RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy258
(238 letters)
>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 = 103 bits (259), Expect = 6e-29
Identities = 37/132 (28%), Positives = 56/132 (42%), Gaps = 32/132 (24%)
Query: 37 LPKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPK 96
LI N D+F + + E+L + K
Sbjct: 4 GSSGLIACVANDDVFS-------------------------ESETRAKFESLFRTYDKDT 38
Query: 97 SFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMTPFDSADQHLQPPA 156
+FQY KSF+R+R+N+ + +AA AR+ LH++ F ++ +YF Q + HL PP
Sbjct: 39 TFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHI---GSSHLAPPN 95
Query: 157 PTKQFLISPPSS 168
P K S PSS
Sbjct: 96 PDK----SGPSS 103
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 59.7 bits (144), Expect = 2e-10
Identities = 39/266 (14%), Positives = 78/266 (29%), Gaps = 88/266 (33%)
Query: 18 LKD--TGDMGDSLDDLINDEQLPKSLI---------ITNLNPDLFKDDALKEQIETLLSQ 66
L++ + + + D++ P + +++L K + + L++
Sbjct: 33 LQEQFNKILPEPTEGFAADDE-PTTPAELVGKFLGYVSSLVEPS-KVGQFDQVLNLCLTE 90
Query: 67 FGKPKSFQYLK-NDALKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLH 125
F YL+ ND I L ++ + +K+ ++ + A +
Sbjct: 91 FEN----CYLEGND-----IHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKS 141
Query: 126 QS-VFASSK---------------INVYF-------------VQPMTPFDSADQHLQP-- 154
S +F + + YF V + + + L
Sbjct: 142 NSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDL--IKFSAETLSELI 199
Query: 155 ------------------------PAPTKQFLISPPSS-PPVGWEPRPESEPLVNYDLLA 189
P K +L+S P S P +G L +Y + A
Sbjct: 200 RTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGV------IQLAHYVVTA 253
Query: 190 AIASLTPG-LSHELHAPSESQPGIVV 214
+ TPG L L + G+V
Sbjct: 254 KLLGFTPGELRSYLKGATGHSQGLVT 279
Score = 36.2 bits (83), Expect = 0.009
Identities = 46/249 (18%), Positives = 78/249 (31%), Gaps = 80/249 (32%)
Query: 18 LKDTGDMGD-------SLDDLINDEQLPKSLIITNLNPDLFKDDALKEQIETLL----SQ 66
L+D+ + + S+ +L EQ+ + N L +Q+E L
Sbjct: 324 LEDSLENNEGVPSPMLSISNL-TQEQVQD--YVNKTNSHLPAG----KQVEISLVNGAKN 376
Query: 67 F---GKPKSFQYLKNDALKEQIETLLSQ----FG--KPK-SFQYLKSFRRMRVN------ 110
G P+S L K + + L Q F K K S ++L V
Sbjct: 377 LVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFL------PVASPFHSH 430
Query: 111 -YESSAAAAKARINLHQSVFASS--KINVYFVQPMTPFDSAD-QHLQPPAPTKQFLISPP 166
++ + + F + +I VY FD +D + L + ++
Sbjct: 431 LLVPASDLINKDLVKNNVSFNAKDIQIPVYD-----TFDGSDLRVLSGSISER--IVDCI 483
Query: 167 SSPPVGWEPRPESEPLVNYDLLAAIASLT------PGLSHELHAPSESQPGIVVHVCEDG 220
PV WE T PG + L G++ H +DG
Sbjct: 484 IRLPVKWE-------------TTTQFKATHILDFGPGGASGL--------GVLTHRNKDG 522
Query: 221 AMVGTKRIM 229
G + I+
Sbjct: 523 T--GVRVIV 529
Score = 28.5 bits (63), Expect = 2.2
Identities = 17/130 (13%), Positives = 33/130 (25%), Gaps = 53/130 (40%)
Query: 111 YESSAAAAKARINLHQSVFASSKINVYFVQPMTPFDSADQHLQ--------------PPA 156
Y++S AA ++ AD H + P
Sbjct: 1636 YKTSKAAQDV------------------------WNRADNHFKDTYGFSILDIVINNPVN 1671
Query: 157 PTKQFLISPPSSPPV-----------GWEPRPESEPLVNYDLLAAIASLT-PGLSHELHA 204
T F + + + ++E + ++ S T L A
Sbjct: 1672 LTIHF--GGEKGKRIRENYSAMIFETIVDGKLKTEKIFK-EINEHSTSYTFRSEKGLLSA 1728
Query: 205 PSESQPGIVV 214
+QP + +
Sbjct: 1729 TQFTQPALTL 1738
>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 = 46.0 bits (108), Expect = 6e-06
Identities = 39/250 (15%), Positives = 74/250 (29%), Gaps = 53/250 (21%)
Query: 2 EEDEDDHKMIINAIDNLKDTGDMGDSLDDLINDEQLPKSLIITNL----NPDLFKDDALK 57
D I I +++ L L+ + L++ L N + +A
Sbjct: 214 TSRSDHSSNIKLRIHSIQA------ELRRLLKSKPYENCLLV--LLNVQNAKAW--NAFN 263
Query: 58 EQIETLLSQFGKPKS-FQYLKNDALKE-QIETLLSQFGKPKSFQYLKSFRRMRVNYESSA 115
+ LL+ + K +L ++ + L + R +
Sbjct: 264 LSCKILLTT--RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRP--QDLP 319
Query: 116 AAAKARINLHQSVFASSKINV-----YFVQPM-----TPFDSADQHLQPPAPTKQFL--- 162
S+ A S + + T +S+ L+P K F
Sbjct: 320 REVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS 379
Query: 163 ISPPSSP-PVG-----WEPRPESEP------LVNYDLLA-----AIASLTPGLSHELHAP 205
+ PPS+ P W +S+ L Y L+ + S+ P + EL
Sbjct: 380 VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI-PSIYLELKVK 438
Query: 206 SESQPGIVVH 215
E++ +H
Sbjct: 439 LENEY--ALH 446
Score = 38.7 bits (89), Expect = 0.001
Identities = 30/160 (18%), Positives = 54/160 (33%), Gaps = 27/160 (16%)
Query: 2 EEDEDDHK---MIINAIDNLK---DTGDMGDSLDDLINDEQLPKSLIITNLNPDLFKDDA 55
E E ++ ++ D D D+ D +++ E++ +I++ D
Sbjct: 10 ETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEI-DHIIMS---KD--AVSG 63
Query: 56 LKEQIETLLSQFGKPKS-FQYLKNDALKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESS 114
TLLS K + Q + L+ + L+S + + M Y
Sbjct: 64 TLRLFWTLLS---KQEEMVQKFVEEVLRINYKFLMSPI----KTEQ-RQPSMMTRMYIE- 114
Query: 115 AAAAKARINLHQSVFASSKINVYFVQPMTPFDSADQHLQP 154
R L+ +K NV +QP A L+P
Sbjct: 115 -----QRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRP 149
Score = 35.2 bits (80), Expect = 0.017
Identities = 22/118 (18%), Positives = 39/118 (33%), Gaps = 31/118 (26%)
Query: 1 MEEDEDDHKMIINAIDNLK--DTGDMGDSLDD----------LINDEQLPKSLIITNLNP 48
+E + H+ I++ + K D+ D+ D L N E + L
Sbjct: 439 LENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPER----MTLFR 494
Query: 49 DLFKDDA-LKEQIE-------------TLLSQFGKPKSFQYLKNDALKEQIETLLSQF 92
+F D L+++I L Q K + ND E++ + F
Sbjct: 495 MVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPY-ICDNDPKYERLVNAILDF 551
Score = 28.7 bits (63), Expect = 2.3
Identities = 13/117 (11%), Positives = 34/117 (29%), Gaps = 28/117 (23%)
Query: 5 EDDHKMIINAIDNLKDTGD-----MG---------DSLDDLINDEQLPKS---LIITNLN 47
+ + A+ L+ + + D ++ L + N N
Sbjct: 134 LQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCN 193
Query: 48 PDLFKDDALKEQIETLLSQFGKPKSFQ-------YLKNDALKEQIETLLSQFGKPKS 97
+ + E ++ LL Q + + L+ +++ ++ LL
Sbjct: 194 ----SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246
>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 = 40.0 bits (94), Expect = 3e-04
Identities = 14/101 (13%), Positives = 26/101 (25%), Gaps = 24/101 (23%)
Query: 41 LIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQY 100
L +TN P + +++ LL L + +F + F Y
Sbjct: 120 LWMTNFPPS-YTQRNIRD----LLQDINVVALSIRLPSL-----------RFNTSRRFAY 163
Query: 101 LKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
++ S A L+ + P
Sbjct: 164 --------IDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP 196
Score = 36.9 bits (86), Expect = 0.004
Identities = 14/103 (13%), Positives = 38/103 (36%), Gaps = 23/103 (22%)
Query: 39 KSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSF 98
+ ++I NL+ +L ++ L+E FG + +
Sbjct: 211 REIMIRNLSTELLDENLLRE----SFEGFGSIEKINIPAGQ----------KEHSFNNCC 256
Query: 99 QYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
+ + +E+ +A +A + +++S+ + +I+V
Sbjct: 257 AF--------MVFENKDSAERA-LQMNRSLLGNREISVSLADK 290
>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 = 38.4 bits (90), Expect = 9e-04
Identities = 16/101 (15%), Positives = 34/101 (33%), Gaps = 24/101 (23%)
Query: 41 LIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQY 100
L + NL P +E L+ FG + + ++ + G+ K + +
Sbjct: 98 LCVANLPPS-LTQQQFEE----LVRPFGSLERCFLVYSE-----------RTGQSKGYGF 141
Query: 101 LKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
Y +AA+A+ +L + V++
Sbjct: 142 --------AEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDA 174
Score = 38.0 bits (89), Expect = 0.001
Identities = 22/106 (20%), Positives = 32/106 (30%), Gaps = 24/106 (22%)
Query: 39 KSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSF 98
+ L + L P DAL LS P Q G+ K F
Sbjct: 185 RCLCVDRLPPGFNDVDALCR----ALSAVHSPTFCQLACGQD------------GQLKGF 228
Query: 99 QYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMTP 144
+ + YE++ A +A+ S + V F P P
Sbjct: 229 ----AV----LEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP 266
Score = 29.9 bits (68), Expect = 0.60
Identities = 16/110 (14%), Positives = 30/110 (27%), Gaps = 31/110 (28%)
Query: 34 DEQLPKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFG 93
+ + ++I L D+ + + + LLS + F
Sbjct: 18 QFRNRRKILIRGLPGDV-TNQEVHD----LLSDYELKYCFV------------------D 54
Query: 94 KPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMT 143
K K + V + A A HQS +++V
Sbjct: 55 KYKGTAF--------VTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDA 96
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 36.9 bits (86), Expect = 0.001
Identities = 14/74 (18%), Positives = 32/74 (43%), Gaps = 13/74 (17%)
Query: 75 YLKN---DALKEQIETLLSQFGKPKSFQYLKSFRRMR----VNYESSAAAAKARINLHQS 127
+++ D + ++ + FG +K + + V +E + +AAKA +H
Sbjct: 35 FVRPFPLDVQESELNEIFGPFGP------MKEVKILNGFAFVEFEEAESAAKAIEEVHGK 88
Query: 128 VFASSKINVYFVQP 141
FA+ + V + +
Sbjct: 89 SFANQPLEVVYSKL 102
>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 = 36.1 bits (84), Expect = 0.001
Identities = 16/103 (15%), Positives = 38/103 (36%), Gaps = 23/103 (22%)
Query: 39 KSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSF 98
++ I NLN + K D LK+ + + S+FG+ ++ K +
Sbjct: 9 HTIYINNLNEKI-KKDELKKSLHAIFSRFGQILDILVSRS--------------LKMRGQ 53
Query: 99 QYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
+ V ++ ++A A ++ F + + + +
Sbjct: 54 AF--------VIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 88
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 36.8 bits (85), Expect = 0.001
Identities = 14/103 (13%), Positives = 35/103 (33%), Gaps = 23/103 (22%)
Query: 39 KSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSF 98
+ ++ITN+NP++ K+ L+ + L S G +D + ++
Sbjct: 30 QVVLITNINPEVPKEK-LQALLYALASSQGDILDIVVDLSDDNSGK------------AY 76
Query: 99 QYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
+ + + +A F + + + F +
Sbjct: 77 ----------IVFATQESAQAFVEAFQGYPFQGNPLVITFSET 109
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 35.8 bits (82), Expect = 0.001
Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 7/72 (9%)
Query: 72 SFQYLKNDALKEQIE-----TLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQ 126
S+ LKN L QI+ TL Q G SF + Y + A KA++ L+
Sbjct: 8 SWLLLKN--LTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNN 65
Query: 127 SVFASSKINVYF 138
V A++ I
Sbjct: 66 CVLANTTIFAES 77
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 36.2 bits (84), Expect = 0.002
Identities = 16/99 (16%), Positives = 34/99 (34%), Gaps = 24/99 (24%)
Query: 38 PKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKS 97
K + LN ++ + LK+ + ++G+ + + L + T K
Sbjct: 6 LKEVTFARLNDNVRETF-LKD----MCRKYGEVEEVEILLHP------RT-----RKHLG 49
Query: 98 FQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINV 136
V + S+ A + NLH + + I+
Sbjct: 50 LAR--------VLFTSTRGAKETVKNLHLTSVMGNIIHA 80
>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 = 35.5 bits (82), Expect = 0.002
Identities = 21/97 (21%), Positives = 31/97 (31%), Gaps = 21/97 (21%)
Query: 75 YLKN---DALKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFAS 131
+KN D+ +++ LL + K ++ R V + A A HQ F
Sbjct: 9 LVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRG 67
Query: 132 SKINVYFVQPMTPFDSADQHLQPPAPTKQFLISPPSS 168
+ V PT L S PSS
Sbjct: 68 KDLIVQL-----------------QPTDALLCSGPSS 87
>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 = 36.1 bits (84), Expect = 0.002
Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 13/74 (17%)
Query: 75 YLKN---DALKEQIETLLSQFGKPKSFQYLKSFRRMR----VNYESSAAAAKARINLHQS 127
+++N +E +E SQFGK L+ ++++ ++++ A KA ++
Sbjct: 15 FVRNLANTVTEEILEKAFSQFGK------LERVKKLKDYAFIHFDERDGAVKAMEEMNGK 68
Query: 128 VFASSKINVYFVQP 141
I + F +P
Sbjct: 69 DLEGENIEIVFAKP 82
>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 = 36.8 bits (84), Expect = 0.003
Identities = 24/173 (13%), Positives = 53/173 (30%), Gaps = 25/173 (14%)
Query: 39 KSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSF 98
++ I NLN + K D LK+ + + SQFG+ ++ K +
Sbjct: 10 HTIYINNLNEKI-KKDELKKSLYAIFSQFGQILDILVSRS--------------LKMRGQ 54
Query: 99 QYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMTPFDSADQHLQPPAPT 158
+ V ++ ++A A ++ F + + + + T D +
Sbjct: 55 AF--------VIFKEVSSATNALRSMQGFPFYDKPMRIQYAK--TDSDIIAKMKGTFVER 104
Query: 159 KQFLISPPSSPPVGWEPRPESEPLVNYDLLAAIASLTPGLSHELHAPSESQPG 211
+ + + ++ A+ PG+ AP
Sbjct: 105 DRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHM 157
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 35.1 bits (81), Expect = 0.003
Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 3/72 (4%)
Query: 75 YLKNDALKEQIETLLSQFGKPKSFQYLKSFR---RMRVNYESSAAAAKARINLHQSVFAS 131
+ E +++LL Q+G +S + + + + V Y S A +A L+ +
Sbjct: 22 NIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLEN 81
Query: 132 SKINVYFVQPMT 143
+ V ++
Sbjct: 82 FTLKVAYIPDEM 93
>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 = 35.0 bits (81), Expect = 0.004
Identities = 23/133 (17%), Positives = 47/133 (35%), Gaps = 26/133 (19%)
Query: 12 INAIDNLKDTGDMGDSLDDLINDEQLPKSLIITNLNPDLFKDDALKEQIETLLSQFGKPK 71
I++ + +++ D + E L +T+++ + +D+ I+ +G+ K
Sbjct: 2 IHSYERVRNEDDDELEPGPQRSVE--GWILFVTSIHEEAQEDE-----IQEKFCDYGEIK 54
Query: 72 SFQYLKNDALKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFAS 131
+ L D T G K + V YE+ A A+ L+ +
Sbjct: 55 NIH-LNLDR-----RT-----GFSKGYAL--------VEYETHKQALAAKEALNGAEIMG 95
Query: 132 SKINVYFVQPMTP 144
I V + P
Sbjct: 96 QTIQVDWCFVKGP 108
>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 = 35.8 bits (83), Expect = 0.005
Identities = 23/104 (22%), Positives = 33/104 (31%), Gaps = 24/104 (23%)
Query: 38 PKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKS 97
L I L L DD +KE LL+ FG K+F +K+ S G K
Sbjct: 114 AHKLFIGGLPNYL-NDDQVKE----LLTSFGPLKAFNLVKD-----------SATGLSKG 157
Query: 98 FQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
+ + Y +A L+ K+ V
Sbjct: 158 YAF--------CEYVDINVTDQAIAGLNGMQLGDKKLLVQRASV 193
>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 = 33.7 bits (78), Expect = 0.010
Identities = 16/96 (16%), Positives = 32/96 (33%), Gaps = 19/96 (19%)
Query: 58 EQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAA 117
EQI L S G + + + D +T G+ K + + + + ++
Sbjct: 17 EQILDLCSNVGPVINLK-MMFDP-----QT-----GRSKGYAF--------IEFRDLESS 57
Query: 118 AKARINLHQSVFASSKINVYFVQPMTPFDSADQHLQ 153
A A NL+ S + + + +H
Sbjct: 58 ASAVRNLNGYQLGSRFLKCGYSSNSDISGVSLEHHH 93
>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 = 33.0 bits (76), Expect = 0.015
Identities = 14/70 (20%), Positives = 22/70 (31%), Gaps = 8/70 (11%)
Query: 83 EQIETLLSQFGKPKSFQYLKS----FRRMRVNYESSAAAAKARINLHQSVFASSKINVYF 138
+ S FG F V YE +A +A L+ + S ++ V
Sbjct: 28 TLLRGAFSPFGNIIDLSMDPPRNCAF----VTYEKMESADQAVAELNGTQVESVQLKVNI 83
Query: 139 VQPMTPFDSA 148
+ DS
Sbjct: 84 ARKQPMLDSG 93
>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 = 32.6 bits (75), Expect = 0.021
Identities = 15/75 (20%), Positives = 30/75 (40%), Gaps = 11/75 (14%)
Query: 75 YLKN---DALKEQIETLLSQFGKPKSFQYLKSFRRMR----VNYESSAAAAKARINLHQS 127
Y++N +E IE + + +++R V++ + A +A L+
Sbjct: 19 YVRNLMLSTSEEMIEKEFNNIKPGAV----ERVKKIRDYAFVHFSNREDAVEAMKALNGK 74
Query: 128 VFASSKINVYFVQPM 142
V S I V +P+
Sbjct: 75 VLDGSPIEVTLAKPV 89
>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 = 33.2 bits (76), Expect = 0.021
Identities = 14/73 (19%), Positives = 23/73 (31%), Gaps = 8/73 (10%)
Query: 82 KEQIETLLSQFGKPKSFQYLKS----FRRMRVNYESSAAAAKARINLHQSVFASSKINVY 137
+ S FG F V YE +A +A L+ + S ++ V
Sbjct: 51 PTLLRGAFSPFGNIIDLSMDPPRNCAF----VTYEKMESADQAVAELNGTQVESVQLKVN 106
Query: 138 FVQPMTPFDSADQ 150
+ D+A
Sbjct: 107 IARKQPMLDAATG 119
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 32.7 bits (75), Expect = 0.027
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 4/63 (6%)
Query: 83 EQIETLLSQFGKPKSFQYLKSFRRMR----VNYESSAAAAKARINLHQSVFASSKINVYF 138
+ + QFGK + + + R + V +E+SA A +AR LH +V KI V
Sbjct: 44 PDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 103
Query: 139 VQP 141
Sbjct: 104 ATA 106
>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 = 32.8 bits (75), Expect = 0.029
Identities = 18/112 (16%), Positives = 39/112 (34%), Gaps = 18/112 (16%)
Query: 39 KSLIITNL-NPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKS 97
+++ N+ +P DD L+ ++ +FG + K
Sbjct: 21 TVMVLRNMVDPKDIDDD-LEGEVTEECGKFGAVNRVIIYQE---------------KQGE 64
Query: 98 FQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMTPFDSAD 149
+ + ++ V + ++ KA L+ FA K+ FD++D
Sbjct: 65 EEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVY-DQERFDNSD 115
>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 = 33.5 bits (76), Expect = 0.032
Identities = 13/129 (10%), Positives = 36/129 (27%), Gaps = 28/129 (21%)
Query: 41 LIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQY 100
L++ L+ D + + +G + +++K+
Sbjct: 7 LMVYGLDQSKMNCDRVFN----VFCLYGNVEKVKFMKSK----------------PGAAM 46
Query: 101 LKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMTPFDSADQHLQPPAPTKQ 160
V A +A +L+ + K+NV + L+ + + +
Sbjct: 47 --------VEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYK 98
Query: 161 FLISPPSSP 169
++
Sbjct: 99 DFSESRNNR 107
Score = 26.6 bits (58), Expect = 6.3
Identities = 7/71 (9%), Positives = 21/71 (29%), Gaps = 8/71 (11%)
Query: 76 LKNDALKEQIETLLSQFGKPKSFQYLKSFRRMR-------VNYESSAAAAKARINLHQSV 128
+ +E + + G + +K F + ++S + A + L+
Sbjct: 131 APLEVTEENFFEICDELGVKRPTS-VKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQ 189
Query: 129 FASSKINVYFV 139
+ +
Sbjct: 190 MKNPNGPYPYT 200
>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 = 31.7 bits (73), Expect = 0.044
Identities = 16/88 (18%), Positives = 29/88 (32%), Gaps = 18/88 (20%)
Query: 57 KEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAA 116
K+ I + S +GK K + + ++ K + Y V +E+
Sbjct: 18 KDHIMEIFSTYGKIKMID-MPVE----RMHP-----HLSKGYAY--------VEFENPDE 59
Query: 117 AAKARINLHQSVFASSKINVYFVQPMTP 144
A KA ++ +I V P
Sbjct: 60 AEKALKHMDGGQIDGQEITATAVLAPWP 87
>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar
mRNA localization, translation; 1.90A {Drosophila
melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A
Length = 165
Score = 32.5 bits (74), Expect = 0.053
Identities = 20/106 (18%), Positives = 37/106 (34%), Gaps = 24/106 (22%)
Query: 39 KSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSF 98
L +T+++ + +D+ I+ +G+ K+ L D T G K +
Sbjct: 73 WILFVTSIHEEAQEDE-----IQEKFCDYGEIKNIH-LNLDR-----RT-----GFSKGY 116
Query: 99 QYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMTP 144
V YE+ A A+ L+ + I V + P
Sbjct: 117 AL--------VEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP 154
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 32.0 bits (73), Expect = 0.056
Identities = 7/41 (17%), Positives = 11/41 (26%)
Query: 109 VNYESSAAAAKARINLHQSVFASSKINVYFVQPMTPFDSAD 149
V++ A L F +I T + S
Sbjct: 69 VSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQSGP 109
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition
motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 99
Score = 31.5 bits (72), Expect = 0.064
Identities = 15/77 (19%), Positives = 26/77 (33%), Gaps = 8/77 (10%)
Query: 76 LKNDALKEQIETLLSQFGKPKSFQYLKS----FRRMRVNYESSAAAAKARINLHQSVFAS 131
L D +E++ L ++GK K F + E+ A A++ L
Sbjct: 23 LPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGF----IRLETRTLAEIAKVELDNMPLRG 78
Query: 132 SKINVYFVQPMTPFDSA 148
++ V F S
Sbjct: 79 KQLRVRFACHSASLTSG 95
>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 31.0 bits (71), Expect = 0.079
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 10/65 (15%)
Query: 76 LKNDALKEQIETLLSQFGKPKSFQYLKSFRRMR----VNYESSAAAAKARINLHQSVFAS 131
L +A +++I +L Q+GK + ++ V+ E AA A NLH
Sbjct: 16 LPREATEQEIRSLFEQYGK------VLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHG 69
Query: 132 SKINV 136
INV
Sbjct: 70 VNINV 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 = 32.2 bits (73), Expect = 0.095
Identities = 16/98 (16%), Positives = 27/98 (27%), Gaps = 28/98 (28%)
Query: 41 LIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQY 100
L+++NLNP+ +L L +G + + L N K
Sbjct: 6 LLVSNLNPERVTPQSLFI----LFGVYGDVQRVKILFNK----------------KENAL 45
Query: 101 LKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYF 138
V A A +L+ I +
Sbjct: 46 --------VQMADGNQAQLAMSHLNGHKLHGKPIRITL 75
Score = 29.5 bits (66), Expect = 0.62
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 6/70 (8%)
Query: 75 YLKN---DALKEQIETLLSQFGKP-KSFQYLKSFRRM-RVNYESSAAAAKARINLH-QSV 128
+L N +E ++ L S G K F++ + R+M + S A +A I+LH +
Sbjct: 124 HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDL 183
Query: 129 FASSKINVYF 138
+ + V F
Sbjct: 184 GENHHLRVSF 193
>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 = 32.3 bits (73), Expect = 0.097
Identities = 19/127 (14%), Positives = 33/127 (25%), Gaps = 29/127 (22%)
Query: 41 LIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQY 100
L+++NLNP+ +L L +G + + L K
Sbjct: 37 LLVSNLNPERVTPQSLFI----LFGVYGDVQRVKILF----------------NKKENAL 76
Query: 101 LKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMTPFDSADQHLQPPAPTKQ 160
V A A +L+ I + + + TK
Sbjct: 77 --------VQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQG-LTKD 127
Query: 161 FLISPPS 167
+ SP
Sbjct: 128 YGNSPLH 134
Score = 28.8 bits (64), Expect = 1.4
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 6/70 (8%)
Query: 75 YLKN---DALKEQIETLLSQFGKP-KSFQYLKSFRRMR-VNYESSAAAAKARINLH-QSV 128
+L N +E ++ L S G K F++ + R+M + S A +A I+LH +
Sbjct: 155 HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDL 214
Query: 129 FASSKINVYF 138
+ + V F
Sbjct: 215 GENHHLRVSF 224
>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 = 30.3 bits (69), Expect = 0.11
Identities = 9/64 (14%), Positives = 27/64 (42%), Gaps = 1/64 (1%)
Query: 76 LKNDALKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARIN-LHQSVFASSKI 134
L + + + QFG+ ++ ++ + + + + AA A ++ + ++
Sbjct: 20 LGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRL 79
Query: 135 NVYF 138
NV +
Sbjct: 80 NVKW 83
>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 = 31.8 bits (73), Expect = 0.11
Identities = 16/104 (15%), Positives = 35/104 (33%), Gaps = 29/104 (27%)
Query: 38 PKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKS 97
++L+ NL+ ++ +D LKE + + + + GK K
Sbjct: 99 ARTLLAKNLSFNI-TEDELKE----VFEDALEIRLVS-----------QD-----GKSKG 137
Query: 98 FQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
Y + ++S A A K + +++Y+
Sbjct: 138 IAY--------IEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173
Score = 28.3 bits (64), Expect = 1.4
Identities = 20/109 (18%), Positives = 36/109 (33%), Gaps = 26/109 (23%)
Query: 33 NDEQLPKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQF 92
++ P +L I NLNP+ LK +S+ +
Sbjct: 8 SESTTPFNLFIGNLNPNK-SVAELKV----AISELFAKNDLAVVDVRT------------ 50
Query: 93 GKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
G + F Y V++ES+ KA + L ++I + +
Sbjct: 51 GTNRKFGY--------VDFESAEDLEKA-LELTGLKVFGNEIKLEKPKG 90
>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 = 30.9 bits (70), Expect = 0.13
Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 10/70 (14%)
Query: 82 KEQIETLLSQFGKPKSFQYLKSFRRMR--------VNYESSAAAAKARINLHQS--VFAS 131
+E+I +++ + + + + V YES AAA AR L
Sbjct: 22 REEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWG 81
Query: 132 SKINVYFVQP 141
+I V + +P
Sbjct: 82 HQIAVDWAEP 91
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 30.8 bits (70), Expect = 0.13
Identities = 19/117 (16%), Positives = 34/117 (29%), Gaps = 20/117 (17%)
Query: 34 DEQLPKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALK--EQIETLLSQ 91
D ++ + L + E + Q G K+ + + ET
Sbjct: 3 DNSDNNTIFVQGLGEN-----VTIESVADYFKQIGIIKTNKKTGQPMINLYTDRET---- 53
Query: 92 FGKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMTPFDSA 148
GK K V+++ +A A F+ + I V F F+
Sbjct: 54 -GKLKGEAT--------VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRG 101
>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 = 30.7 bits (70), Expect = 0.14
Identities = 21/106 (19%), Positives = 40/106 (37%), Gaps = 24/106 (22%)
Query: 39 KSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSF 98
++ +TNL+ D ++ L+E L FG K+ T G+ K F
Sbjct: 16 ATIRVTNLSEDT-RETDLQE----LFRPFGSISRIYLAKDK------TT-----GQSKGF 59
Query: 99 QYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMTP 144
+ +++ AA+A + + +NV + +P T
Sbjct: 60 AF--------ISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTN 97
>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 = 30.3 bits (69), Expect = 0.14
Identities = 21/100 (21%), Positives = 33/100 (33%), Gaps = 19/100 (19%)
Query: 58 EQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAA 117
EQ++ + S+ G SF+ L D ET GKPK + + Y+ A
Sbjct: 23 EQLKDIFSEVGPVVSFR-LVYDR-----ET-----GKPKGYGF--------CEYQDQETA 63
Query: 118 AKARINLHQSVFASSKINVYFVQPMTPFDSADQHLQPPAP 157
A NL+ F+ + V +
Sbjct: 64 LSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAPV 103
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 30.3 bits (69), Expect = 0.15
Identities = 22/104 (21%), Positives = 35/104 (33%), Gaps = 25/104 (24%)
Query: 38 PKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKS 97
L I+ L KE++E + G K + + N A GKPK
Sbjct: 17 KHKLFISGLPFS-----CTKEELEEICKAHGTVKDLRLVTNRA------------GKPKG 59
Query: 98 FQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
Y V YE+ + A++A + + + I V
Sbjct: 60 LAY--------VEYENESQASQAVMKMDGMTIKENIIKVAISNS 95
>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 = 31.0 bits (71), Expect = 0.17
Identities = 15/102 (14%), Positives = 35/102 (34%), Gaps = 24/102 (23%)
Query: 40 SLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQ 99
+LI+ L D D L L G + + +++ + G +
Sbjct: 5 NLIVNYLPQD-MTDRELYA----LFRAIGPINTCRIMRD-----------YKTGYSYGYA 48
Query: 100 YLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
+ V++ S + +A L+ + ++ V + +P
Sbjct: 49 F--------VDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP 82
>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 = 30.0 bits (68), Expect = 0.23
Identities = 9/68 (13%), Positives = 24/68 (35%), Gaps = 12/68 (17%)
Query: 83 EQIETLLSQFGKPKSFQYLKSFRRMR------VNYESSAAAAKARINLHQSVFASSKINV 136
+ + S FG+ + R V + + +AA A ++++ + +
Sbjct: 40 QLMRQTFSPFGQ------IMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKC 93
Query: 137 YFVQPMTP 144
Y+ +
Sbjct: 94 YWGKESPD 101
>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 = 30.0 bits (68), Expect = 0.27
Identities = 20/105 (19%), Positives = 37/105 (35%), Gaps = 24/105 (22%)
Query: 40 SLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQ 99
L +T ++ + ++D I +++G+ K+ +L D T G K +
Sbjct: 24 ILFVTGVHEEATEED-----IHDKFAEYGEIKNI-HLNLDR-----RT-----GYLKGYT 67
Query: 100 YLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMTP 144
V YE+ A A L+ I+V + P
Sbjct: 68 L--------VEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 104
>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 = 30.8 bits (70), Expect = 0.28
Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 8/71 (11%)
Query: 75 YLKNDALKEQIETLLSQFGKPKSFQYLKS----FRRMRVNYESSAAAAKARINLHQSVFA 130
L D +E + L ++G+P + F + ES A A+ L ++
Sbjct: 29 NLPTDITEEDFKRLFERYGEPSEVFINRDRGFGF----IRLESRTLAEIAKAELDGTILK 84
Query: 131 SSKINVYFVQP 141
S + + F
Sbjct: 85 SRPLRIRFATH 95
>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 = 29.5 bits (67), Expect = 0.34
Identities = 19/111 (17%), Positives = 36/111 (32%), Gaps = 25/111 (22%)
Query: 33 NDEQLPKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQF 92
EQ P +L I+NL P + L+ +L FG+ S + L++ +
Sbjct: 20 QQEQDPTNLYISNL-PLSMDEQELEN----MLKPFGQVISTRILRDSS------------ 62
Query: 93 GKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMT 143
G + F ES+ + + + +P+
Sbjct: 63 GTSRGV----GF----ARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLL 105
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 29.1 bits (66), Expect = 0.44
Identities = 7/63 (11%), Positives = 20/63 (31%), Gaps = 10/63 (15%)
Query: 78 NDALKEQIETLLSQFGKPKSFQYLKSFRRMR----VNYESSAAAAKARINLHQSVFASSK 133
+ KE + + S +G + + +++ + A Q + K
Sbjct: 21 KNVSKEDLFRIFSPYGH------IMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKK 74
Query: 134 INV 136
+ +
Sbjct: 75 LIL 77
>3mm5_B Sulfite reductase, dissimilatory-type subunit BET;
alpha-beta-protein, oxidoreductase; HET: SRM; 1.80A
{Archaeoglobus fulgidus} PDB: 3c7b_B* 3mm6_B* 3mm7_B*
3mm8_B* 3mm9_B* 3mma_B* 3mmb_B* 3mmc_B*
Length = 366
Score = 30.4 bits (69), Expect = 0.49
Identities = 8/31 (25%), Positives = 14/31 (45%), Gaps = 5/31 (16%)
Query: 200 HELHAPSESQPGIVVHVCEDGAMVGTKRIMQ 230
HE+ +PG++ V E G ++ R
Sbjct: 33 HEVV-----KPGVIKRVAESGDVIYVVRFGT 58
>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 = 29.0 bits (65), Expect = 0.51
Identities = 13/79 (16%), Positives = 27/79 (34%), Gaps = 9/79 (11%)
Query: 79 DALKEQIETLLSQFGKPKSFQYLKSFR--------RMRVNYESSAAAAKARINLHQSVFA 130
+ + E + S++G KS + + ++ V + S KA L FA
Sbjct: 26 EEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFA 85
Query: 131 SSKINVYFVQPMTPFDSAD 149
+ + + + D
Sbjct: 86 NRVVVTKYC-DPDSYHRRD 103
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 28.8 bits (65), Expect = 0.56
Identities = 20/105 (19%), Positives = 36/105 (34%), Gaps = 24/105 (22%)
Query: 40 SLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQ 99
L +T ++ + ++D I +++G+ K+ L D T G K +
Sbjct: 25 ILFVTGVHEEATEED-----IHDKFAEYGEIKNIH-LNLDR-----RT-----GYLKGYT 68
Query: 100 YLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMTP 144
V YE+ A A L+ I+V + P
Sbjct: 69 L--------VEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 105
>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 = 28.5 bits (64), Expect = 0.88
Identities = 14/69 (20%), Positives = 27/69 (39%), Gaps = 14/69 (20%)
Query: 82 KEQIETLLSQFGK------PKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKIN 135
K +ET+ S++G+ K + +F V Y + A A + + V A ++
Sbjct: 42 KSDVETIFSKYGRVAGCSVHKGY----AF----VQYSNERHARAAVLGENGRVLAGQTLD 93
Query: 136 VYFVQPMTP 144
+ P
Sbjct: 94 INMAGEPKP 102
>1nvp_D Transcription initiation factor IIA gamma chain; transcription
regulation, DNA, complex, transcription/DNA complex;
2.10A {Homo sapiens} SCOP: a.32.1.1 b.56.1.1
Length = 108
Score = 28.3 bits (63), Expect = 0.91
Identities = 13/54 (24%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 26 DSLDDLINDEQLPKSLIITNLNP-DLFKDDALKEQIETLLSQFGKPKSFQYLKN 78
+SLD+LI +Q+ L + L D + AL +++ ++ G ++++ N
Sbjct: 16 ESLDELIQSQQITPQLALQVLLQFDKAINAALAQRVRNRVNFRGSLNTYRFCDN 69
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 27.7 bits (62), Expect = 1.3
Identities = 10/58 (17%), Positives = 18/58 (31%), Gaps = 8/58 (13%)
Query: 83 EQIETLLSQFGKPKSFQYLKS----FRRMRVNYESSAAAAKARINLHQSVFASSKINV 136
+ L FG F++ F + Y++ AA + L F +
Sbjct: 42 ADLIPLFQNFGFILDFKHYPEKGCCF----IKYDTHEQAAVCIVALANFPFQGRNLRT 95
>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 = 28.3 bits (64), Expect = 1.3
Identities = 18/102 (17%), Positives = 36/102 (35%), Gaps = 24/102 (23%)
Query: 40 SLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQ 99
+LI+ L + + + L G+ +S + +++ T G+ +
Sbjct: 4 NLIVNYLPQN-MTQEEFRS----LFGSIGEIESCKLVRD------KIT-----GQSLGYG 47
Query: 100 YLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
+ VNY A KA L+ + I V + +P
Sbjct: 48 F--------VNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP 81
>3aow_A Putative uncharacterized protein PH0207; protein-PLP-AKG triple
complex, schiff-base linkage, kynuren aminotransferase;
HET: PLP AKG; 1.56A {Pyrococcus horikoshii} PDB: 3aov_A*
3ath_A* 3av7_A* 1x0m_A 1wst_A*
Length = 448
Score = 28.8 bits (65), Expect = 1.7
Identities = 9/53 (16%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 46 LNPDLFKDDALKEQIETLLSQFGKPKSFQYLK---NDALKEQIETLLSQFGKP 95
NP F + +++ + ++ ++ K+ QY L+E + L +
Sbjct: 86 PNPKTFPKEIIRDILVEIMEKYA-DKALQYGTTKGFTPLRETLMKWLGKRYGI 137
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 28.6 bits (63), Expect = 1.8
Identities = 11/54 (20%), Positives = 26/54 (48%)
Query: 72 SFQYLKNDALKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLH 125
+ ++LK ++ +I + S+ G +Y++S V ++ A A A+ +
Sbjct: 147 NSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMS 200
>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 = 26.7 bits (60), Expect = 2.0
Identities = 22/99 (22%), Positives = 33/99 (33%), Gaps = 24/99 (24%)
Query: 38 PKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKS 97
L I L P D L + L +GK S + + + T K K
Sbjct: 5 SSGLYIRGLQPG-TTDQDLVK----LCQPYGKIVSTKAILD------KTT-----NKCKG 48
Query: 98 FQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINV 136
+ F V+++S +AA KA L S +
Sbjct: 49 Y----GF----VDFDSPSAAQKAVTALKASGVQAQMAKQ 79
>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 = 28.3 bits (62), Expect = 2.4
Identities = 16/143 (11%), Positives = 39/143 (27%), Gaps = 24/143 (16%)
Query: 39 KSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSF 98
K+L + +N D + + +G K + + + GKP+ +
Sbjct: 103 KTLFVARVNYDTTESK-----LRREFEVYGPIKRIHMVYSK-----------RSGKPRGY 146
Query: 99 QYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMTPFDSADQHLQPPAPT 158
+ + YE A + ++ V + T + L
Sbjct: 147 AF--------IEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGG 198
Query: 159 KQFLISPPSSPPVGWEPRPESEP 181
+ + + G + +
Sbjct: 199 TRRGGADVNIRHSGRDDTSRYDE 221
>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 = 27.0 bits (60), Expect = 2.4
Identities = 22/117 (18%), Positives = 35/117 (29%), Gaps = 20/117 (17%)
Query: 34 DEQLPKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALK--EQIETLLSQ 91
++ ++ + LN + + Q G K + + ET
Sbjct: 11 EDSDNSAIYVQGLNDS-----VTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET---- 61
Query: 92 FGKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMTPFDSA 148
GKPK V+YE A A F SK+ V + P +S
Sbjct: 62 -GKPKGDAT--------VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSG 109
>3or1_B Sulfite reductase beta; dissimilatory sulfite reductase, sulfate
reduction, oxidored sulfite reduction; HET: SRM; 1.76A
{Desulfovibrio gigas} PDB: 3or2_B* 2v4j_B* 2xsj_B*
Length = 386
Score = 28.1 bits (63), Expect = 2.5
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 5/29 (17%)
Query: 200 HELHAPSESQPGIVVHVCEDGAMVGTKRI 228
HE+ +PGI+VHV ++G V T R
Sbjct: 44 HEIL-----EPGILVHVAKNGDKVFTVRC 67
>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 = 26.8 bits (59), Expect = 2.8
Identities = 14/104 (13%), Positives = 33/104 (31%), Gaps = 9/104 (8%)
Query: 41 LIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQ- 99
+ + N+ +++ Q L Q ++ +E + ++G+ +
Sbjct: 4 IALLNI----YRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNV 59
Query: 100 YLKSFRRMR----VNYESSAAAAKARINLHQSVFASSKINVYFV 139
+ V + A KA I+L+ F I+
Sbjct: 60 CDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103
>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 = 26.9 bits (60), Expect = 3.0
Identities = 18/57 (31%), Positives = 24/57 (42%), Gaps = 5/57 (8%)
Query: 109 VNYESSAAAAKARINLHQSVFASSKINVYFVQPMTPFDSADQHLQPPAPTKQFLISP 165
V S AAA A LH FA I +V P+ + + L P + T L+ P
Sbjct: 60 VKCPSIAAAIAAVNALHGRWFAGKMITAAYV-PLPTYHN----LFPDSMTATQLLVP 111
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 27.8 bits (61), Expect = 3.2
Identities = 12/70 (17%), Positives = 21/70 (30%), Gaps = 18/70 (25%)
Query: 106 RMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPMTPFDSADQHLQPPAPTKQFLISP 165
++VNY S + V P+ S + K+FL+
Sbjct: 119 AIQVNYSSEVKENSVDSDDKAKV-----------PPLIRIVSGLELSDTKQKGKKFLV-- 165
Query: 166 PSSPPVGWEP 175
+ +EP
Sbjct: 166 -----IAYEP 170
>3kan_A D-dopachrome tautomerase; immune response, cytokine,
cytokine-inhibitor C; HET: RW1; 1.13A {Homo sapiens}
PDB: 1dpt_A* 3ker_A*
Length = 117
Score = 26.8 bits (59), Expect = 3.5
Identities = 8/32 (25%), Positives = 10/32 (31%)
Query: 42 IITNLNPDLFKDDALKEQIETLLSQFGKPKSF 73
+ TNL + K S GKP
Sbjct: 5 LDTNLPANRVPAGLEKRLCAAAASILGKPADR 36
>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 = 26.1 bits (58), Expect = 3.9
Identities = 9/49 (18%), Positives = 17/49 (34%), Gaps = 8/49 (16%)
Query: 93 GKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
GK K Y + ++S A A K + +++Y+
Sbjct: 50 GKSKGIAY--------IEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 90
>1nh2_D Transcription initiation factor IIA small chain;
transcription/DNA; HET: 5IU; 1.90A {Saccharomyces
cerevisiae} SCOP: a.32.1.1 b.56.1.1 PDB: 1ytf_D* 1rm1_B
Length = 121
Score = 26.5 bits (58), Expect = 4.3
Identities = 14/54 (25%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 26 DSLDDLINDEQLPKSLIITNLNP-DLFKDDALKEQIETLLSQFGKPKSFQYLKN 78
D+LD LI+D ++ SL + L D + LK+ ++ L+ G ++ + +
Sbjct: 20 DALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLTVKGNLDTYGFCDD 73
>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 = 26.8 bits (60), Expect = 4.4
Identities = 19/101 (18%), Positives = 34/101 (33%), Gaps = 28/101 (27%)
Query: 41 LIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQY 100
L I ++ + I + S FG+ + + L+ G +
Sbjct: 98 LFIGMISKKC--TE---NDIRVMFSSFGQIEECRILRGPD------------GLSRGC-- 138
Query: 101 LKSFRRMRVNYESSAAAAKARINLHQSVF---ASSKINVYF 138
+F V + + A A A +HQ+ SS + V F
Sbjct: 139 --AF----VTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKF 173
Score = 26.8 bits (60), Expect = 5.3
Identities = 16/101 (15%), Positives = 32/101 (31%), Gaps = 22/101 (21%)
Query: 41 LIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQY 100
+ + + + L+E L Q+G L++ P+S
Sbjct: 6 MFVGQVPRTW-SEKDLRE----LFEQYGAVYEINVLRD-----------RSQNPPQSKGC 49
Query: 101 LKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
F V + + AA +A+ LH + ++P
Sbjct: 50 --CF----VTFYTRKAALEAQNALHNMKVLPGMHHPIQMKP 84
>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 = 26.2 bits (58), Expect = 5.2
Identities = 21/129 (16%), Positives = 39/129 (30%), Gaps = 25/129 (19%)
Query: 23 DMGDSLDDLINDEQLPKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALK 82
D+ DS + L+++NL D ++E L ++FG K + +
Sbjct: 20 DLFDSGCGGGEGVETGAKLLVSNL-DFGVSDADIQE----LFAEFGTLKKAAVDYDRS-- 72
Query: 83 EQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQPM 142
G+ V++E A A KA +++ V
Sbjct: 73 ----------GRSLGTAD--------VHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 114
Query: 143 TPFDSADQH 151
+ H
Sbjct: 115 IDLEHHHHH 123
>2ijq_A Hypothetical protein; structural genomics, PSI, protein structure
initiative, NEW YORK SGX research center for structural
genomics; 1.88A {Haloarcula marismortui} SCOP: a.246.2.1
Length = 161
Score = 26.6 bits (58), Expect = 5.3
Identities = 10/47 (21%), Positives = 17/47 (36%), Gaps = 1/47 (2%)
Query: 158 TKQFLISPPSSPPVGWEPRPESEP-LVNYDLLAAIASLTPGLSHELH 203
T+ + P P GW + E + ++ + G HE H
Sbjct: 6 TRDPTVKAPDGNPSGWRTDGQWEHETLRRAVVHGVRLYNSGEFHESH 52
>2hhi_A Antigen MPT64, immunogenic protein MPT64; secreted antigen,
residual dipolar COUP solution structure, beta-grAsp,
unknown function; NMR {Mycobacterium tuberculosis}
Length = 204
Score = 26.8 bits (59), Expect = 6.0
Identities = 10/57 (17%), Positives = 22/57 (38%), Gaps = 4/57 (7%)
Query: 27 SLDDLINDEQLPKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQ--YLKNDAL 81
+ D L + P ++ + +L K + I + P ++Q + ND +
Sbjct: 119 TYDTLWQADTDPLPVVFPIVQGELSKQTGQQVSIAP--NAGLDPVNYQNFAVTNDGV 173
>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing
system, phosphoryltransferase, HEL helix motif,
transcription regulator; 3.20A {Streptococcus
pneumoniae}
Length = 158
Score = 26.4 bits (58), Expect = 6.1
Identities = 11/53 (20%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 27 SLDDLINDEQLPKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKND 79
S D++ ++++ + L K + +KE+ LLS+ + + Q + D
Sbjct: 56 SYVDIVGEDKMLNPVEDYELT---LKIEIVKERGANLLSRLYRYQDSQGISID 105
>1vp4_A Aminotransferase, putative; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI; HET: MSE PLP; 1.82A {Thermotoga maritima} SCOP:
c.67.1.1
Length = 425
Score = 26.5 bits (59), Expect = 8.9
Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 4/54 (7%)
Query: 47 NPDLFKDDALKEQIETLLSQFGKPKSFQYLK---NDALKEQIETLLSQFGKPKS 97
+P+ F L E + ++ + + QY + LK+QI LL +
Sbjct: 54 DPETFPRKELAEIAKEIIEKEY-HYTLQYSTTEGDPVLKQQILKLLERMYGITG 106
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.314 0.132 0.382
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,573,107
Number of extensions: 203790
Number of successful extensions: 488
Number of sequences better than 10.0: 1
Number of HSP's gapped: 473
Number of HSP's successfully gapped: 89
Length of query: 238
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 147
Effective length of database: 4,160,982
Effective search space: 611664354
Effective search space used: 611664354
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (25.9 bits)