFATMGETVMSVKIIRNRLT--GIPAGYCFVEFADLATAEKC 68
Query: 75 LDYFNNTYV----FSSRIKVEKCSNLGDTTKPKSWSKYAPDSSA 114
L N + + R K+ +++ Y+ SS
Sbjct: 69 LHKINGKPLPGATPAKRFKL-------------NYATYSGPSSG 99
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 105
Score = 60.3 bits (147), Expect = 2e-11
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 4/83 (4%)
Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
S S E G++FV L ++ T++ L F +YG + + ++ DK T++++GF
Sbjct: 2 SSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61
Query: 382 LVTFLMPEHATQA----YQHLDG 400
V F P LDG
Sbjct: 62 FVKFKDPNCVGTVLASRPHTLDG 84
Score = 57.6 bits (140), Expect = 2e-10
Identities = 20/95 (21%), Positives = 42/95 (44%), Gaps = 6/95 (6%)
Query: 567 ENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLS 626
+ L++ L++++T++++R +F + G + + KD + Q S
Sbjct: 3 SGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVI--MKDKTT-NQ--S 57
Query: 627 MGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKR 661
G+GFV+F + L + +LD I+ K
Sbjct: 58 RGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP 91
Score = 38.4 bits (90), Expect = 0.001
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 1/62 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
K+ V + + Q + F +GE+ + K + RGFGFV+F N +
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVI-MKDKTTNQSRGFGFVKFKDPNCVGTVL 75
Query: 746 KA 747
+
Sbjct: 76 AS 77
Score = 35.3 bits (82), Expect = 0.014
Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 1/51 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALD 76
+ TQE L++ F + G V D + + R F F+ + + L
Sbjct: 26 WSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 76
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics,
RRM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 116
Score = 60.4 bits (147), Expect = 2e-11
Identities = 36/130 (27%), Positives = 62/130 (47%), Gaps = 17/130 (13%)
Query: 557 DNQQGVPEVEENV-EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK 615
G+ + E V E ++RE E L+I L+F +TE+S+R ++++ G + V
Sbjct: 3 SGSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV--M 60
Query: 616 KDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKR 675
+DP S + S G+GFV F + ++ A+ + S+D +E KR V R
Sbjct: 61 RDPAS-KR--SRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKR----------AVAR 106
Query: 676 KSSNVAKQTG 685
+ S +G
Sbjct: 107 EESGSGPSSG 116
Score = 58.8 bits (143), Expect = 9e-11
Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+ ++F+ LS+ TE+ L +E++G L + ++ D + +++GF VTF A
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 85
Query: 395 ----YQHLDG 400
+DG
Sbjct: 86 MAARPHSIDG 95
Score = 47.7 bits (114), Expect = 7e-07
Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 1/86 (1%)
Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM 721
+ +E TV + K+ K+ + + F+ + + ++ +G+L + +
Sbjct: 4 GSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV-MRD 62
Query: 722 VGSGLHRGFGFVEFITKNEAKRAMKA 747
S RGFGFV F + E AM A
Sbjct: 63 PASKRSRGFGFVTFSSMAEVDAAMAA 88
Score = 34.9 bits (81), Expect = 0.021
Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAAL 75
++ T+E L+ +E+ G +TD + + R F F+ + + AA+
Sbjct: 37 FETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
>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 = 60.4 bits (147), Expect = 2e-11
Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 4/70 (5%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
++F+ LS+ T++ L + F ++G + E ++ D T +++GF VTF+ +
Sbjct: 24 SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 83
Query: 395 ----YQHLDG 400
LD
Sbjct: 84 LAQSRHELDS 93
Score = 53.8 bits (130), Expect = 4e-09
Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 6/89 (6%)
Query: 573 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFV 632
++I L++ +T++ +R +F + G + V +DP + + S G+GFV
Sbjct: 18 GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLV--MRDPLT-KR--SRGFGFV 72
Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELKR 661
F + +++ L LD I+ K
Sbjct: 73 TFMDQAGVDKVLAQ-SRHELDSKTIDPKV 100
Score = 41.1 bits (97), Expect = 1e-04
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
+G K+ + + +Q Q + E F FGE+K + + + RGFGFV F+ +
Sbjct: 21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLV-MRDPLTKRSRGFGFVTFMDQAG 79
Query: 741 AKRAMKA 747
+ +
Sbjct: 80 VDKVLAQ 86
Score = 33.8 bits (78), Expect = 0.048
Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAAL 75
++ TQE L+ F + G V + + + R F F+ + + L
Sbjct: 35 WQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 59.0 bits (144), Expect = 2e-11
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA--- 394
++F+ LS+ T++ L + F ++G + E ++ D T +++GF VTF+ +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 395 -YQHLDG 400
LD
Sbjct: 62 SRHELDS 68
Score = 54.4 bits (132), Expect = 9e-10
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
++I L++ +T++ +R +F + G + V +DP + + S G+GFV F + +++
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLV--MRDPLT-KR--SRGFGFVTFMDQAGVDK 57
Query: 643 ALKVLQNSSLDEHQIELKR 661
L LD I+ K
Sbjct: 58 VLAQ-SRHELDSKTIDPKV 75
Score = 40.6 bits (96), Expect = 8e-05
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ + + +Q Q + E F FGE+K + + + RGFGFV F+ + + +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLV-MRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Query: 747 A 747
Sbjct: 61 Q 61
Score = 35.2 bits (82), Expect = 0.006
Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAAL 75
++ TQE L+ F + G V + + + R F F+ + + L
Sbjct: 10 WQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>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 = 59.9 bits (146), Expect = 3e-11
Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 3/78 (3%)
Query: 326 SVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
S + ++ + V L + TE DL + F +G + V + D +T +KGF V F
Sbjct: 5 SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
Query: 386 LMPEHATQA---YQHLDG 400
E + +DG
Sbjct: 65 TEYETQVKVMSQRHMIDG 82
Score = 57.2 bits (139), Expect = 3e-10
Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 7/87 (8%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
R + + L + L + +TE ++ +F G + V V KKD K+ G S G+GFV+F
Sbjct: 10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQV--KKDLKT-GH--SKGFGFVRF 64
Query: 635 YTRESLNQALKVLQNSSLDEHQIELKR 661
E+ + + Q +D + K
Sbjct: 65 TEYETQVKVMS--QRHMIDGRWCDCKL 89
Score = 41.4 bits (98), Expect = 8e-05
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
A Q S ++V +P++ + +++E F FGE+ V++ KK + +G +GFGFV
Sbjct: 5 SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQV-KKDLKTGHSKGFGFVR 63
Query: 735 FITKNEAKRAMKA 747
F + M
Sbjct: 64 FTEYETQVKVMSQ 76
Score = 34.1 bits (79), Expect = 0.033
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALD 76
+K T++ LK F G V VQ+K + G + F F+ + + +
Sbjct: 25 WKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 59.6 bits (145), Expect = 3e-11
Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 6/80 (7%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+FV V L++ F +GP+A V+ +DK+ FA+V
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVV--MDKD---KGVFAIVEMGDVGAREAVLS- 63
Query: 398 LDGTVFLGRMLHLIPGKPKE 417
G L + P + KE
Sbjct: 64 QSQHSLGGHRLRVRPREQKE 83
Score = 51.9 bits (125), Expect = 1e-08
Identities = 12/80 (15%), Positives = 28/80 (35%), Gaps = 11/80 (13%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
++++ + +F GP+ASV + + K + V+ +
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKG----------VFAIVEMGDVGARE 59
Query: 642 QALKVLQNSSLDEHQIELKR 661
L SL H++ ++
Sbjct: 60 AVLS-QSQHSLGGHRLRVRP 78
Score = 48.9 bits (117), Expect = 1e-07
Identities = 20/74 (27%), Positives = 27/74 (36%), Gaps = 10/74 (13%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ V P +++ E F AFG + V + K F VE +
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD------KGVFAIVEMGDVGARE---A 60
Query: 747 ALCQSTH-LYGRRL 759
L QS H L G RL
Sbjct: 61 VLSQSQHSLGGHRL 74
Score = 37.3 bits (87), Expect = 0.002
Identities = 12/66 (18%), Positives = 20/66 (30%), Gaps = 5/66 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ QL F G V V + FA + +A L + +
Sbjct: 18 RGVDSAQLSEYFLAFGPVASVVMDKDK----GVFAIVEMGDVGAREAVLSQ-SQHSLGGH 72
Query: 87 RIKVEK 92
R++V
Sbjct: 73 RLRVRP 78
Score = 34.6 bits (80), Expect = 0.016
Identities = 17/74 (22%), Positives = 28/74 (37%), Gaps = 9/74 (12%)
Query: 222 RQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASV-----RTTFLGMAYIGFKDEKNCNKAL 275
++ V P GV L YF P+ASV + F A + D L
Sbjct: 6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVF---AIVEMGDVGAREAVL 62
Query: 276 NKNKSFWKGKQLNI 289
++++ G +L +
Sbjct: 63 SQSQHSLGGHRLRV 76
Score = 34.6 bits (80), Expect = 0.018
Identities = 12/57 (21%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 444 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAA 499
+ R + V P L F FG + V++ G+ +VE +A
Sbjct: 5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAV 61
>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 = 59.1 bits (144), Expect = 3e-11
Identities = 21/90 (23%), Positives = 46/90 (51%), Gaps = 6/90 (6%)
Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
+ + E +++ L++++++ ++ +F K G + T+ K DP + G+ S G+GF
Sbjct: 3 NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTI--KMDPNT-GR--SRGFGF 57
Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKR 661
+ F S+ + L + LD I+ K+
Sbjct: 58 ILFKDAASVEKVLDQ-KEHRLDGRVIDPKK 86
Score = 57.6 bits (140), Expect = 1e-10
Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
++G++FV LS+ ++ DL F K+G + + + +D T +++GF + F +
Sbjct: 10 DAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKV 69
Query: 395 ----YQHLDG 400
LDG
Sbjct: 70 LDQKEHRLDG 79
Score = 41.4 bits (98), Expect = 6e-05
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
K+ V + + + ++++ F FGE+ + K +G RGFGF+ F ++ +
Sbjct: 12 GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTI-KMDPNTGRSRGFGFILFKDAASVEKVL 70
Query: 746 KA 747
Sbjct: 71 DQ 72
Score = 34.9 bits (81), Expect = 0.013
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALD 76
+ +++ LK F + G V D +K G+ R F FI + + LD
Sbjct: 21 WDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD 71
>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 = 59.1 bits (143), Expect = 7e-11
Identities = 13/105 (12%), Positives = 41/105 (39%), Gaps = 12/105 (11%)
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
+ ++++ ++++V +P ++++ + G++ + + + G G VE
Sbjct: 6 GRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--------GTGVVE 57
Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
F+ K + A++ L +T + D + +
Sbjct: 58 FVRKEDMTYAVRKL-DNTKFRSHEGETAYIRVK---VDGPRSPSY 98
Score = 57.5 bits (139), Expect = 2e-10
Identities = 17/80 (21%), Positives = 27/80 (33%), Gaps = 7/80 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+ V L + + DL + G + + G +V F+ E T A +
Sbjct: 18 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKEDMTYAVRK 70
Query: 398 LDGTVFLGRMLHLIPGKPKE 417
LD T F + K
Sbjct: 71 LDNTKFRSHEGETAYIRVKV 90
Score = 54.4 bits (131), Expect = 3e-09
Identities = 15/87 (17%), Positives = 32/87 (36%), Gaps = 12/87 (13%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
+ + + L + + ++ H ++ G + V R G G V+F
Sbjct: 11 PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------------GTGVVEF 58
Query: 635 YTRESLNQALKVLQNSSLDEHQIELKR 661
+E + A++ L N+ H+ E
Sbjct: 59 VRKEDMTYAVRKLDNTKFRSHEGETAY 85
Score = 46.4 bits (110), Expect = 2e-06
Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 1/74 (1%)
Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 504
RS+ ++V LP DLK GD+ V G TG+VEF++K A L
Sbjct: 14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFVRKEDMTYAVRKLD 72
Query: 505 YTKFKEVPLYLEWA 518
TKF+ +
Sbjct: 73 NTKFRSHEGETAYI 86
Score = 38.6 bits (90), Expect = 0.001
Identities = 13/91 (14%), Positives = 28/91 (30%), Gaps = 6/91 (6%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ + LK E G V + + + R++ A+ +NT S
Sbjct: 26 PSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKLDNTKFRSH 79
Query: 87 RIKVEKCSNLGDTTKPKSWSKYAPDSSAYQK 117
+ D + S+ + S + +
Sbjct: 80 EGETAYIRVKVDGPRSPSYGRSRSRSRSRSR 110
Score = 36.3 bits (84), Expect = 0.006
Identities = 13/75 (17%), Positives = 30/75 (40%), Gaps = 2/75 (2%)
Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTFLGMAYIGFKDEKNCNK 273
P +R + +VV LP +DLK + + + G + F +++
Sbjct: 7 RYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTY 66
Query: 274 ALNK-NKSFWKGKQL 287
A+ K + + ++ +
Sbjct: 67 AVRKLDNTKFRSHEG 81
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 58.6 bits (142), Expect = 7e-11
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 338 RIFVRNL------SYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
I V N+ ++ + K+F K+G + P +E KTKG+ + + P HA
Sbjct: 17 VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHA 74
Query: 392 TQAYQHLDGTVFLGR 406
A ++ DG +
Sbjct: 75 VDAVKNADGYKLDKQ 89
Score = 46.6 bits (111), Expect = 1e-06
Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 9/70 (12%)
Query: 685 GSKILVRNIP------FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 738
S I+V N+P + ++ + ++F FG++ P++ G +G+ F+E+ +
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE---DGKTKGYIFLEYASP 71
Query: 739 NEAKRAMKAL 748
A A+K
Sbjct: 72 AHAVDAVKNA 81
Score = 44.7 bits (106), Expect = 5e-06
Identities = 16/90 (17%), Positives = 35/90 (38%), Gaps = 13/90 (14%)
Query: 570 EEDEEREPEPDTTLYIKNL------NFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQ 623
++ + D+ + + N+ ++ I + F K G I + P+ G+
Sbjct: 5 KDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY-----PEEDGK 59
Query: 624 FLSMGYGFVQFYTRESLNQALKVLQNSSLD 653
+ GY F+++ + A+K LD
Sbjct: 60 --TKGYIFLEYASPAHAVDAVKNADGYKLD 87
Score = 38.2 bits (89), Expect = 0.001
Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 1/55 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT 81
+ + + F + G +T+ GK + + F+ Y A A+ +
Sbjct: 31 LEKLKNVIHKIFSKFGKITNDFYPEED-GKTKGYIFLEYASPAHAVDAVKNADGY 84
Score = 30.5 bits (69), Expect = 0.58
Identities = 14/72 (19%), Positives = 23/72 (31%), Gaps = 12/72 (16%)
Query: 448 RIILVKNLPYRT------LPTDLKALFEPFGDLGRVLVP-----PYGITGLVEFLQKNQA 496
+I+V N+P L + +F FG + P G +E+ A
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGY-IFLEYASPAHA 74
Query: 497 KAAFNSLAYTKF 508
A + K
Sbjct: 75 VDAVKNADGYKL 86
>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 = 58.0 bits (141), Expect = 8e-11
Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 7/87 (8%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
++FV + +T ++L + F +YG + +V +P + FA VTF + A
Sbjct: 10 HGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSL 64
Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGN 421
+ + G +H+ +PK N+ N
Sbjct: 65 CG--EDLIIKGISVHISNAEPKHNKLN 89
Score = 49.5 bits (119), Expect = 8e-08
Identities = 8/88 (9%), Positives = 28/88 (31%), Gaps = 12/88 (13%)
Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
+ +++ + T + +++ F + G + V + K + + FV
Sbjct: 5 HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI--PKPFR--------AFAFVT 54
Query: 634 FYTRESLNQALKVLQNSSLDEHQIELKR 661
F + ++ + + +
Sbjct: 55 FADDKVAQSLCG--EDLIIKGISVHISN 80
Score = 47.6 bits (114), Expect = 3e-07
Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 6/71 (8%)
Query: 676 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
+ S+ GSK+ V E+++ F +GE+ V +PK R F FV F
Sbjct: 2 RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP------FRAFAFVTF 55
Query: 736 ITKNEAKRAMK 746
A+
Sbjct: 56 ADDKVAQSLCG 66
Score = 35.3 bits (82), Expect = 0.009
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAAL 75
+T E+L+ F + G V DV + FR FAF+ + + AQ+
Sbjct: 21 EDMTAEELQQFFCQYGEVVDVFIP----KPFRAFAFVTFADDKVAQSLC 65
>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 = 58.8 bits (142), Expect = 9e-11
Identities = 17/108 (15%), Positives = 39/108 (36%), Gaps = 10/108 (9%)
Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKC---GPIASVTVARKKDPKSPGQFLSMGYG 630
E + ++ L ++ + + ++ C +A V ++ + G
Sbjct: 11 GPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR------QSGEA 64
Query: 631 FVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSS 678
FV+ + + + ALK S+ IE+ +S+R +S
Sbjct: 65 FVELESEDDVKLALK-KDRESMGHRYIEVFKSHRTEMDWVLKHSGPNS 111
Score = 57.6 bits (139), Expect = 2e-10
Identities = 16/100 (16%), Positives = 35/100 (35%), Gaps = 8/100 (8%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAF---GELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
G + +R +P+ +V+ + V G G FVE ++++
Sbjct: 16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR--QSGEAFVELESEDD 73
Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRY 780
K A+K + G R + + ++ + K +
Sbjct: 74 VKLALK---KDRESMGHRYIEVFKSHRTEMDWVLKHSGPN 110
Score = 54.9 bits (132), Expect = 2e-09
Identities = 14/100 (14%), Positives = 30/100 (30%), Gaps = 3/100 (3%)
Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEV--ILPIDKETDKTKG 379
S + + E + +R L ++ + +D+ V + I + G
Sbjct: 3 SGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSG 62
Query: 380 FALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
A V + A + D R + + E +
Sbjct: 63 EAFVELESEDDVKLALK-KDRESMGHRYIEVFKSHRTEMD 101
Score = 45.7 bits (108), Expect = 4e-06
Identities = 11/87 (12%), Positives = 32/87 (36%), Gaps = 10/87 (11%)
Query: 220 HKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLA----SVR------TTFLGMAYIGFKDEK 269
+ + + ++ LP +D++ + + V G A++ + E
Sbjct: 13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESED 72
Query: 270 NCNKALNKNKSFWKGKQLNIYKYSKDN 296
+ AL K++ + + ++K +
Sbjct: 73 DVKLALKKDRESMGHRYIEVFKSHRTE 99
Score = 31.4 bits (71), Expect = 0.33
Identities = 10/66 (15%), Positives = 20/66 (30%), Gaps = 10/66 (15%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPF---GDLGRVLVP------PYGITGLVEFLQK 493
E ++ ++ LP+ D++ + V G VE +
Sbjct: 13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGE-AFVELESE 71
Query: 494 NQAKAA 499
+ K A
Sbjct: 72 DDVKLA 77
>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 = 57.6 bits (140), Expect = 1e-10
Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 7/88 (7%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
+ S +FV + +TED+L + F +YG + +V +P + FA VTF + A
Sbjct: 3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQS 57
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGN 421
+ + G +H+ +PK N +
Sbjct: 58 LCG--EDLIIKGISVHISNAEPKHNSNS 83
Score = 46.8 bits (112), Expect = 6e-07
Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 6/66 (9%)
Query: 681 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
S + V + E+ E F +G++ V +PK R F FV F
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP------FRAFAFVTFADDQI 54
Query: 741 AKRAMK 746
A+
Sbjct: 55 AQSLCG 60
Score = 46.8 bits (112), Expect = 7e-07
Identities = 11/79 (13%), Positives = 27/79 (34%), Gaps = 12/79 (15%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ + TED +R F + G + V + K + + FV F +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFI--PKPFR--------AFAFVTFADDQIAQS 57
Query: 643 ALKVLQNSSLDEHQIELKR 661
++ + + +
Sbjct: 58 LCG--EDLIIKGISVHISN 74
Score = 35.7 bits (83), Expect = 0.005
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAAL 75
+T+++L+ F + G V DV + FR FAF+ + + AQ+
Sbjct: 15 GDMTEDELREFFSQYGDVMDVFIP----KPFRAFAFVTFADDQIAQSLC 59
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 58.3 bits (141), Expect = 1e-10
Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 3/73 (4%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RI ++NL + DL L + T G + F E +A +
Sbjct: 30 RITMKNLPEGCSWQDLKDLARENSL---ETTFSSVNTRDFDGTGALEFPSEEILVEALER 86
Query: 398 LDGTVFLGRMLHL 410
L+ F G ++ +
Sbjct: 87 LNNIEFRGSVITV 99
Score = 54.4 bits (131), Expect = 3e-09
Identities = 16/92 (17%), Positives = 32/92 (34%), Gaps = 8/92 (8%)
Query: 570 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGY 629
+ P + +KNL + ++ ++ T + G
Sbjct: 18 GSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE--TTFSSVNTRDFDG------T 69
Query: 630 GFVQFYTRESLNQALKVLQNSSLDEHQIELKR 661
G ++F + E L +AL+ L N I ++R
Sbjct: 70 GALEFPSEEILVEALERLNNIEFRGSVITVER 101
Score = 53.7 bits (129), Expect = 5e-09
Identities = 19/102 (18%), Positives = 39/102 (38%), Gaps = 10/102 (9%)
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFV 733
+ +I ++N+P ++++L + E F V + G G +
Sbjct: 18 GSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSS-----VNTRDFDGTGAL 72
Query: 734 EFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRK 775
EF ++ A++ L + G + + E DN IR+
Sbjct: 73 EFPSEEILVEALERL-NNIEFRGSVITV---ERDDNPPPIRR 110
Score = 39.4 bits (92), Expect = 4e-04
Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 6/89 (6%)
Query: 207 SDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL-----GMA 261
S VP S + + I +KNLP G +DLK + L + ++ G
Sbjct: 11 SSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTG 70
Query: 262 YIGFKDEKNCNKALNK-NKSFWKGKQLNI 289
+ F E+ +AL + N ++G + +
Sbjct: 71 ALEFPSEEILVEALERLNNIEFRGSVITV 99
Score = 37.1 bits (86), Expect = 0.003
Identities = 15/66 (22%), Positives = 22/66 (33%), Gaps = 2/66 (3%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ + LK E T T F + + E+ AL+ NN S
Sbjct: 38 EGCSWQDLKDLARENSLETTFSSVNT--RDFDGTGALEFPSEEILVEALERLNNIEFRGS 95
Query: 87 RIKVEK 92
I VE+
Sbjct: 96 VITVER 101
Score = 36.0 bits (83), Expect = 0.008
Identities = 18/80 (22%), Positives = 27/80 (33%), Gaps = 3/80 (3%)
Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFG---DLGRVLVPPYGITGLVEFLQKNQAKAAFN 501
+ I +KNLP DLK L V + TG +EF + A
Sbjct: 26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALE 85
Query: 502 SLAYTKFKEVPLYLEWAPEG 521
L +F+ + +E
Sbjct: 86 RLNNIEFRGSVITVERDDNP 105
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 57.0 bits (138), Expect = 2e-10
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 339 IFVRNL------SYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
I V N+ ++ + K+F K+G + P +E KTKG+ + + P HA
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAV 61
Query: 393 QAYQHLDGTVFLGR 406
A ++ DG +
Sbjct: 62 DAVKNADGYKLDKQ 75
Score = 46.2 bits (110), Expect = 1e-06
Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 9/69 (13%)
Query: 686 SKILVRNIP------FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN 739
S I+V N+P + ++ + ++F FG++ P++ G +G+ F+E+ +
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE---DGKTKGYIFLEYASPA 58
Query: 740 EAKRAMKAL 748
A A+K
Sbjct: 59 HAVDAVKNA 67
Score = 43.5 bits (103), Expect = 8e-06
Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 13/80 (16%)
Query: 580 DTTLYIKNL------NFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
D+ + + N+ ++ I + F K G I + P+ G+ + GY F++
Sbjct: 1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY-----PEEDGK--TKGYIFLE 53
Query: 634 FYTRESLNQALKVLQNSSLD 653
+ + A+K LD
Sbjct: 54 YASPAHAVDAVKNADGYKLD 73
Score = 38.9 bits (91), Expect = 4e-04
Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 1/55 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT 81
+ + + F + G +T+ GK + + F+ Y A A+ +
Sbjct: 17 LEKLKNVIHKIFSKFGKITNDFYPEED-GKTKGYIFLEYASPAHAVDAVKNADGY 70
Score = 32.0 bits (73), Expect = 0.12
Identities = 15/70 (21%), Positives = 24/70 (34%), Gaps = 10/70 (14%)
Query: 449 IILVKNLP------YRTLPTDLKALFEPFGDLGRVLVPPY-GIT---GLVEFLQKNQAKA 498
+I+V N+P L + +F FG + P G T +E+ A
Sbjct: 3 VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVD 62
Query: 499 AFNSLAYTKF 508
A + K
Sbjct: 63 AVKNADGYKL 72
>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 = 57.9 bits (140), Expect = 2e-10
Identities = 13/94 (13%), Positives = 33/94 (35%), Gaps = 10/94 (10%)
Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKC---GPIASVTVARKKDPKSPGQFLSMGYG 630
E E + + + L ++ T + + F C + +D K G
Sbjct: 5 EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGK------RRGDA 58
Query: 631 FVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
++ + + + +AL+ + + +E+ N
Sbjct: 59 LIEMESEQDVQKALE-KHRMYMGQRYVEVYEINN 91
Score = 57.2 bits (138), Expect = 2e-10
Identities = 14/99 (14%), Positives = 34/99 (34%), Gaps = 8/99 (8%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAF---GELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
I + +P+ +V F + G RG +E ++ +
Sbjct: 10 DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGK--RRGDALIEMESEQD 67
Query: 741 AKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNR 779
++A++ + G+R V + ++V+ + K
Sbjct: 68 VQKALE---KHRMYMGQRYVEVYEINNEDVDALMKSLQV 103
Score = 53.3 bits (128), Expect = 5e-09
Identities = 13/89 (14%), Positives = 30/89 (33%), Gaps = 3/89 (3%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEV--ILPIDKETDKTKGFALVTFLMP 388
E++ + I + L ++ T +D+ F I + K +G AL+
Sbjct: 6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE 65
Query: 389 EHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
+ +A R + + ++
Sbjct: 66 QDVQKA-LEKHRMYMGQRYVEVYEINNED 93
Score = 42.9 bits (101), Expect = 3e-05
Identities = 16/91 (17%), Positives = 34/91 (37%), Gaps = 10/91 (10%)
Query: 215 SKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLASV----------RTTFLGMAYIG 264
SK I + LP +D+ +F + + G A I
Sbjct: 2 SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIE 61
Query: 265 FKDEKNCNKALNKNKSFWKGKQLNIYKYSKD 295
+ E++ KAL K++ + + + +Y+ + +
Sbjct: 62 MESEQDVQKALEKHRMYMGQRYVEVYEINNE 92
Score = 30.2 bits (68), Expect = 0.74
Identities = 11/65 (16%), Positives = 19/65 (29%), Gaps = 8/65 (12%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLG-----RVLVPPYGIT---GLVEFLQKN 494
E +I + LP+ D+ F L+ G L+E +
Sbjct: 7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQ 66
Query: 495 QAKAA 499
+ A
Sbjct: 67 DVQKA 71
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 57.5 bits (139), Expect = 2e-10
Identities = 18/99 (18%), Positives = 34/99 (34%), Gaps = 8/99 (8%)
Query: 321 KSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGF 380
++ S + +R L V E DL + +++GP++ V++ K
Sbjct: 6 HHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQ 59
Query: 381 ALVTFLMPEHATQAYQHLDGT--VFLGRMLHLIPGKPKE 417
ALV F A A + G + ++
Sbjct: 60 ALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK 98
Score = 54.0 bits (130), Expect = 3e-09
Identities = 13/93 (13%), Positives = 34/93 (36%), Gaps = 9/93 (9%)
Query: 674 KRKSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 732
+ K S ++ +R + ++++ E + FG + +V + +
Sbjct: 9 MENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-------KKRQAL 61
Query: 733 VEFITKNEAKRAMKALCQST-HLYGRRLVLEWA 764
VEF A A+ + ++ G + ++
Sbjct: 62 VEFEDVLGACNAVNYAADNQIYIAGHPAFVNYS 94
Score = 51.3 bits (123), Expect = 2e-08
Identities = 14/78 (17%), Positives = 26/78 (33%), Gaps = 11/78 (14%)
Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
D+ + ++I+ L E + ++ GPI+ V V KK
Sbjct: 13 DDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK-----------RQAL 61
Query: 632 VQFYTRESLNQALKVLQN 649
V+F A+ +
Sbjct: 62 VEFEDVLGACNAVNYAAD 79
Score = 47.4 bits (113), Expect = 5e-07
Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 2/73 (2%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
++ ++ L + DL + FG + V+V P LVEF A A N A +
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQ 81
Query: 508 FKEV--PLYLEWA 518
P ++ ++
Sbjct: 82 IYIAGHPAFVNYS 94
Score = 38.2 bits (89), Expect = 0.001
Identities = 11/67 (16%), Positives = 24/67 (35%), Gaps = 7/67 (10%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT--YVF 84
+ + L +E G ++ V + +R A + + A A++Y + Y+
Sbjct: 31 DGVVEADLVEALQEFGPISYVVV-----MPKKRQALVEFEDVLGACNAVNYAADNQIYIA 85
Query: 85 SSRIKVE 91
V
Sbjct: 86 GHPAFVN 92
Score = 34.7 bits (80), Expect = 0.018
Identities = 20/92 (21%), Positives = 33/92 (35%), Gaps = 15/92 (16%)
Query: 208 DPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRT-TFLGMAYIGF 265
DP P S + ++ L GV + DL + P++ V A + F
Sbjct: 14 DPHKTPASP---------VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEF 64
Query: 266 KDEKNCNKALN---KNKSFWKGKQLNIYKYSK 294
+D A+N N+ + G + YS
Sbjct: 65 EDVLGACNAVNYAADNQIYIAGHPAFV-NYST 95
>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 = 57.2 bits (138), Expect = 4e-10
Identities = 19/94 (20%), Positives = 33/94 (35%), Gaps = 8/94 (8%)
Query: 328 QFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLM 387
S I +R L VTE ++ L +G + +++ K K A +
Sbjct: 23 DSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNT 76
Query: 388 PEHATQA--YQHLDGTVFLGRMLHLIPGKPKENE 419
E A Y V G+ +++ KE +
Sbjct: 77 EEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELK 110
Score = 54.2 bits (130), Expect = 4e-09
Identities = 15/93 (16%), Positives = 38/93 (40%), Gaps = 9/93 (9%)
Query: 674 KRKSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 732
+ + S+++ +R +P + EV L FG++ + + K + F
Sbjct: 19 SHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-------GKNQAF 71
Query: 733 VEFITKNEAKRAMKALC-QSTHLYGRRLVLEWA 764
+E T+ A + + L G+ + ++++
Sbjct: 72 IEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS 104
Score = 47.2 bits (112), Expect = 1e-06
Identities = 12/87 (13%), Positives = 29/87 (33%), Gaps = 11/87 (12%)
Query: 566 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
+ D P ++I+ L + TE + G + ++ + + K
Sbjct: 17 RGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK--------- 67
Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSL 652
F++ T E+ N + + +
Sbjct: 68 --NQAFIEMNTEEAANTMVNYYTSVTP 92
Score = 46.8 bits (111), Expect = 2e-06
Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 2/73 (2%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
R+I ++ LP ++ +L PFG + +L+ +E + A N
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 91
Query: 508 --FKEVPLYLEWA 518
+ P+Y++++
Sbjct: 92 PVLRGQPIYIQFS 104
Score = 35.3 bits (81), Expect = 0.018
Identities = 12/67 (17%), Positives = 29/67 (43%), Gaps = 7/67 (10%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYF--NNTYVF 84
+T+ ++ + G VT++ + K + AFI + E+ A ++Y+ +
Sbjct: 41 IDVTEGEVISLGLPFGKVTNLLM-----LKGKNQAFIEMNTEEAANTMVNYYTSVTPVLR 95
Query: 85 SSRIKVE 91
I ++
Sbjct: 96 GQPIYIQ 102
Score = 32.2 bits (73), Expect = 0.17
Identities = 14/99 (14%), Positives = 35/99 (35%), Gaps = 6/99 (6%)
Query: 201 SKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTFL- 258
++ P + + I ++ LP V + ++ + P + ++
Sbjct: 8 HHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK 67
Query: 259 GMAYIGFKDEKNCNKALN---KNKSFWKGKQLNIYKYSK 294
A+I E+ N +N +G+ + I ++S
Sbjct: 68 NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI-QFSN 105
>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 = 56.9 bits (137), Expect = 4e-10
Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ L V+ + L + EK G + +++P + K ++ + E + +AY L
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTL 83
Query: 399 DGTVFLGRMLHLIP 412
+G + + I
Sbjct: 84 NGKEVVDDLGQKIT 97
Score = 54.9 bits (132), Expect = 2e-09
Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 13/85 (15%)
Query: 570 EEDEEREPEPDTTLYIKN--LNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 627
E E +L + N L + + + +KCG + ++ + K
Sbjct: 15 HEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK----------- 63
Query: 628 GYGFVQFYTRESLNQALKVLQNSSL 652
Y F ++ T E +A L +
Sbjct: 64 PYSFARYRTTEESKRAYVTLNGKEV 88
Score = 46.8 bits (111), Expect = 1e-06
Identities = 9/61 (14%), Positives = 25/61 (40%), Gaps = 7/61 (11%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ + ++++ + + G + + +P ++ + F + T E+KRA
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-------NKPYSFARYRTTEESKRAYVT 82
Query: 748 L 748
L
Sbjct: 83 L 83
Score = 43.8 bits (103), Expect = 1e-05
Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 7/82 (8%)
Query: 444 ARSKRIILVKN--LPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN 501
+ + + ++V N L L + E G + +L+PP + ++K A+
Sbjct: 22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYV 81
Query: 502 SLAYTKF-----KEVPLYLEWA 518
+L + +++ LYL +
Sbjct: 82 TLNGKEVVDDLGQKITLYLNFV 103
Score = 37.6 bits (87), Expect = 0.002
Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 5/61 (8%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
+++ QL E+ G V + + + ++F Y ++++ A N V
Sbjct: 39 VSRNQLLPVLEKCGLVDALLMP-----PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLG 93
Query: 89 K 89
+
Sbjct: 94 Q 94
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 55.6 bits (134), Expect = 8e-10
Identities = 19/98 (19%), Positives = 32/98 (32%), Gaps = 8/98 (8%)
Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
S I +R L VTE ++ L +G + +++ K K A
Sbjct: 2 RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQA 55
Query: 382 LVTFLMPEHATQA--YQHLDGTVFLGRMLHLIPGKPKE 417
+ E A Y V G+ +++ KE
Sbjct: 56 FIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE 93
Score = 54.1 bits (130), Expect = 3e-09
Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 9/81 (11%)
Query: 686 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
S+++ +R +P + EV L FG++ + + K + F+E T+ A
Sbjct: 16 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-------GKNQAFIEMNTEEAANTM 68
Query: 745 MKALCQST-HLYGRRLVLEWA 764
+ T L G+ + ++++
Sbjct: 69 VNYYTSVTPVLRGQPIYIQFS 89
Score = 47.9 bits (114), Expect = 4e-07
Identities = 15/90 (16%), Positives = 33/90 (36%), Gaps = 13/90 (14%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
P ++I+ L + TE + G + ++ + + K F++ T
Sbjct: 13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK-----------NQAFIEMNT 61
Query: 637 RESLNQALKVLQNSS--LDEHQIELKRSNR 664
E+ N + + + L I ++ SN
Sbjct: 62 EEAANTMVNYYTSVTPVLRGQPIYIQFSNH 91
Score = 47.9 bits (114), Expect = 5e-07
Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 2/73 (2%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
R+I ++ LP ++ +L PFG + +L+ +E + A N
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 76
Query: 508 --FKEVPLYLEWA 518
+ P+Y++++
Sbjct: 77 PVLRGQPIYIQFS 89
Score = 35.6 bits (82), Expect = 0.010
Identities = 12/67 (17%), Positives = 29/67 (43%), Gaps = 7/67 (10%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYF--NNTYVF 84
+T+ ++ + G VT++ + K + AFI + E+ A ++Y+ +
Sbjct: 26 IDVTEGEVISLGLPFGKVTNLLM-----LKGKNQAFIEMNTEEAANTMVNYYTSVTPVLR 80
Query: 85 SSRIKVE 91
I ++
Sbjct: 81 GQPIYIQ 87
Score = 30.6 bits (69), Expect = 0.47
Identities = 13/74 (17%), Positives = 30/74 (40%), Gaps = 6/74 (8%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVR-TTFLGMAYIGFKDEKNCNKALN---KNKS 280
I ++ LP V + ++ + P + ++ A+I E+ N +N
Sbjct: 18 VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTP 77
Query: 281 FWKGKQLNIYKYSK 294
+G+ + I ++S
Sbjct: 78 VLRGQPIYI-QFSN 90
>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 = 54.8 bits (132), Expect = 1e-09
Identities = 18/95 (18%), Positives = 33/95 (34%), Gaps = 8/95 (8%)
Query: 325 DSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVT 384
S D A S + +R L VTE ++ L +G + +++ K K A +
Sbjct: 4 GSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLE 57
Query: 385 FLMPEHATQAYQH--LDGTVFLGRMLHLIPGKPKE 417
E A + + +++ KE
Sbjct: 58 LATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE 92
Score = 51.4 bits (123), Expect = 2e-08
Identities = 17/91 (18%), Positives = 40/91 (43%), Gaps = 9/91 (9%)
Query: 676 KSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
S + S++L +R +P + ++EV L FG++ + + K + F+E
Sbjct: 5 SSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-------GKNQAFLE 57
Query: 735 FITKNEAKRAMKALC-QSTHLYGRRLVLEWA 764
T+ A + + HL + + ++++
Sbjct: 58 LATEEAAITMVNYYSAVTPHLRNQPIYIQYS 88
Score = 49.0 bits (117), Expect = 2e-07
Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
R++ ++ LP T++ AL PFG + +L+ +E + A N +
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVT 75
Query: 508 --FKEVPLYLEWA 518
+ P+Y++++
Sbjct: 76 PHLRNQPIYIQYS 88
Score = 46.7 bits (111), Expect = 9e-07
Identities = 15/95 (15%), Positives = 32/95 (33%), Gaps = 13/95 (13%)
Query: 572 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
++ + P L+I+ L TE + G + ++ + + K F
Sbjct: 7 GDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK-----------NQAF 55
Query: 632 VQFYTRESLNQALKVLQNS--SLDEHQIELKRSNR 664
++ T E+ + L I ++ SN
Sbjct: 56 LELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH 90
Score = 36.0 bits (83), Expect = 0.007
Identities = 12/67 (17%), Positives = 31/67 (46%), Gaps = 7/67 (10%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYF--NNTYVF 84
++T+ ++ A G VT++ + K + AF+ E+ A ++Y+ ++
Sbjct: 25 GEVTETEVIALGLPFGKVTNILM-----LKGKNQAFLELATEEAAITMVNYYSAVTPHLR 79
Query: 85 SSRIKVE 91
+ I ++
Sbjct: 80 NQPIYIQ 86
Score = 30.9 bits (70), Expect = 0.43
Identities = 13/95 (13%), Positives = 32/95 (33%), Gaps = 15/95 (15%)
Query: 205 APSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTT-FLGMAY 262
+ D S+ + ++ LP V + ++ A P + ++ A+
Sbjct: 5 SSGDKMDGAPSR---------VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAF 55
Query: 263 IGFKDEKNCNKALNK---NKSFWKGKQLNIYKYSK 294
+ E+ +N + + + I +YS
Sbjct: 56 LELATEEAAITMVNYYSAVTPHLRNQPIYI-QYSN 89
>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 = 60.4 bits (146), Expect = 2e-09
Identities = 46/247 (18%), Positives = 79/247 (31%), Gaps = 73/247 (29%)
Query: 588 LNFNSTEDSI-------------RRHFKKCGPIASVTVARKKDPKSP----GQFLSMGYG 630
L+ S E + + F K P + A +P +P G+FL G
Sbjct: 11 LSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFL----G 66
Query: 631 FVQFYTRES-LNQALKVLQNSSLD--EHQIELKRSN-----RNLESEATTVKRKSSNV-- 680
+V S + Q +VL L E+ L+ ++ L E T K+ +
Sbjct: 67 YVSSLVEPSKVGQFDQVLN-LCLTEFENCY-LEGNDIHALAAKLLQENDTTLVKTKELIK 124
Query: 681 ----AKQTGSKILVRNIP---FQAKQSEVEELFKAFG----------EL-KFVRLPKKMV 722
A+ + + F+A +L FG EL + +V
Sbjct: 125 NYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLV 184
Query: 723 GSGLHRGFGFVEFITKNEAKRAMKALCQSTH----LYGRRL-VLEWAEEADNVEDIRKRT 777
G + I + + L ++T ++ + L +LEW E N D
Sbjct: 185 G----------DLI--KFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPD----- 227
Query: 778 NRYFGTA 784
Y +
Sbjct: 228 KDYLLSI 234
Score = 48.9 bits (116), Expect = 7e-06
Identities = 83/545 (15%), Positives = 152/545 (27%), Gaps = 177/545 (32%)
Query: 225 HTIVVKNLPAG--VKKKDLKAYF-KPLPLASVRTT--------------FLGMAYIGFKD 267
H ++V P L+ F K LP + FLG Y+
Sbjct: 18 HVLLV---PTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLG--YVSSLV 72
Query: 268 EKNCNKALNK---------NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKA- 317
E + ++ + +G +I+ + AK D + E IK
Sbjct: 73 EPSKVGQFDQVLNLCLTEFENCYLEGN--DIHALA----AKLLQENDTTLVKTKELIKNY 126
Query: 318 --------KHWKSQEDSVQFAEDIAESGRIFV------RNLSYTVTEDDLTKLFEKYGPL 363
+ + + +S F + ++ Y ++L L++ Y L
Sbjct: 127 ITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYF---EELRDLYQTYHVL 183
Query: 364 AEVILPIDKETDKTKGFALVTFL-MPEHATQAYQH-LDGTVFLGRMLHLIPGKPKENEGN 421
++ K + +T L + A + + L+ + L P N +
Sbjct: 184 VGDLI---KFSAET----LSELIRTTLDAEKVFTQGLN----ILEWLE----NP-SNTPD 227
Query: 422 VDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKAL-FEPFGDLGRVLVP 480
D + IS I +++ Y K L F P G+L L
Sbjct: 228 KDYLLSIPIS------CPL--------IGVIQLAHYVVT---AKLLGFTP-GELRSYLK- 268
Query: 481 PYGITGLVEFLQKNQAKAAFNSLAYTK---FKEVPLYLEWAPEGVF---AEAKEK--SKG 532
G TG + L A + + F V + F E +
Sbjct: 269 --GATGHSQGL----VTAVAIAETDSWESFFVSVRKAITVL----FFIGVRCYEAYPNTS 318
Query: 533 KEKEKNEEEGEEGEEEKKENTAEEDNQQGVP------------EVEENVEEDEEREPEPD 580
E+ E E GVP +V++ V + P
Sbjct: 319 LPPSILEDSLENNE--------------GVPSPMLSISNLTQEQVQDYVNKTNSHLPA-G 363
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIAS----VTVARK-KDPKSPGQ------------ 623
+ I +L N ++ GP S RK K P Q
Sbjct: 364 KQVEI-SL-VNG-----AKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKF 416
Query: 624 ---FLSMGYGFVQF---YTRESLNQALKVLQNSSLDEHQIELK------RSNRNLESEAT 671
FL + F + + K L +++ + +++ +L +
Sbjct: 417 SNRFLPV---ASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSG 473
Query: 672 TVKRK 676
++ +
Sbjct: 474 SISER 478
Score = 48.5 bits (115), Expect = 1e-05
Identities = 88/538 (16%), Positives = 146/538 (27%), Gaps = 189/538 (35%)
Query: 32 EQLKAKFE------EKGTVTDVQLKYTTE--GKFRRFAFIGYHREDQAQ--------AAL 75
QL+ +F +G D + E GKF ++ E L
Sbjct: 31 SQLQEQFNKILPEPTEGFAADDEPTTPAELVGKF--LGYVSSLVEPSKVGQFDQVLNLCL 88
Query: 76 DYFNNTYVFSSRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTK-- 133
F N Y+ + I L + +K Y +A + K ++
Sbjct: 89 TEFENCYLEGNDIHALAAKLLQENDTTLVKTKEL--IKNYITARIMAKRPFDKKSNSALF 146
Query: 134 DSKPGKKSK----------NDPTFSDFLQLHGKDVSKLL--PLSNKDGEEKEEENEDESN 181
+ ++ D F + L+ +L L E E +
Sbjct: 147 RAVGEGNAQLVAIFGGQGNTDDYFEELRDLY--QTYHVLVGDLIKFSAETLSELIRTTLD 204
Query: 182 NQIAHADISD-MEYLKLKTKSKDTAPSDP---SVPPVSKAP-------VHKRQYHTIVVK 230
+ + +E+L ++ P S+ P+S P H Y + K
Sbjct: 205 AEKVFTQGLNILEWL----ENPSNTPDKDYLLSI-PIS-CPLIGVIQLAH---Y-VVTAK 254
Query: 231 NLPAGVKKKDLKAYFK-----------PLPLASVRT--TFLGMA--------YIGF---- 265
L G +L++Y K + +A + +F +IG
Sbjct: 255 LL--GFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYE 312
Query: 266 ------------KDEKNCN---------------KALNK-----NKSFWKGKQLNIYKYS 293
+D N + + N GKQ+ I S
Sbjct: 313 AYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEI---S 369
Query: 294 KDNSAKY---SGAADD--NNNASMENIKAKHWKSQ----------EDSVQF--------- 329
N AK SG N ++ KA Q + S +F
Sbjct: 370 LVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHS 429
Query: 330 ----------AEDIAESGRIF-VRNLSYTV--TED--DLTKLFEKYGP-LAEVIL--PID 371
+D+ ++ F +++ V T D DL L + + I+ P+
Sbjct: 430 HLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVK 489
Query: 372 KETDKTKGFALVTFLMPEHATQAYQHLD----GTVFLGRMLHLIPGKPKENEGNVDGK 425
ET T H LD G LG + H N DG
Sbjct: 490 WET--------TTQFKATHI------LDFGPGGASGLGVLTH----------RNKDGT 523
Score = 42.7 bits (100), Expect = 6e-04
Identities = 71/487 (14%), Positives = 140/487 (28%), Gaps = 163/487 (33%)
Query: 145 PT--FSDFLQLHGKDV-SKLLPLSNKDGEEKEEENEDESNNQIAHADISDMEYLKLKTKS 201
PT F QL ++ +K+LP + E ++E + ++ ++L +
Sbjct: 23 PTASFFIASQL--QEQFNKILP---EPTEGFAADDEPTTPAELV------GKFLGYVSSL 71
Query: 202 KDTAPSDPSVPPVSKAPVH-KRQY------HTIVVKNLPAGVKKKDLKAYFKPLPLASVR 254
+ + ++ + Y H + K L +K ++
Sbjct: 72 VEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAK-LLQENDTTLVKTK------ELIK 124
Query: 255 TTFLGMAYIGFKDEKNCNKALNKNKS---------FWKGKQ---------L-NIYK-YSK 294
+K N AL + F G Q L ++Y+ Y
Sbjct: 125 NYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF--GGQGNTDDYFEELRDLYQTYHV 182
Query: 295 ------DNSAKY----SGAADDNNNASMENIKAKHWKSQEDS------------------ 326
SA+ D + + W +
Sbjct: 183 LVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIG 242
Query: 327 -VQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKY----GPLAEVI--LPIDKETDKTKG 379
+Q A + + + L +T E L G ++ + I ETD +
Sbjct: 243 VIQLAHYV-----VTAKLLGFTPGE-----LRSYLKGATGHSQGLVTAVAI-AETDSWES 291
Query: 380 F------AL-VTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE----NEG------NV 422
F A+ V F + +AY + L P ++ NEG ++
Sbjct: 292 FFVSVRKAITVLFFIGVRCYEAYPNTS----------LPPSILEDSLENNEGVPSPMLSI 341
Query: 423 DGKVHCCISERKLDAFNQVVEARSKRI-ILVKNLPYRTLPTDLKALFEPFGDLGRVLV-- 479
+ + ++ N + K++ I + N + LV
Sbjct: 342 SNLTQEQV-QDYVNKTNSHL-PAGKQVEISLVNGA-------------------KNLVVS 380
Query: 480 -PPYGITGLVEFLQK-------NQAKAAFNSLA---YTKFKEV--PL---YLEWAPEGVF 523
PP + GL L+K +Q++ F+ +F V P L A + +
Sbjct: 381 GPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLIN 440
Query: 524 AEAKEKS 530
+ + +
Sbjct: 441 KDLVKNN 447
Score = 36.2 bits (83), Expect = 0.047
Identities = 44/283 (15%), Positives = 87/283 (30%), Gaps = 92/283 (32%)
Query: 228 VVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQL 287
+V N P +L +F +R + M + D K + + K +
Sbjct: 1664 IVINNP-----VNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKE----INEHS 1714
Query: 288 NIYKYSKDNSAKYSGAADDNNN----------ASMENIKAKHWKSQEDSVQFA-----E- 331
Y + + G A+ E++K+K D+ FA E
Sbjct: 1715 TSYTFRSEK-----GLLSATQFTQPALTLMEKAAFEDLKSKGLI-PADAT-FAGHSLGEY 1767
Query: 332 ----DIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLM 387
+A+ +S + L ++ G +V +P D+ G +
Sbjct: 1768 AALASLADV-------MSI----ESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAIN--- 1813
Query: 388 PEHATQAYQHLDGTVFLGRM--------LHLIPGKPKENEG--------NVDGK--VHCC 429
P GR+ L + + + G NV+ + V
Sbjct: 1814 P----------------GRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYV--- 1854
Query: 430 IS--ERKLDAFNQVV-EARSKRIILVKNLPYRTLPTDLKA-LF 468
+ R LD V+ + ++I +++ L +++ LF
Sbjct: 1855 AAGDLRALDTVTNVLNFIKLQKIDIIE-LQKSLSLEEVEGHLF 1896
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 55.4 bits (133), Expect = 2e-09
Identities = 15/95 (15%), Positives = 29/95 (30%), Gaps = 8/95 (8%)
Query: 669 EATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAF---GELKFVRLPKKMVGSG 725
+ G + +R +P+ +V+ V G
Sbjct: 28 QQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGR- 86
Query: 726 LHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV 760
G FVE ++++ K A+K + G R +
Sbjct: 87 -QSGEAFVELGSEDDVKMALK---KDRESMGHRYI 117
Score = 55.0 bits (132), Expect = 3e-09
Identities = 16/101 (15%), Positives = 36/101 (35%), Gaps = 10/101 (9%)
Query: 567 ENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKC---GPIASVTVARKKDPKSPGQ 623
E + ++ L ++ + + ++ C A V ++ +
Sbjct: 31 GRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGR---- 86
Query: 624 FLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNR 664
G FV+ + + + ALK S+ IE+ +S+R
Sbjct: 87 --QSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHR 124
Score = 51.5 bits (123), Expect = 5e-08
Identities = 14/101 (13%), Positives = 31/101 (30%), Gaps = 3/101 (2%)
Query: 321 KSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPL--AEVILPIDKETDKTK 378
+ S+ + E + +R L ++ + +D+ A + I +
Sbjct: 29 QMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQS 88
Query: 379 GFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
G A V + A + D R + + E +
Sbjct: 89 GEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHRTEMD 128
Score = 45.0 bits (106), Expect = 9e-06
Identities = 15/113 (13%), Positives = 35/113 (30%), Gaps = 13/113 (11%)
Query: 203 DTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPLPLA----SVR---- 254
+ + ++ LP +D++ + + V
Sbjct: 23 SMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYT 82
Query: 255 --TTFLGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSK---DNSAKYSG 302
G A++ E + AL K++ + + ++K + D K+SG
Sbjct: 83 REGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTEMDWVLKHSG 135
Score = 28.0 bits (62), Expect = 5.5
Identities = 9/65 (13%), Positives = 19/65 (29%), Gaps = 8/65 (12%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLG-----RVLVPPYGIT---GLVEFLQKN 494
E ++ ++ LP+ D++ + G VE ++
Sbjct: 40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSED 99
Query: 495 QAKAA 499
K A
Sbjct: 100 DVKMA 104
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 54.0 bits (130), Expect = 3e-09
Identities = 14/71 (19%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 575 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
+ + ++YIK ++T D I+ + G + ++ + R G FV F
Sbjct: 6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFK------GSIFVVF 59
Query: 635 YTRESLNQALK 645
+ ES + ++
Sbjct: 60 DSIESAKKFVE 70
Score = 52.8 bits (127), Expect = 8e-09
Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 2/74 (2%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++++ T DD+ + E G + + + KG V F E A + +
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-T 71
Query: 399 DGTVFLGRMLHLIP 412
G + L ++
Sbjct: 72 PGQKYKETDLLILF 85
Score = 52.4 bits (126), Expect = 1e-08
Identities = 11/80 (13%), Positives = 34/80 (42%), Gaps = 4/80 (5%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ ++ P A +++E + G++ +++ + +G FV F + AK+ ++
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT--LHKAFKGSIFVVFDSIESAKKFVE 70
Query: 747 ALCQSTHLYGRRLVLEWAEE 766
L++ + ++
Sbjct: 71 T--PGQKYKETDLLILFKDD 88
Score = 46.3 bits (110), Expect = 2e-06
Identities = 13/58 (22%), Positives = 27/58 (46%)
Query: 25 FIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY 82
F T + +K E+KG V ++Q++ T F+ F+ + + A+ ++ Y
Sbjct: 19 FPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKY 76
Score = 41.6 bits (98), Expect = 7e-05
Identities = 17/98 (17%), Positives = 33/98 (33%), Gaps = 6/98 (6%)
Query: 443 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-----TGLVEFLQKNQAK 497
R + +K P D+K E G + + + + V F AK
Sbjct: 7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66
Query: 498 AAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEK 535
K+KE L + + + + +E+ + K +
Sbjct: 67 KFVE-TPGQKYKETDLLILFKDDYFAKKNEERKQNKVE 103
Score = 40.9 bits (96), Expect = 1e-04
Identities = 11/76 (14%), Positives = 28/76 (36%), Gaps = 7/76 (9%)
Query: 221 KRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVR------TTFLGMAYIGFKDEKNCNK 273
+ ++ +K P D+K + + + +++ F G ++ F ++ K
Sbjct: 8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 67
Query: 274 ALNKNKSFWKGKQLNI 289
+ +K L I
Sbjct: 68 FVETPGQKYKETDLLI 83
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 53.8 bits (130), Expect = 3e-09
Identities = 23/87 (26%), Positives = 37/87 (42%), Gaps = 7/87 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPL---AEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+FV +L+ V + L + F K P +V+L +T +KG+ V F +A
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD---QTGVSKGYGFVKFTDELEQKRA 67
Query: 395 YQHLDGTVFLG-RMLHLIPGKPKENEG 420
G V LG + + L PK +
Sbjct: 68 LTECQGAVGLGSKPVRLSVAIPKASRV 94
Score = 48.8 bits (117), Expect = 2e-07
Identities = 20/91 (21%), Positives = 35/91 (38%), Gaps = 8/91 (8%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR-KKDPKSPGQFLSMGYGFVQF 634
P+ +L++ +L + + + F K P S + D +S GYGFV+F
Sbjct: 5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYP--SCRGGKVVLDQTG----VSKGYGFVKF 58
Query: 635 YTRESLNQALKVLQNS-SLDEHQIELKRSNR 664
+AL Q + L + L +
Sbjct: 59 TDELEQKRALTECQGAVGLGSKPVRLSVAIP 89
Score = 41.9 bits (99), Expect = 6e-05
Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 703 EELFKAFGELKF--VRLPKKMV-GSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL 759
L++ F + + R K ++ +G+ +G+GFV+F + E KRA+ + L + +
Sbjct: 24 GMLYEFFVK-VYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPV 82
Query: 760 VLEWA 764
L A
Sbjct: 83 RLSVA 87
>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 = 55.6 bits (133), Expect = 7e-09
Identities = 11/79 (13%), Positives = 34/79 (43%), Gaps = 4/79 (5%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ ++ P A +++E + G++ +++ + +G FV F + AK+ ++
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT--LHKAFKGSIFVVFDSIESAKKFVET 169
Query: 748 LCQSTHLYGRRLVLEWAEE 766
L++ + ++
Sbjct: 170 P--GQKYKETDLLILFKDD 186
Score = 51.8 bits (123), Expect = 1e-07
Identities = 17/117 (14%), Positives = 39/117 (33%), Gaps = 2/117 (1%)
Query: 296 NSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTK 355
+ S A + I+ K + ++ ++ ++++ T DD+ +
Sbjct: 69 EALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKE 128
Query: 356 LFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIP 412
E G + + + KG V F E A + + G + L ++
Sbjct: 129 WLEDKGQVLNIQMRRTLHK-AFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF 183
Score = 45.6 bits (107), Expect = 2e-05
Identities = 13/59 (22%), Positives = 27/59 (45%)
Query: 24 EFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY 82
F T + +K E+KG V ++Q++ T F+ F+ + + A+ ++ Y
Sbjct: 116 GFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKY 174
Score = 44.8 bits (105), Expect = 3e-05
Identities = 18/105 (17%), Positives = 37/105 (35%), Gaps = 7/105 (6%)
Query: 563 PEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 622
P DE + + ++YIK ++T D I+ + G + ++ + R
Sbjct: 92 PSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH----- 146
Query: 623 QFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLE 667
G FV F + ES + ++ E + + +
Sbjct: 147 -KAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDYFA 189
Score = 42.1 bits (98), Expect = 2e-04
Identities = 23/171 (13%), Positives = 50/171 (29%), Gaps = 15/171 (8%)
Query: 368 LPIDK----ETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVD 423
LP DK + +G+ + ++ + +
Sbjct: 29 LPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKS---KAELMEISEDK 85
Query: 424 GKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG 483
K+ S+ + ++ R + +K P D+K E G + + +
Sbjct: 86 TKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL 145
Query: 484 I-----TGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEK 529
+ V F AK + K+KE L + + + + K +
Sbjct: 146 HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDD--YFAKKNE 193
Score = 39.8 bits (92), Expect = 0.001
Identities = 11/77 (14%), Positives = 29/77 (37%), Gaps = 7/77 (9%)
Query: 220 HKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVR------TTFLGMAYIGFKDEKNCN 272
+ + ++ +K P D+K + + + +++ F G ++ F ++
Sbjct: 105 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 164
Query: 273 KALNKNKSFWKGKQLNI 289
K + +K L I
Sbjct: 165 KFVETPGQKYKETDLLI 181
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 52.3 bits (125), Expect = 2e-08
Identities = 16/86 (18%), Positives = 31/86 (36%), Gaps = 4/86 (4%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETD--KTKGFALVTFLMPEHAT 392
S ++FV L + ED++T F ++GPL + KG+A + F
Sbjct: 7 GSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQ 66
Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKEN 418
G++ + ++
Sbjct: 67 ALID--ACLEEDGKLYLCVSSPTIKD 90
Score = 41.9 bits (98), Expect = 6e-05
Identities = 15/86 (17%), Positives = 35/86 (40%), Gaps = 6/86 (6%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ L + ED I F++ GP+ + + F GY F+ F S+
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSY---FPPKGYAFLLFQEESSVQ- 66
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLES 668
++ ++ ++ L S+ ++
Sbjct: 67 --ALIDACLEEDGKLYLCVSSPTIKD 90
Score = 39.2 bits (91), Expect = 7e-04
Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 1/62 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV-GSGLHRGFGFVEFITKNEAKRAM 745
K+ V +P + E+ F+ FG L K +G+ F+ F ++ + +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69
Query: 746 KA 747
A
Sbjct: 70 DA 71
Score = 34.6 bits (79), Expect = 0.026
Identities = 10/51 (19%), Positives = 22/51 (43%), Gaps = 3/51 (5%)
Query: 29 ITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALD 76
I ++++ A F G + + + + +AF+ + E QA +D
Sbjct: 20 IDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
>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 = 57.2 bits (137), Expect = 2e-08
Identities = 89/642 (13%), Positives = 180/642 (28%), Gaps = 176/642 (27%)
Query: 220 HKRQYHTIVVKNLPAGVKK---KDLKAYFKPLPLASVRTTFLGMAYIGFKDEKNCNKALN 276
H+ QY I+ A V KD++ K + L+ + I KD + L
Sbjct: 14 HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSI-LSKEEIDHI----IMSKDAVSGTLRL- 67
Query: 277 KNKSFW--KGKQLNIYKYSKDNSAKYSGAADDNN-NASMENIKAKHWKSQEDSVQFAED- 332
FW KQ + + K+ N M IK + + + + E
Sbjct: 68 ----FWTLLSKQEEMVQ-------KFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQR 116
Query: 333 --IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKT----KGF---ALV 383
+ ++F + Y V+ + Y L + +L + + G +
Sbjct: 117 DRLYNDNQVFAK---YNVSR------LQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVA 167
Query: 384 TFLMPEHATQAYQHLDGTVF---LGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFN- 439
+ + Q +D +F L P E + ++ + R + N
Sbjct: 168 LDVCLSYKVQ--CKMDFKIFWLNLKNC--NSPETVLEMLQKLLYQIDPNWTSRSDHSSNI 223
Query: 440 ----QVVEARSKRIILVKNLPYRTL--------PTDLKALFEPFGDLG-RVLVPPYGITG 486
++A +R++ K L A F +L ++L+ T
Sbjct: 224 KLRIHSIQAELRRLLKSKPYE-NCLLVLLNVQNAKAWNA-F----NLSCKILL----TT- 272
Query: 487 LVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEE-----E 541
+ K + L+ + L S ++ +
Sbjct: 273 --------RFKQVTDFLSAATTTHISL-------------DHHSMTLTPDEVKSLLLKYL 311
Query: 542 GEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSI---- 597
++ +E N + + + E++ + T K++N + I
Sbjct: 312 DCRPQDLPRE--VLTTNPRRLSIIAESIRDG------LATWDNWKHVNCDKLTTIIESSL 363
Query: 598 --------RRHFKKCG--PIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVL 647
R+ F + P P LS+ + V + + L
Sbjct: 364 NVLEPAEYRKMFDRLSVFP---------PSAHIPTILLSLIWFDVIKSDVMVV---VNKL 411
Query: 648 QNSSLDE----------H--QIELKRSNRN--------LESEATTVKRKSSNVAKQTGSK 687
SL E +ELK N ++ S ++ +
Sbjct: 412 HKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471
Query: 688 ILVRNIPF---QAKQSEVEELF-KAFGELKFVRLPKKMVGSGLHRGFG------------ 731
+I + E LF F + +F+ +K+
Sbjct: 472 YFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLE--QKIRHDSTAWNASGSILNTLQQLKF 529
Query: 732 FVEFITKNEAK--RAMKALCQSTHLYGRRLVLEWAEEADNVE 771
+ +I N+ K R + A+ L+ ++ D +
Sbjct: 530 YKPYICDNDPKYERLVNAILDFLPKIEENLIC--SKYTDLLR 569
Score = 52.2 bits (124), Expect = 6e-07
Identities = 35/231 (15%), Positives = 67/231 (29%), Gaps = 54/231 (23%)
Query: 584 YIKNLNFNSTEDSIRRHFKKCGPIASVT-VARKKDPKSPGQFL-----SMGYGFVQFYTR 637
++ N + +D + K + + KD S L S VQ +
Sbjct: 29 FVDNFDCKDVQDMPKSILSK----EEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVE 84
Query: 638 ESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQA 697
E L K L + + E ++ + R ++ Q +K N+
Sbjct: 85 EVLRINYKFL----MSPIKTEQRQPSMMTRMYIEQRDRLYNDN--QVFAK---YNVS--- 132
Query: 698 KQSEVEELFKAFGELKFVRLPKK------MVGSG-------------LHRGFGF-VEFIT 737
+ +L +A EL+ P K ++GSG + F + ++
Sbjct: 133 RLQPYLKLRQALLELR----PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN 188
Query: 738 KNEAKRAMKALCQSTHLYGRRLVLEWAEEAD-------NVEDIRKRTNRYF 781
L L ++ W +D + I+ R
Sbjct: 189 LKNCNSPETVLEMLQKLL-YQIDPNWTSRSDHSSNIKLRIHSIQAELRRLL 238
Score = 51.4 bits (122), Expect = 1e-06
Identities = 50/402 (12%), Positives = 109/402 (27%), Gaps = 151/402 (37%)
Query: 508 FKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGE----EGEEEKKENTAEEDNQQGVP 563
K+V P+ + + KE+ K+ G K+E ++
Sbjct: 35 CKDVQDM----PKSILS--KEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQK------- 81
Query: 564 EVEENVEED----------EEREPEPDTTLYIKNLN--FNSTE-------------DSIR 598
VEE + + E+R+P T +YI+ + +N + +R
Sbjct: 82 FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLR 141
Query: 599 RHFKKCGPIASVTV---------------ARKKDPKS--PGQ-F-LSMGYGFVQFYTRES 639
+ + P +V + + + F L++ S
Sbjct: 142 QALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKN-------CNS 194
Query: 640 LNQALKVLQN--SSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQT------------- 684
L++LQ +D + + N++ +++ + + K
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ 254
Query: 685 ----------GSKILV--RNI---------------------PFQAKQSEVEELFKAFGE 711
KIL+ R EV+ L + +
Sbjct: 255 NAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLT--PDEVKSLLLKYLD 312
Query: 712 LKFVRLPK----------KMVGSGLHRGFG-------------------FVEFITKNEAK 742
+ LP+ ++ + G + + E +
Sbjct: 313 CRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYR 372
Query: 743 RAMKALC---QSTHLYGRRLVLEWAE-EADNVEDIRKRTNRY 780
+ L S H+ L L W + +V + + ++Y
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY 414
Score = 51.0 bits (121), Expect = 1e-06
Identities = 98/694 (14%), Positives = 190/694 (27%), Gaps = 228/694 (32%)
Query: 131 HTKDSKPGK-KSKNDPTFSDFLQ-----LHGKDVSKLLP--LSNKDGE----EKEEEN-- 176
H D + G+ + + S F KDV + LS ++ + K+ +
Sbjct: 5 HHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGT 64
Query: 177 -------EDESNNQIAHA--DISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTI 227
+ + ++ + Y L + K T PS+ R Y+
Sbjct: 65 LRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIK-TEQRQPSMMTRMYIEQRDRLYNDN 123
Query: 228 VV---KNLPAGVKKKDLKAYFKPL-PLASVRTTFLGMAYIGFKDEKNC--NKALNK---- 277
V N+ L+ L P +V G+ G K
Sbjct: 124 QVFAKYNVSRLQPYLKLRQALLELRPAKNV--LIDGVLGSG----KTWVALDVCLSYKVQ 177
Query: 278 ----NKSFWKGKQLNIYKYSKDNS-------------AKYSGAADDNNNASM--ENIK-- 316
K FW LN+ + + ++ +D ++N + +I+
Sbjct: 178 CKMDFKIFW----LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233
Query: 317 ----------------------AKHWK-----------SQEDSVQFAEDIAESGRIFVRN 343
AK W ++ V A + I + +
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDH 293
Query: 344 LSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF--LMPEHAT--QAYQHLD 399
S T+T D++ L KY LP +E T L + + ++H++
Sbjct: 294 HSMTLTPDEVKSLLLKYLDCRPQDLP--REVLTTNPRRLSIIAESIRDGLATWDNWKHVN 351
Query: 400 GTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRT 459
D ++E+ S + L
Sbjct: 352 -----------------------------------CDKLTTIIES-S-----LNVLE--- 367
Query: 460 LPTDLKALFEPFG----DLGRVLVPP--------YGITGLVE-FLQKNQAKAAFNSLAYT 506
P + + +F+ +P I V + K SL
Sbjct: 368 -PAEYRKMFDRLSVFPPS---AHIPTILLSLIWFDVIKSDVMVVVNKLHKY----SLVEK 419
Query: 507 KFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVE 566
+ KE + + ++ E K K E E + + N +
Sbjct: 420 QPKESTISI----PSIYLELKVKL-------------ENEYALHRSIVDHYN------IP 456
Query: 567 ENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLS 626
+ + D+ P D Y + I H K +T+ R FL
Sbjct: 457 KTFDSDDLIPPYLDQ--YF--YSH------IGHHLKNIEHPERMTLFRMV-------FLD 499
Query: 627 MGYGFVQ---------FYTRESLNQALKVLQN--SSLDEHQIELKRSNRNLESEATTVKR 675
+ F++ + S+ L+ L+ + ++ + +R + + +
Sbjct: 500 --FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAIL---DFLPK 554
Query: 676 KSSNVAKQTGSKILVRNIPFQAKQSEV-EELFKA 708
N+ + +L I A+ + EE K
Sbjct: 555 IEENLICSKYTDLL--RIALMAEDEAIFEEAHKQ 586
Score = 51.0 bits (121), Expect = 1e-06
Identities = 63/409 (15%), Positives = 109/409 (26%), Gaps = 135/409 (33%)
Query: 3 NHLSGPVVPRNHISLLDLDEVE-------F-----IYKITQEQLKAKFEEKGTVTDVQLK 50
L LL L V+ F I T+ + F T T + L
Sbjct: 236 RLLKSKPYEN---CLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLD 292
Query: 51 YTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVEKCSNL-----GDTTK--PK 103
+ + D+ ++ L + + +V + ++ +
Sbjct: 293 HHSMT----LT------PDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA 342
Query: 104 SWSKYAPDSSAYQKLHNIAPK--QDLKPEHTKDSKPGKKSKNDPTFSDF--LQLHGKDV- 158
+W + KL I L+P + F
Sbjct: 343 TWDNW--KHVNCDKLTTIIESSLNVLEPAEYRKM-----------FDRLSVFP---PSAH 386
Query: 159 --SKLLPL--SNKDGEEKEEE----------NEDESNNQIAHADISDMEYLKLKTKSKDT 204
+ LL L + + + + I+ I YL+LK K ++
Sbjct: 387 IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI----YLELKVKLEN- 441
Query: 205 APSDPSVPPVSKAPVHKR---QYHTIVVKNLPAGVKKKDLKA-----YF--------KPL 248
+ +H+ Y N+P DL YF K +
Sbjct: 442 -----------EYALHRSIVDHY------NIPKTFDSDDLIPPYLDQYFYSHIGHHLKNI 484
Query: 249 PLA----SVRTTFLGMAYIGFKDEKNCNKALNKNKSFWKGK--------QLNIYK-YSKD 295
R FL ++ K + + + W QL YK Y D
Sbjct: 485 EHPERMTLFRMVFLDFRFLEQK--------IRHDSTAWNASGSILNTLQQLKFYKPYICD 536
Query: 296 NSAKYSGAADD--NN--NASMENIKAKHWKSQEDSVQFAEDIAESGRIF 340
N KY + + I +K+ D ++ A +AE IF
Sbjct: 537 NDPKYERLVNAILDFLPKIEENLICSKY----TDLLRIAL-MAEDEAIF 580
Score = 46.8 bits (110), Expect = 3e-05
Identities = 36/206 (17%), Positives = 65/206 (31%), Gaps = 68/206 (33%)
Query: 16 SLLDLDEVEFIYKI--TQEQLKAKFEEKGTVTDVQL-KYTTEGKFRR------------F 60
SL++ E I +LK K E + + + Y F +
Sbjct: 415 SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFY 474
Query: 61 AFIGYH--REDQAQAALDYFNNTYVFSSRIKVEKCSNLGDTTKPKSW--SKYAPDSSAYQ 116
+ IG+H + + + F ++ + + K DS+A+
Sbjct: 475 SHIGHHLKNIEHPE-RMTLFRMVFL-----------DF-------RFLEQKIRHDSTAWN 515
Query: 117 KLHNIAPK-QDLK--PEHTKDSKPGKKSKNDPTFS-------DFLQLHGKDV--SKL--- 161
+I Q LK + D NDP + DFL +++ SK
Sbjct: 516 ASGSILNTLQQLKFYKPYICD--------NDPKYERLVNAILDFLPKIEENLICSKYTDL 567
Query: 162 --LPLSNKDGEEKEEENEDESNNQIA 185
+ L +D E E++ Q+
Sbjct: 568 LRIALMAEDEAIFE-----EAHKQVQ 588
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 52.9 bits (126), Expect = 8e-08
Identities = 18/94 (19%), Positives = 30/94 (31%), Gaps = 20/94 (21%)
Query: 581 TTLYIKNLNFNST---------EDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
TLY+ ++ E IR F + G I + K GF
Sbjct: 135 KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK-----------NCGF 183
Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKRSNRN 665
V+F + + A + + N +L + R
Sbjct: 184 VKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRRE 217
Score = 46.3 bits (109), Expect = 1e-05
Identities = 14/125 (11%), Positives = 34/125 (27%), Gaps = 15/125 (12%)
Query: 307 NNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVT---------EDDLTKLF 357
+ K +ED ++ ++V + + E + +F
Sbjct: 105 RTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVF 164
Query: 358 EKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
+ G + + ++K V F +A A + + L + +
Sbjct: 165 SRLGDIDRIRYV------ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREG 218
Query: 418 NEGNV 422
V
Sbjct: 219 TGLLV 223
Score = 43.6 bits (102), Expect = 1e-04
Identities = 16/90 (17%), Positives = 36/90 (40%), Gaps = 18/90 (20%)
Query: 691 RNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL-- 748
+++ +S + +F G++ +R + + GFV+F + A+ A +A+
Sbjct: 149 KHLKPAQIESRIRFVFSRLGDIDRIRYVES-------KNCGFVKFKYQANAEFAKEAMSN 201
Query: 749 ---------CQSTHLYGRRLVLEWAEEADN 769
G L+++WA E +
Sbjct: 202 QTLLLPSDKEWDDRREGTGLLVKWANEDPD 231
Score = 36.7 bits (84), Expect = 0.019
Identities = 15/100 (15%), Positives = 36/100 (36%), Gaps = 6/100 (6%)
Query: 19 DLDEVEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYF 78
L+ + +++ F G + ++ + + F+ + + A+ A +
Sbjct: 145 ALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-----ESKNCGFVKFKYQANAEFAKEAM 199
Query: 79 NNTYVFSSRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKL 118
+N + K G K W+ PD +A ++L
Sbjct: 200 SNQTLLLPSDKEWDDRREGTGLLVK-WANEDPDPAAQKRL 238
Score = 34.8 bits (79), Expect = 0.068
Identities = 11/68 (16%), Positives = 25/68 (36%)
Query: 453 KNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVP 512
K+L + + ++ +F GD+ R+ G V+F + A+ A +++
Sbjct: 149 KHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPS 208
Query: 513 LYLEWAPE 520
Sbjct: 209 DKEWDDRR 216
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 49.6 bits (118), Expect = 2e-07
Identities = 24/73 (32%), Positives = 33/73 (45%), Gaps = 4/73 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RI V NL Y VT D L ++F K+G + ++I T + AL+ + P A A
Sbjct: 30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYADPVSAQHAKLS 85
Query: 398 LDGTVFLGRMLHL 410
LDG L
Sbjct: 86 LDGQNIYNACCTL 98
Score = 42.3 bits (99), Expect = 7e-05
Identities = 14/92 (15%), Positives = 28/92 (30%), Gaps = 11/92 (11%)
Query: 571 EDEEREPEPDTTL--YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMG 628
+ L ++NL + T D + + F K G + + K +
Sbjct: 17 DAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---------NQF 67
Query: 629 YGFVQFYTRESLNQALKVLQNSSLDEHQIELK 660
+Q+ S A L ++ L+
Sbjct: 68 QALLQYADPVSAQHAKLSLDGQNIYNACCTLR 99
Score = 40.0 bits (93), Expect = 5e-04
Identities = 18/107 (16%), Positives = 42/107 (39%), Gaps = 12/107 (11%)
Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKIL---VRNIPFQAKQSEVEELFKAFGELKFVRLP 718
N L + A V + +A S +L V N+ + + ++F FG + +
Sbjct: 5 GNLALAASAAAV---DAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF 61
Query: 719 KKMVGSGLHRGFGFVEFITKNEAKRAMKALC-QSTHLYGRRLVLEWA 764
K ++ +++ A+ A +L Q+ + L ++++
Sbjct: 62 TK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 103
Score = 35.8 bits (82), Expect = 0.013
Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP--YGITGLVEFLQKNQAKAA 499
I+V+NL Y L +F FG + +++ L+++ A+ A
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHA 82
Score = 32.3 bits (73), Expect = 0.24
Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 3/64 (4%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
Y +T + L F + GTV T + A + Y AQ A + ++++
Sbjct: 38 YPVTLDVLHQIFSKFGTV---LKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNA 94
Query: 87 RIKV 90
+
Sbjct: 95 CCTL 98
>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 = 50.1 bits (119), Expect = 2e-07
Identities = 24/73 (32%), Positives = 33/73 (45%), Gaps = 4/73 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RI V NL Y VT D L ++F K+G + ++I T + AL+ + P A A
Sbjct: 48 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYADPVSAQHAKLS 103
Query: 398 LDGTVFLGRMLHL 410
LDG L
Sbjct: 104 LDGQNIYNACCTL 116
Score = 43.2 bits (101), Expect = 7e-05
Identities = 14/92 (15%), Positives = 28/92 (30%), Gaps = 11/92 (11%)
Query: 571 EDEEREPEPDTTL--YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMG 628
+ L ++NL + T D + + F K G + + K +
Sbjct: 35 DAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---------NQF 85
Query: 629 YGFVQFYTRESLNQALKVLQNSSLDEHQIELK 660
+Q+ S A L ++ L+
Sbjct: 86 QALLQYADPVSAQHAKLSLDGQNIYNACCTLR 117
Score = 42.4 bits (99), Expect = 1e-04
Identities = 16/94 (17%), Positives = 37/94 (39%), Gaps = 11/94 (11%)
Query: 676 KSSNVAKQTGSKIL---VRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFG 731
+ +A S +L V N+ + + ++F FG LK + K +
Sbjct: 34 VDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN------QFQA 87
Query: 732 FVEFITKNEAKRAMKALC-QSTHLYGRRLVLEWA 764
+++ A+ A +L Q+ + L ++++
Sbjct: 88 LLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 121
Score = 35.8 bits (82), Expect = 0.021
Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 2/82 (2%)
Query: 423 DGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP- 481
G + S +DA + I+V+NL Y L +F FG + +++
Sbjct: 22 SGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK 81
Query: 482 -YGITGLVEFLQKNQAKAAFNS 502
L+++ A+ A S
Sbjct: 82 NNQFQALLQYADPVSAQHAKLS 103
Score = 33.5 bits (76), Expect = 0.13
Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 3/65 (4%)
Query: 26 IYKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y +T + L F + GTV T + A + Y AQ A + +++
Sbjct: 55 FYPVTLDVLHQIFSKFGTV---LKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN 111
Query: 86 SRIKV 90
+ +
Sbjct: 112 ACCTL 116
>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 = 47.2 bits (112), Expect = 8e-07
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 350 EDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLH 409
E+ T++ EKYG + E+ + D D G V F E A +A L+ F G+ +H
Sbjct: 41 EEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99
Score = 34.1 bits (78), Expect = 0.033
Identities = 14/96 (14%), Positives = 39/96 (40%), Gaps = 8/96 (8%)
Query: 1 MFNH----LSGPVVPRNHISLLDLDE-VEFIYKITQEQLKAKFEEKGTVTDVQLKYTTEG 55
++ + R+ +S +++ E + ++ +++ K+ G V ++ +
Sbjct: 9 IYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKY---GEVEEMNVCDNLGD 65
Query: 56 KFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE 91
++ + RE+ A+ A+ NN + I E
Sbjct: 66 HLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101
Score = 29.8 bits (67), Expect = 1.1
Identities = 9/50 (18%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 699 QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+ E+ + +GE++ + + G +V+F + +A++A+ L
Sbjct: 41 EEVFTEMEEKYGEVEEMNVCDN--LGDHLVGNVYVKFRREEDAEKAVIDL 88
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 46.2 bits (109), Expect = 3e-06
Identities = 14/73 (19%), Positives = 26/73 (35%), Gaps = 5/73 (6%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+ ++N Y +T D L + G + ++ + A+V F A +A
Sbjct: 27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIV-----IFKRNGIQAMVEFESVLCAQKAKAA 81
Query: 398 LDGTVFLGRMLHL 410
L+G L
Sbjct: 82 LNGADIYAGCCTL 94
Score = 40.1 bits (93), Expect = 4e-04
Identities = 16/98 (16%), Positives = 37/98 (37%), Gaps = 10/98 (10%)
Query: 668 SEATTVKRKSSNVAKQTGSKIL---VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS 724
S + R + G+K+L ++N + + + G+++ + + K+
Sbjct: 5 SSGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR---- 60
Query: 725 GLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE 762
+ VEF + A++A A +Y L+
Sbjct: 61 --NGIQAMVEFESVLCAQKAKAA-LNGADIYAGCCTLK 95
Score = 38.5 bits (89), Expect = 0.001
Identities = 13/97 (13%), Positives = 28/97 (28%), Gaps = 10/97 (10%)
Query: 564 EVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQ 623
+ D+ L I+N + T D + G + + + ++
Sbjct: 9 RITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNG------ 62
Query: 624 FLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELK 660
V+F + +A L + + LK
Sbjct: 63 ----IQAMVEFESVLCAQKAKAALNGADIYAGCCTLK 95
Score = 31.6 bits (71), Expect = 0.33
Identities = 11/65 (16%), Positives = 22/65 (33%), Gaps = 4/65 (6%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
Y IT + L G V ++ + A + + AQ A N +++
Sbjct: 35 YPITVDVLYTVCNPVGKVQ--RIVIFKRNGIQ--AMVEFESVLCAQKAKAALNGADIYAG 90
Query: 87 RIKVE 91
++
Sbjct: 91 CCTLK 95
Score = 31.2 bits (70), Expect = 0.42
Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 3/72 (4%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLV-PPYGITGLVEFLQKNQAKAAFNSLAYTKF 508
+ ++N Y L + P G + R+++ GI +VEF A+ A +L
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADI 87
Query: 509 --KEVPLYLEWA 518
L +E+A
Sbjct: 88 YAGCCTLKIEYA 99
>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 = 45.7 bits (108), Expect = 3e-06
Identities = 18/92 (19%), Positives = 32/92 (34%), Gaps = 9/92 (9%)
Query: 322 SQEDSVQFAEDIAESGRIFVRNLSY-TVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGF 380
+ +F + I + NL + ++ + KL E YG + IL + K
Sbjct: 11 EGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL------MRMKSQ 64
Query: 381 ALVTFLMPEHATQA--YQHLDGTVFLGRMLHL 410
A + E A + F GR + +
Sbjct: 65 AFIEMETREDAMAMVDHCLKKALWFQGRCVKV 96
Score = 41.1 bits (96), Expect = 1e-04
Identities = 17/105 (16%), Positives = 42/105 (40%), Gaps = 9/105 (8%)
Query: 662 SNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQA-KQSEVEELFKAFGELKFVRLPKK 720
S+ + + + + ++ G I + N+P S V +L + +G++K L +
Sbjct: 2 SSGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR- 60
Query: 721 MVGSGLHRGFGFVEFITKNEAKRAMKALCQST-HLYGRRLVLEWA 764
+ F+E T+ +A + + GR + ++ +
Sbjct: 61 ------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS 99
Score = 40.3 bits (94), Expect = 3e-04
Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 6/73 (8%)
Query: 448 RIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYT 506
R+I + NLP+ + + L EP+G + ++ +E + A A +
Sbjct: 26 RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVD----- 80
Query: 507 KFKEVPLYLEWAP 519
+ L+ +
Sbjct: 81 HCLKKALWFQGRC 93
Score = 36.1 bits (83), Expect = 0.008
Identities = 13/108 (12%), Positives = 40/108 (37%), Gaps = 14/108 (12%)
Query: 563 PEVEENVEEDEEREPEPDTTLYIKNL-NFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 621
+ E ++ +++ E +++ NL + ++ ++ + + G I + + R K
Sbjct: 8 KKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK----- 62
Query: 622 GQFLSMGYGFVQFYTRESLNQALKVLQNSS--LDEHQIELKRSNRNLE 667
F++ TRE + + +++ S + +
Sbjct: 63 ------SQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKK 104
Score = 32.6 bits (74), Expect = 0.11
Identities = 9/54 (16%), Positives = 18/54 (33%), Gaps = 5/54 (9%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT 81
+ + E G + + L + + AFI + A A +D+
Sbjct: 37 GYSDSAVLKLAEPYGKIKNYIL-----MRMKSQAFIEMETREDAMAMVDHCLKK 85
>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 = 40.9 bits (96), Expect = 1e-04
Identities = 16/66 (24%), Positives = 25/66 (37%), Gaps = 2/66 (3%)
Query: 346 YTVTEDDLTKLFEKYGPLAEVILP--IDKETDKTKGFALVTFLMPEHATQAYQHLDGTVF 403
Y +D+ KYG + + +P +D G V F +A Q L G F
Sbjct: 25 YEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF 84
Query: 404 LGRMLH 409
R++
Sbjct: 85 ANRVVV 90
Score = 32.8 bits (75), Expect = 0.076
Identities = 13/55 (23%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 695 FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHR-GFGFVEFITKNEAKRAMKAL 748
++ +V + +G +K + +P+ + G + G FVEF + + ++AM+ L
Sbjct: 25 YEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL 79
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 39.8 bits (93), Expect = 3e-04
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 447 KRIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN 501
+R++ + + + L L L EPFG + L+ +E A+AA +
Sbjct: 15 RRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVD 70
Score = 33.7 bits (77), Expect = 0.039
Identities = 8/60 (13%), Positives = 19/60 (31%), Gaps = 7/60 (11%)
Query: 339 IFVRNLSY-TVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+ + + L +L E +G ++ ++ A + E A A +
Sbjct: 18 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL------NKINEAFIEMATTEDAQAAVDY 71
Score = 30.6 bits (69), Expect = 0.46
Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 7/65 (10%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT--YVFSS 86
+ QL E G +++ + AFI + AQAA+DY+ T VF
Sbjct: 28 NLRYQLLQLVEPFGVISNHLI-----LNKINEAFIEMATTEDAQAAVDYYTTTPALVFGK 82
Query: 87 RIKVE 91
++V
Sbjct: 83 PVRVH 87
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 39.3 bits (91), Expect = 3e-04
Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 8/81 (9%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ ++NL+ + L L ++GPL + +G AL + E A +A L
Sbjct: 10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMAL 63
Query: 399 DGTVFLGRMLHLIPGKPKENE 419
+ V + P ENE
Sbjct: 64 NNCVLANTT--IFAESPSENE 82
Score = 35.8 bits (82), Expect = 0.007
Identities = 19/77 (24%), Positives = 30/77 (38%), Gaps = 11/77 (14%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
+ L +KNL ++R + GP+ S +L+ G ++ TRE
Sbjct: 8 SWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHP-----------YLNQGIALCKYTTREEA 56
Query: 641 NQALKVLQNSSLDEHQI 657
N+A L N L I
Sbjct: 57 NKAQMALNNCVLANTTI 73
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 39.2 bits (91), Expect = 5e-04
Identities = 20/93 (21%), Positives = 30/93 (32%), Gaps = 14/93 (15%)
Query: 332 DIAESGRIFVRNLSYTVTEDDLTKLFEKY-----GPLAEVILPIDKETDKTKGFALVTFL 386
+ + VR L V ++ LT FE GP+ + ++TF
Sbjct: 4 GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW--------QRLGCGGVLTFR 55
Query: 387 MPEHATQAYQHLDGTVFLGRMLHLIPGKPKENE 419
P A + D G L L P P+
Sbjct: 56 EPADAERVLAQAD-HELHGAQLSLRPAPPRAPA 87
Score = 32.2 bits (73), Expect = 0.15
Identities = 15/80 (18%), Positives = 30/80 (37%), Gaps = 7/80 (8%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL------PLASVRTTFLGMAYIGFKDEKNCNKALNKNK 279
+ V+ LP V + L YF+ P+ S + + F++ + + L +
Sbjct: 10 AVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRL-GCGGVLTFREPADAERVLAQAD 68
Query: 280 SFWKGKQLNIYKYSKDNSAK 299
G QL++ A+
Sbjct: 69 HELHGAQLSLRPAPPRAPAR 88
Score = 28.8 bits (64), Expect = 2.6
Identities = 16/83 (19%), Positives = 28/83 (33%), Gaps = 18/83 (21%)
Query: 683 QTGSKILVRNIPFQAKQSEVEELFKAF-----GELKFVRLPKKMVGSGLHRGFGFVEFIT 737
G + VR +P + F+ G + + G + F
Sbjct: 6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRL---------GCGGVLTFRE 56
Query: 738 KNEAKRAMKALCQSTH-LYGRRL 759
+A+R L Q+ H L+G +L
Sbjct: 57 PADAER---VLAQADHELHGAQL 76
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 39.0 bits (91), Expect = 7e-04
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 350 EDDLTKLFEKYGPLAEVILP-IDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRML 408
E + + EKYG + + ++ I D + F E A +A L+G F GR++
Sbjct: 27 EVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV 86
Query: 409 H 409
Sbjct: 87 K 87
>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 = 38.5 bits (90), Expect = 0.001
Identities = 24/77 (31%), Positives = 33/77 (42%), Gaps = 6/77 (7%)
Query: 350 EDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLH 409
+DL K+G + +++L D+ D G A V+F PE A Q LDG F GR +
Sbjct: 40 REDLRVECSKFGQIRKLLLF-DRHPD---GVASVSFRDPEEADYCIQTLDGRWFGGRQIT 95
Query: 410 --LIPGKPKENEGNVDG 424
G G G
Sbjct: 96 AQAWDGTTDYQSGPSSG 112
Score = 28.5 bits (64), Expect = 3.4
Identities = 9/50 (18%), Positives = 19/50 (38%), Gaps = 5/50 (10%)
Query: 699 QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+ ++ FG+++ + L + G V F EA ++ L
Sbjct: 40 REDLRVECSKFGQIRKLLLFDRH-----PDGVASVSFRDPEEADYCIQTL 84
>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 = 38.2 bits (89), Expect = 0.001
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 350 EDDLTKLFEKYGPLAEVILPI----DKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLG 405
E ++T+ K+G + VI+ ++E + V F + +A Q L+G F G
Sbjct: 39 EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG 98
Query: 406 RMLH 409
R +
Sbjct: 99 RKVV 102
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 38.6 bits (89), Expect = 0.004
Identities = 11/68 (16%), Positives = 26/68 (38%), Gaps = 5/68 (7%)
Query: 516 EWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE- 574
+W E + ++ + E+E E ++ E + ++Q N D+
Sbjct: 89 KWREE--QRKRLQE-LDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAF 145
Query: 575 -REPEPDT 581
++P+ D
Sbjct: 146 YQQPDADI 153
>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 = 36.2 bits (84), Expect = 0.008
Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 4/60 (6%)
Query: 350 EDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLH 409
+DD+ + K+G + + + + G V A A L G F G+M+
Sbjct: 31 KDDVIEECNKHGGVIHIYVDKNSAQ----GNVYVKCPSIAAAIAAVNALHGRWFAGKMIT 86
Score = 27.3 bits (61), Expect = 7.9
Identities = 10/50 (20%), Positives = 20/50 (40%), Gaps = 5/50 (10%)
Query: 699 QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+ +V E G + + + K +G +V+ + A A+ AL
Sbjct: 31 KDDVIEECNKHGGVIHIYVDKN-----SAQGNVYVKCPSIAAAIAAVNAL 75
>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 = 35.7 bits (82), Expect = 0.008
Identities = 15/90 (16%), Positives = 35/90 (38%), Gaps = 17/90 (18%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRH----FKKCGPIASVTVARKKDPKSPGQFLSMGYGF 631
+ + N+++ + +++ F + G + SV ++ D
Sbjct: 5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTD--------YQLKAV 56
Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKR 661
VQ E+L A+ + +SL ++I K+
Sbjct: 57 VQM---ENLQDAIGAV--NSLHRYKIGSKK 81
Score = 33.0 bits (75), Expect = 0.067
Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 2/64 (3%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
K Q+ L+ F G V V+L T+ + A + A A++ + + S +
Sbjct: 24 KELQQLLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKK 81
Query: 88 IKVE 91
I V
Sbjct: 82 ILVS 85
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 38.2 bits (88), Expect = 0.009
Identities = 21/110 (19%), Positives = 46/110 (41%), Gaps = 13/110 (11%)
Query: 317 AKHWKSQEDSVQFAEDIAESGRIFVRN--LSYTVTEDDLTKLFEKYGPLAEVILPIDKET 374
AKH + + ++ + + V N L V+ + L + EK G + +++P +
Sbjct: 1 AKHTLLRHEGIETVSY--ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN--- 55
Query: 375 DKTKGFALVTFLMPEHATQAYQHLDGTV---FLGRMLHLIPGKPKENEGN 421
K ++ + E + +AY L+G LG+ + L ++ +
Sbjct: 56 ---KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWK 102
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 34.0 bits (77), Expect = 0.029
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 5/52 (9%)
Query: 349 TEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
++D L +L +KYG + ++L K G A+V F + A A Q+ G
Sbjct: 30 SKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG 76
Score = 30.5 bits (68), Expect = 0.56
Identities = 11/53 (20%), Positives = 25/53 (47%), Gaps = 10/53 (18%)
Query: 593 TEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALK 645
++D + R +K G + ++ ++ KK G V+F T ++ A++
Sbjct: 30 SKDVLLRLLQKYGEVLNLVLSSKK----------PGTAVVEFATVKAAELAVQ 72
>3cx5_F Cytochrome B-C1 complex subunit 6; complex III, electron transfer
complex, cytochrome BC1 complex,
mitochondrialtransmembrane complex; HET: M3L SUC 6PH UMQ
HEM SMA 8PE 9PE CN5 7PH CN3; 1.90A {Saccharomyces
cerevisiae} SCOP: f.28.1.1 PDB: 3cxh_F* 1ezv_H* 1kb9_F*
1p84_F* 2ibz_H* 1kyo_F*
Length = 146
Score = 34.9 bits (79), Expect = 0.038
Identities = 17/59 (28%), Positives = 28/59 (47%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTL 583
A E ++ E+ EGEE EEE + +ED + + ++ EE+EE + L
Sbjct: 22 AAAEDDDNEQHEEKAAEGEEKEEENGDEDEDEDEDEDDDDDDDEDEEEEEEVTDQLEDL 80
Score = 29.9 bits (66), Expect = 1.6
Identities = 12/51 (23%), Positives = 28/51 (54%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 574
E KE+ G E E +E+ ++ +++ ++ EE+ + ++ E+ + EE
Sbjct: 39 GEEKEEENGDEDEDEDEDEDDDDDDDEDEEEEEEVTDQLEDLREHFKNTEE 89
Score = 28.7 bits (63), Expect = 3.9
Identities = 11/58 (18%), Positives = 26/58 (44%)
Query: 523 FAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 580
+ + K +++ E+ EE+ E +E+ E E+ E+D++ + E +
Sbjct: 10 WEQLKITVVPVVAAAEDDDNEQHEEKAAEGEEKEEENGDEDEDEDEDEDDDDDDDEDE 67
>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 = 33.4 bits (76), Expect = 0.060
Identities = 16/85 (18%), Positives = 24/85 (28%), Gaps = 13/85 (15%)
Query: 339 IFVRNLSYTVTEDDLTK-----LFEKYGPLAE-VILPIDKETDKTKGFALVTFLMPEHAT 392
+ + V + T+ LF Y K + F P A
Sbjct: 8 LIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKR-------VRINFSNPLSAA 60
Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKE 417
A L T FLG+ + L +
Sbjct: 61 DARLRLHKTEFLGKEMKLYFAQTLH 85
>2cg9_A ATP-dependent molecular chaperone HSP82; chaperone complex, HSP90,
heat shock protein, ATP-binding, heat shock,
nucleotide-binding, acetylation; HET: ATP; 3.1A
{Saccharomyces cerevisiae}
Length = 677
Score = 35.1 bits (81), Expect = 0.10
Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 505 YTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPE 564
+++F P+ L K KE EEE ++ E++ +E E+D + + E
Sbjct: 197 HSEFVAYPIQLV----------VTKEVEKEVPIPEEEKKDEEKKDEEKKDEDDKKPKLEE 246
Query: 565 VEENVEEDEEREPEPDTTLYIKNLN 589
V+E E+ + + + I+ LN
Sbjct: 247 VDEEEEKKPKTKKVKEEVQEIEELN 271
>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T*
1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S*
3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z
1pnu_T 1pny_T 1vor_W ...
Length = 237
Score = 33.9 bits (78), Expect = 0.12
Identities = 10/62 (16%), Positives = 21/62 (33%)
Query: 519 PEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE 578
PE E+ + E + + E+ + V E + ++EE + E
Sbjct: 164 PELTVVSVLPPRLTAEELEAEVQAAQVAGLVAAGELSEEAAEAVLEGDASLEEVKAEASE 223
Query: 579 PD 580
+
Sbjct: 224 DN 225
>3gdb_A Endo-D, putative uncharacterized protein SPR0440;
alpha-beta-barrels, cell WALL, peptidoglycan-anchor,
secreted, hydrolase; HET: PGE; 1.87A {Streptococcus
pneumoniae} PDB: 2xqx_A
Length = 937
Score = 34.6 bits (78), Expect = 0.17
Identities = 11/59 (18%), Positives = 24/59 (40%), Gaps = 1/59 (1%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 582
+ A ++ E + + EE+ E AE + + P+ ++ E E + D +
Sbjct: 76 SPASNEAATTETAEAASAAKP-EEKASEVVAETPSAEAKPKSDKETEAKPEATNQGDES 133
Score = 28.8 bits (63), Expect = 9.7
Identities = 10/39 (25%), Positives = 13/39 (33%)
Query: 544 EGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 582
G + EN + + VPE E E E T
Sbjct: 8 HGHHHQLENLYFQGEETAVPENSGANTELVSGESEHSTN 46
>4ani_A Protein GRPE; chaperone cycle, complementary assay; 4.09A
{Geobacillus kaustophilus}
Length = 213
Score = 32.8 bits (75), Expect = 0.28
Identities = 13/56 (23%), Positives = 18/56 (32%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 580
+A +E+ EE + EEE EE + E E EE
Sbjct: 11 QATYDEPEREQPIEEEAAPQPEEESGGVPLEEAGGEEAAEPAEKAPTAEELAAAKA 66
>1dkg_A Nucleotide exchange factor GRPE; HSP70, GRPE, nucleotide exchange
factor, coiled-coil, complex (HSP24/HSP70); 2.80A
{Escherichia coli} SCOP: b.73.1.1 h.1.9.1
Length = 197
Score = 32.3 bits (74), Expect = 0.36
Identities = 10/43 (23%), Positives = 17/43 (39%)
Query: 534 EKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 576
KE+ EG+ EE + E + + E+ DE+
Sbjct: 3 SKEQKTPEGQAPEEIIMDQHEEIEAVEPEASAEQVDPRDEKVA 45
>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 = 31.8 bits (71), Expect = 0.38
Identities = 9/35 (25%), Positives = 13/35 (37%), Gaps = 20/35 (57%)
Query: 89 KVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAP 123
K++ ++L K YA DS AP
Sbjct: 24 KLQ--ASL----KL-----YADDS---------AP 38
Score = 28.4 bits (62), Expect = 5.3
Identities = 7/37 (18%), Positives = 14/37 (37%), Gaps = 15/37 (40%)
Query: 171 EKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPS 207
EK+ + ++ LK + D+AP+
Sbjct: 18 EKQA--------------LKKLQA-SLKLYADDSAPA 39
>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1
a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F*
2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H
Length = 423
Score = 32.5 bits (74), Expect = 0.57
Identities = 17/88 (19%), Positives = 36/88 (40%), Gaps = 7/88 (7%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEE-EKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTL 583
+ ++ + +E E E EE E+ E + + + + +E+D PE L
Sbjct: 2 KKSKRKNAQAQEAQETEVLVQEEAEELPEFPEGEPDPDLEDPDLALEDDLLDLPEEGEGL 61
Query: 584 YIK------NLNFNSTEDSIRRHFKKCG 605
++ + ST D +R++ + G
Sbjct: 62 DLEEEEEDLPIPKISTSDPVRQYLHEIG 89
>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A
{Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A*
1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A*
1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A*
2ga2_A* 2oaz_A*
Length = 478
Score = 32.2 bits (73), Expect = 0.79
Identities = 18/117 (15%), Positives = 36/117 (30%)
Query: 100 TKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKPGKKSKNDPTFSDFLQLHGKDVS 159
S S D + A + + + K K + + + G V
Sbjct: 6 EVAASGSHLNGDLDPDDREEGAASTAEEAAKKKRRKKKKSKGPSAAGEQEPDKESGASVD 65
Query: 160 KLLPLSNKDGEEKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSK 216
++ + E +E +ED+ + + + K K K +DP P+
Sbjct: 66 EVARQLERSALEDKERDEDDEDGDGDGDGATGKKKKKKKKKRGPKVQTDPPSVPICD 122
Score = 28.7 bits (64), Expect = 8.4
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 580
EA +K + K+K+ +E KE+ A D ++E + ED+ER+ + +
Sbjct: 33 EAAKKKRRKKKKSKGPSAAGEQEPDKESGASVDEVA--RQLERSALEDKERDEDDE 86
>1bw0_A TAT, protein (tyrosine aminotransferase); tyrosine catabolism,
pyridoxal-5'-phosphate, PLP; HET: LLP; 2.50A
{Trypanosoma cruzi} SCOP: c.67.1.1
Length = 416
Score = 30.7 bits (70), Expect = 2.0
Identities = 10/56 (17%), Positives = 20/56 (35%), Gaps = 13/56 (23%)
Query: 312 MENIKAKHWKSQEDSVQFAEDIAESGRIFV------------RNLSYTVTEDDLTK 355
M I + ++ + V+F E + E + V R L+ T + +
Sbjct: 347 MSRIDLEKYRDIKTDVEFFEKLLEEENVQVLPGTIFHAPGFTR-LTTTRPVEVYRE 401
>3nzj_F Proteasome component C1; ubiquitin, protein degradation, N-terminal
nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO
MES; 2.40A {Saccharomyces cerevisiae} PDB: 1z7q_G*
3nzw_F* 3nzx_F* 3un4_F* 3un8_F* 3bdm_F* 1fnt_G* 2zcy_F*
Length = 288
Score = 30.4 bits (69), Expect = 2.3
Identities = 12/87 (13%), Positives = 29/87 (33%), Gaps = 7/87 (8%)
Query: 496 AKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAE 555
AK + + K K+ L + W + ++ G K + +E + ++
Sbjct: 197 AKIIYLAHEDNKEKDFELEISWC-------SLSETNGLHKFVKGDLLQEAIDFAQKEING 249
Query: 556 EDNQQGVPEVEENVEEDEEREPEPDTT 582
+D++ +DE +
Sbjct: 250 DDDEDEDDSDNVMSSDDENAPVATNAN 276
>2xzm_B RPS0E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_B
Length = 241
Score = 29.5 bits (66), Expect = 4.0
Identities = 10/41 (24%), Positives = 16/41 (39%)
Query: 534 EKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 574
K E +E EEE+ AEE + E +++
Sbjct: 200 HKTLPTAEQKEAEEEEGAEGAEEKVAEVKEGEAEQNTDNKN 240
>3dyd_A Tyrosine aminotransferase; PLP, SGC, structural genomics,
structural genomics consortium, disease mutation,
phenylalani catabolism; HET: PLP; 2.30A {Homo sapiens}
PDB: 3pdx_A*
Length = 427
Score = 29.5 bits (67), Expect = 4.1
Identities = 11/56 (19%), Positives = 21/56 (37%), Gaps = 13/56 (23%)
Query: 312 MENIKAKHWKSQEDSVQFAEDIAESGRIFV------------RNLSYTVTEDDLTK 355
M I+ +H+ E+ V+F E + + R + TV E + +
Sbjct: 358 MVGIEMEHFPEFENDVEFTERLVAEQSVHCLPATCFEYPNFIR-VVITVPEVMMLE 412
>1vq8_G Acidic ribosomal protein P0 homolog; ribosome 50S, protein-protein
complex, RNA-RNA complex, PROT complex, peptidyl
transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
2.20A {Haloarcula marismortui} SCOP: j.84.1.1 PDB:
1k73_I* 1k8a_I* 1k9m_I* 1kc8_I* 1kd1_I* 1kqs_G* 1m1k_I*
1m90_I* 1n8r_I* 1nji_I* 1q7y_I* 1q81_I* 1q82_I* 1q86_I*
1qvf_G 1qvg_G 1s72_G* 1vq4_G* 1vq5_G* 1vq6_G* ...
Length = 348
Score = 29.4 bits (65), Expect = 4.4
Identities = 10/75 (13%), Positives = 25/75 (33%), Gaps = 2/75 (2%)
Query: 489 EFLQKNQAKAAFNSLAYTKFKEVPLYLE--WAPEGVFAEAKEKSKGKEKEKNEEEGEEGE 546
+ + K A+ + + +P L+ A ++ E + + + E
Sbjct: 269 DLVSKADAQVRALASQIDDEEALPEELQGVEADVATEEPTDDQDDDTASEDDADADDAAE 328
Query: 547 EEKKENTAEEDNQQG 561
E ++ +ED
Sbjct: 329 EADDDDDDDEDAGDA 343
>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis
lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A*
1u0y_A* 1yt2_A*
Length = 269
Score = 29.1 bits (66), Expect = 4.9
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 529 KSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 576
SK + E+ EE E +EEK+++ E E EE ++ + ++
Sbjct: 215 SSKTETVEEPMEEEEAAKEEKEDSDDEAAV-----EEEEEEKKPKTKK 257
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 27.4 bits (60), Expect = 5.4
Identities = 23/98 (23%), Positives = 38/98 (38%), Gaps = 24/98 (24%)
Query: 579 PDTTLYIKNLNFNSTEDSI----RRHFKKCGPIASVTVARKKDPKSPGQFLSMGYG--FV 632
T LY+ NL N S+ RR CG G+ LS+ +
Sbjct: 8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCG----------------GKVLSITGCSAIL 51
Query: 633 QFYTRESLNQALKVLQNSSLDEHQIELK--RSNRNLES 668
+F ++S +A K ++N + ++I + NR L
Sbjct: 52 RFINQDSAERAQKRMENEDVFGNRIIVSFTPKNRELCE 89
>2qp2_A Unknown protein; toxin, unknown function; 2.00A {Photorhabdus
luminescens subsp}
Length = 511
Score = 28.8 bits (63), Expect = 7.8
Identities = 14/74 (18%), Positives = 22/74 (29%), Gaps = 3/74 (4%)
Query: 288 NIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYT 347
+ S D N S + + + E + ES L
Sbjct: 130 LFFSASLKVDFDTDSLTDFENAFSRIQYTYDLYILKSSAEALKEFLKES---VKTALDKA 186
Query: 348 VTEDDLTKLFEKYG 361
TE+D+ LF +G
Sbjct: 187 DTEEDMNDLFNTWG 200
>3lo3_A Uncharacterized conserved protein; structural genomics, PSI-2,
protein structure initiative, MI center for structural
genomics, MCSG; 2.38A {Colwellia psychrerythraea}
Length = 94
Score = 26.8 bits (60), Expect = 8.4
Identities = 9/57 (15%), Positives = 17/57 (29%), Gaps = 12/57 (21%)
Query: 465 KALFEPFGDLGRVLV----------PPYGITGLVEFLQKNQAKAAFNSLAYTKFKEV 511
+ + G VLV + ++EF + A ++S Y
Sbjct: 27 ASTLAKYS--GEVLVKGSVEQLHGKFEHKAQVILEFPSREDAYNWYHSEEYQALIST 81
>2fiu_A Conserved hypothetical protein; alpha-beta, dimeric alpha-beta
barrels, structural genomics, protein structure
initiative; 2.00A {Agrobacterium tumefaciens str} SCOP:
d.58.4.16
Length = 99
Score = 26.8 bits (60), Expect = 8.8
Identities = 12/57 (21%), Positives = 17/57 (29%), Gaps = 12/57 (21%)
Query: 465 KALFEPFGDLGRVLV----------PPYGITGLVEFLQKNQAKAAFNSLAYTKFKEV 511
K FE FG L ++EF A +NS Y ++
Sbjct: 28 KPAFERFG--ANFLARGGSVTELEGTARARNVVIEFPSVQHAIDCYNSPEYQAAAKI 82
>3u5c_A 40S ribosomal protein S0-A; translation, ribosome, ribosomal,
ribosomal R ribosomal protein, eukaryotic ribosome,
RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB:
3izb_A 3o30_A 3o2z_A 3u5g_A 3jyv_B* 1s1h_B
Length = 252
Score = 28.3 bits (63), Expect = 9.1
Identities = 12/69 (17%), Positives = 23/69 (33%), Gaps = 7/69 (10%)
Query: 521 GVFAEAKEKSKGKEKEKNEEEG-------EEGEEEKKENTAEEDNQQGVPEVEENVEEDE 573
+ A + +G ++ + EE ++ AEE + E E E E
Sbjct: 175 YLLAREVLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTE 234
Query: 574 EREPEPDTT 582
E+ +
Sbjct: 235 EQAEATEWA 243
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 0.131 0.372
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: 11,617,260
Number of extensions: 701823
Number of successful extensions: 3296
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2458
Number of HSP's successfully gapped: 1064
Length of query: 787
Length of database: 6,701,793
Length adjustment: 101
Effective length of query: 686
Effective length of database: 3,881,772
Effective search space: 2662895592
Effective search space used: 2662895592
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)