RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4687
(339 letters)
>3ax1_A Serrate RNA effector molecule; miRNA processing, protein binding;
2.74A {Arabidopsis thaliana}
Length = 358
Score = 127 bits (319), Expect = 5e-34
Identities = 39/190 (20%), Positives = 64/190 (33%), Gaps = 14/190 (7%)
Query: 155 LSSKNPVLQNITDYLIEEASAEEEELLGKSEENTE---ETEQVDPNVLRVLDRLILYLRI 211
L S+ + +N+ E S E+ G + T + +LD L+ YL
Sbjct: 160 LDSEKKIEENVLQGSETEKSGREKLHSGSTGPVVIIRGLTSVKGLEGVELLDTLVTYLWR 219
Query: 212 VHSVDYYNHCEYPNEDEMPNRCGIIHTRGSAPASKVTPQEITDYCSTFQNKMSSLVSSPQ 271
VH +DYY E G+ H R S + + S F + +
Sbjct: 220 VHGLDYYGKVETNE------AKGLRHVRAEGKVS---DAKGDENESKFDSHWQERLKGQD 270
Query: 272 EPTPEELDQLGAKKTDAEVEKFIAANTQEISTDKWLCPLSG--KKFKGPDFIRKHIFNKH 329
+ ++ + E K+ C G K F +F+ KH+ KH
Sbjct: 271 PLEVMAAKEKIDAAATEALDPHVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVYKHLKLKH 330
Query: 330 AEKVEEVKKE 339
E V E+ +
Sbjct: 331 TELVTELTTK 340
>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 = 54.5 bits (130), Expect = 3e-08
Identities = 60/399 (15%), Positives = 117/399 (29%), Gaps = 119/399 (29%)
Query: 9 MLNSYNNIINGGESK---NEPPPRALHRTSSIF--LRNLAPTITKAEVENLCKRYSGFLR 63
+ + +I++ E + T +F L + + + VE + + FL
Sbjct: 38 VQDMPKSILSKEEIDHIIMSKDA--VSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLM 95
Query: 64 VAIA----DPQPDRRWFRRGWVTFRRDVDIKEICWNLNNIRLRDCELGAIVNR-DLSRRV 118
I P R + ++ ++ +N N + + V+R ++
Sbjct: 96 SPIKTEQRQPSMMTRMY----------IEQRDRLYNDNQVFAKY-----NVSRLQPYLKL 140
Query: 119 RTVSGLTSLKP---VVQFDMK------LSLWTDGQEPAQQPMSY-----TLSSKN----- 159
R L L+P V+ + ++L Q M + L + N
Sbjct: 141 RQ--ALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETV 198
Query: 160 -PVLQNITDYLIEEASAEEEELLGKSEENTEETEQVD---------PNVLRVLDRLILYL 209
+LQ + Y I+ + + + N L VL +
Sbjct: 199 LEMLQKLL-YQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLN-VQNA 256
Query: 210 RIVHSVDYYNHCEYPNEDEMPNRCGI-IHTRGSAPASKVTPQEITDYCSTFQNKMSSLVS 268
+ ++ + C I + TR ++TD+ S SL
Sbjct: 257 KAWNAFN--------------LSCKILLTTRFK---------QVTDFLSAATTTHISLDH 293
Query: 269 SPQEPTPEELDQLGAKKTDAEVEK--------------FIAANTQE-IST-DKWLCPLSG 312
TP+E+ L K D + IA + ++ ++T D W ++
Sbjct: 294 HSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWK-HVNC 352
Query: 313 KKFK----------GPDFIRKH-----IFNKHA---EKV 333
K P RK +F A +
Sbjct: 353 DKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTIL 391
Score = 44.5 bits (104), Expect = 4e-05
Identities = 59/353 (16%), Positives = 117/353 (33%), Gaps = 97/353 (27%)
Query: 33 RTSSIFLRNLAPTITKAEVENLCKRYSGFLRVAIAD-PQPDRRWFRRGWVTFRRDVDIKE 91
T+ I L + + T+T EV++L +Y L D P +E
Sbjct: 285 TTTHISLDHHSMTLTPDEVKSLLLKY---LDCRPQDLP--------------------RE 321
Query: 92 ICWNLNNIRLRDCEL-GAIVNRDLSR--RVRTVSG--LTSLKPVVQFDMKLSLWTDGQEP 146
+ R + + L+ + V+ LT++ ++ SL + EP
Sbjct: 322 VL----TTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI-------IESSL--NVLEP 368
Query: 147 A-QQPMSYTLSSKNPVLQ---NITDYLIE---EASAEEE------ELLGKS--EENTEET 191
A + M LS V +I L+ + + +L S E+ +E+
Sbjct: 369 AEYRKMFDRLS----VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKES 424
Query: 192 EQVDPNVLRVLDRLILYLRIVHS--VDYYN-HCEYPNEDEMPNRC-GII------HTRGS 241
P++ L + +H VD+YN + ++D +P H +
Sbjct: 425 TISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNI 484
Query: 242 APASKVT--PQEITDYCSTF-QNKMSSLVSSPQEPTPEELDQLGAKKTDAEV-EKFIAAN 297
++T D+ F + K+ S+ + L+ L + + +I N
Sbjct: 485 EHPERMTLFRMVFLDF--RFLEQKIRH-DSTAWNASGSILNTL----QQLKFYKPYICDN 537
Query: 298 TQEISTDKWLCPLSGKKF-----------KGPDFIRKHIFNKHAEKVEEVKKE 339
+ ++ + + F K D +R + + EE K+
Sbjct: 538 --DPKYERLVNAI--LDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQ 586
Score = 31.0 bits (69), Expect = 0.63
Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 12/67 (17%)
Query: 4 LLNLMM-LNSYNNIINGGESKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRYSGFL 62
+LN + L Y I N+P L FL + + +C +Y+ L
Sbjct: 520 ILNTLQQLKFYKPYI----CDNDPKYERLVNAILDFLPKIEENL-------ICSKYTDLL 568
Query: 63 RVAIADP 69
R+A+
Sbjct: 569 RIALMAE 575
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 37.7 bits (87), Expect = 0.005
Identities = 26/164 (15%), Positives = 50/164 (30%), Gaps = 56/164 (34%)
Query: 11 NSYNNIINGGESKNEPPPRALHRTSSIFLRNLAPT-ITKAEVENLCKR----YSGFLRVA 65
N N++ G PP++L+ + + AP+ + ++ + +R + FL VA
Sbjct: 372 NGAKNLVVSG------PPQSLYGLNLTLRKAKAPSGLDQSRIP-FSERKLKFSNRFLPVA 424
Query: 66 I-------ADPQPDRRWFRRGWVTFRRDVDIKEICWNLNNIRLRDCELGAIV-----NRD 113
+D+ + +N ++ V D
Sbjct: 425 SPFHSHLLVPASD----------LINKDLVKNNVSFNAK-------DIQIPVYDTFDGSD 467
Query: 114 LSRRVRTVSGLTSLKPVVQFDMKLSL---WTDGQEPAQQPMSYT 154
L R +SG S+ + D + L W T
Sbjct: 468 L----RVLSG--SISERI-VDCIIRLPVKW-----ETTTQFKAT 499
Score = 37.0 bits (85), Expect = 0.010
Identities = 44/258 (17%), Positives = 84/258 (32%), Gaps = 72/258 (27%)
Query: 126 SLKPVVQFDMKLSLWTDGQEPAQQ------PMSY-TLSSKNPVLQNITDYLIEEASA--- 175
S+ +V + G E ++ M + T+ + I + E +++
Sbjct: 1660 SILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTF 1719
Query: 176 -EEEELLGKSEENTEETEQVDP-------NVLRVL-DRLILYLRIV---HSVDYYNHCEY 223
E+ LL T+ T Q P L + ++ HS+ EY
Sbjct: 1720 RSEKGLLSA----TQFT-Q--PALTLMEKAAFEDLKSKGLIPADATFAGHSLG-----EY 1767
Query: 224 ----------PNEDEMPNRCGIIHTRGSAPASKVTPQEI--TDY--CSTFQNKMSSLVSS 269
E + ++ RG V E+ ++Y + +++ S
Sbjct: 1768 AALASLADVMSIESLVE----VVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVA--ASF 1821
Query: 270 PQEPTPEELDQLGAKKTDAEVEKFIA----ANTQEIST------DKWLCP-LSGKKFKGP 318
QE ++++ K+T VE I N Q ++ D + L+ K +
Sbjct: 1822 SQEALQYVVERV-GKRTGWLVE--IVNYNVENQQYVAAGDLRALDT-VTNVLNFIKLQKI 1877
Query: 319 DFIR-KHIFNKHAEKVEE 335
D I + E+VE
Sbjct: 1878 DIIELQKSL--SLEEVEG 1893
Score = 32.7 bits (74), Expect = 0.22
Identities = 39/259 (15%), Positives = 70/259 (27%), Gaps = 91/259 (35%)
Query: 125 TSLKPVV--------QFDMKLSLWTDGQEPAQQPMSYTLSSK-NPVLQNITDYLI--EEA 173
S +P+ + + + A Q L + N +L T+ +E
Sbjct: 4 YSTRPLTLSHGSLEHVLLVPTASFF----IASQ-----LQEQFNKILPEPTEGFAADDEP 54
Query: 174 SAEEEELLGK---------SEENTEETEQVDPNVLRVLDRLILYLRIVHSV--------- 215
+ E L+GK + +QV L + L +H++
Sbjct: 55 TTPAE-LVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQEND 113
Query: 216 -----------DYYNHCEYPNEDEMPNRCGIIHTRGSAPASKVTPQ------------EI 252
+Y + +++ E+
Sbjct: 114 TTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEEL 173
Query: 253 TD-YCSTFQNKMSSLVSSPQEPTPEELDQLGAKKTDAEVEKFIAANTQEISTDKWL---- 307
D Y T+ + L+ + E L +L DA EK TQ ++ +WL
Sbjct: 174 RDLY-QTYHVLVGDLIKF----SAETLSELIRTTLDA--EKVF---TQGLNILEWLENPS 223
Query: 308 --------------CPLSG 312
CPL G
Sbjct: 224 NTPDKDYLLSIPISCPLIG 242
>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 = 33.8 bits (78), Expect = 0.016
Identities = 19/108 (17%), Positives = 38/108 (35%), Gaps = 8/108 (7%)
Query: 12 SYNNIINGGESKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRYSGFLRVAIADPQP 71
S ++ ++GG P I++ NL P I ++E++ +Y + + +
Sbjct: 3 SGSSGMSGGGVIRGPAGN---NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR-R 58
Query: 72 DRRWFRRGWVTFRRDVDIKEICWNLNNIRLRDCELGAIVNRDLSRRVR 119
F +V F D ++ + + L V S R
Sbjct: 59 GGPPF--AFVEFEDPRDAEDAVYGRDGYDYDGYRL--RVEFPRSGRGT 102
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 31.7 bits (72), Expect = 0.076
Identities = 6/58 (10%), Positives = 24/58 (41%), Gaps = 5/58 (8%)
Query: 9 MLNSYNNIINGGESKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRYSGFLRVAI 66
M + +++ + + ++ P + + +R L + +A++ + + V +
Sbjct: 1 MGHHHHHHMENYDDPHKTPA-----SPVVHIRGLIDGVVEADLVEALQEFGPISYVVV 53
>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 = 31.3 bits (71), Expect = 0.11
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 6/41 (14%)
Query: 18 NGGESKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRY 58
+ G+ + P R LH +R L +T+ EV L +
Sbjct: 5 SSGDKMDGAPSRVLH------IRKLPGEVTETEVIALGLPF 39
>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 = 31.1 bits (71), Expect = 0.11
Identities = 14/80 (17%), Positives = 32/80 (40%), Gaps = 9/80 (11%)
Query: 28 PRALHRTSSIFLRNL-APTITKAEVENLCKRYSGFLRVAIADPQPDRRWFRRGWVTFRRD 86
PR H S +F+ NL ++K ++ + Y +++ I + F G++ F
Sbjct: 16 PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI------KNAF--GFIQFDNP 67
Query: 87 VDIKEICWNLNNIRLRDCEL 106
+++ + +L
Sbjct: 68 QSVRDAIEXESQEMNFGKKL 87
>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 = 30.5 bits (69), Expect = 0.25
Identities = 5/49 (10%), Positives = 19/49 (38%), Gaps = 5/49 (10%)
Query: 18 NGGESKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRYSGFLRVAI 66
S ++ + + +R L ++ +A++ +++ V +
Sbjct: 4 GSSGSHHKVSV-----SPVVHVRGLCESVVEADLVEALEKFGTICYVMM 47
>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 = 29.2 bits (66), Expect = 0.52
Identities = 7/39 (17%), Positives = 16/39 (41%)
Query: 20 GESKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRY 58
G S + + I ++N+ T++ E+ + Y
Sbjct: 1 GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGY 39
>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 = 29.8 bits (67), Expect = 0.60
Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 5/78 (6%)
Query: 29 RALHRTSSIFLRNLAPTITKAEVENLCKRYSGFLRVAIADPQPDRRWFRRGWVTFRRDVD 88
+ +++ NL K E+E Y V +A + F +V F D
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVA---RNPPGF--AFVEFEDPRD 122
Query: 89 IKEICWNLNNIRLRDCEL 106
+ L+ L C +
Sbjct: 123 AADAVRELDGRTLCGCRV 140
>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 = 29.3 bits (66), Expect = 0.60
Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 6/80 (7%)
Query: 27 PPRALHRTSSIFLRNLAPTITKAEVENLCKRYSGFLRVAIADPQPDRRWFRRGWVTFRRD 86
PP +++RNL IT E+ ++ +Y ++ + + P+ R +V +
Sbjct: 4 PPEV---NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT-PETRGT--AYVVYEDI 57
Query: 87 VDIKEICWNLNNIRLRDCEL 106
D K +L+ + + L
Sbjct: 58 FDAKNAVDHLSGFNVSNRYL 77
>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 = 29.2 bits (66), Expect = 0.61
Identities = 12/81 (14%), Positives = 30/81 (37%), Gaps = 4/81 (4%)
Query: 20 GESKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRYSGFLRVAIADPQPDRRWFRRG 79
G S + + I ++N+ T++ E+ + Y + ++ + + + G
Sbjct: 1 GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGY-QVIPGSVC-LKYNEKGMPTG 58
Query: 80 W--VTFRRDVDIKEICWNLNN 98
V F + +LN+
Sbjct: 59 EAMVAFESRDEATAAVIDLND 79
>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 = 29.5 bits (66), Expect = 0.71
Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 2/48 (4%)
Query: 11 NSYNNIINGGESKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRY 58
+S + G + R I +R L +T+ EV +L +
Sbjct: 10 HSSGLVPRGSHMGDSRSAGVPSRV--IHIRKLPIDVTEGEVISLGLPF 55
>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 = 28.9 bits (65), Expect = 1.0
Identities = 7/39 (17%), Positives = 13/39 (33%)
Query: 20 GESKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRY 58
G S + + N+ +ITK +V +
Sbjct: 1 GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGI 39
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 28.3 bits (63), Expect = 1.2
Identities = 9/37 (24%), Positives = 16/37 (43%), Gaps = 6/37 (16%)
Query: 22 SKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRY 58
+ P R +H +R L +T+ EV +L +
Sbjct: 10 HGSGVPSRVIH------IRKLPIDVTEGEVISLGLPF 40
>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 = 28.4 bits (64), Expect = 1.2
Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 4/75 (5%)
Query: 19 GGESKNEPPPRALHRTS-SIFLRNLAPTITKAEVENLCKRYSGFLRVAIADPQPDR-RWF 76
G +P + T ++F+ NL P + AE++ +A+ D + R F
Sbjct: 1 GSHMLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKF 60
Query: 77 RRGWVTFRRDVDIKE 91
G+V F D+++
Sbjct: 61 --GYVDFESAEDLEK 73
>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator,
structural genomics, PSI-2, protei structure initiative;
NMR {Homo sapiens}
Length = 97
Score = 27.4 bits (61), Expect = 2.1
Identities = 14/67 (20%), Positives = 24/67 (35%), Gaps = 2/67 (2%)
Query: 39 LRNLAPTITKAEVENLCKRYSG--FLRVAIADPQPDRRWFRRGWVTFRRDVDIKEICWNL 96
+R L P +TK ++E + + AD + R ++ FR DI
Sbjct: 14 IRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRF 73
Query: 97 NNIRLRD 103
+ D
Sbjct: 74 DGYIFLD 80
>2wbt_A B-129; zinc finger; 2.70A {Sulfolobus virus 1}
Length = 129
Score = 28.0 bits (61), Expect = 2.2
Identities = 10/72 (13%), Positives = 23/72 (31%)
Query: 262 KMSSLVSSPQEPTPEELDQLGAKKTDAEVEKFIAANTQEISTDKWLCPLSGKKFKGPDFI 321
+ L + + L + ++ + +++CPL F +
Sbjct: 31 RYHQLTPEQKRLIRAIVKTLIHNPQLLDESSYLYRLLASKAISQFVCPLCLMPFSSSVSL 90
Query: 322 RKHIFNKHAEKV 333
++HI KV
Sbjct: 91 KQHIRYTEHTKV 102
Score = 27.2 bits (59), Expect = 4.0
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 308 CPLSGKKFKGPDFIRKHIFNKHA 330
CP+ K+F D H+ KH
Sbjct: 103 CPVCKKEFTSTDSALDHVCKKHN 125
>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 = 27.6 bits (62), Expect = 2.3
Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 9/77 (11%)
Query: 11 NSYNNIINGGESKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRYSGFLRVAIADPQ 70
+S I + P ++L+NL+P +T+ ++ +L R+ I Q
Sbjct: 5 SSGEEIRKIPMFSSYNPGEP---NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPI---Q 58
Query: 71 PDRRWFR-RG--WVTFR 84
R RG ++TF
Sbjct: 59 FRMMTGRMRGQAFITFP 75
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 27.3 bits (61), Expect = 2.3
Identities = 17/70 (24%), Positives = 26/70 (37%), Gaps = 8/70 (11%)
Query: 34 TSSIFLRNLAPTITKAEVENLCKRYSGFLRVA----IADPQPDR-RWFRRGWVTFRRDVD 88
+I LRN+AP + Y L V I D Q + R F +V +D
Sbjct: 9 MDTIILRNIAPHTVVDSIMTALSPY-ASLAVNNIRLIKDKQTQQNRGF--AFVQLSSAMD 65
Query: 89 IKEICWNLNN 98
++ L +
Sbjct: 66 ASQLLQILQS 75
>1htt_A Histidyl-tRNA synthetase; complex (tRNA synthetase/His-adenylate),
aminoacyl-tRNA synthase, ligase; HET: HIS AMP; 2.60A
{Escherichia coli} SCOP: c.51.1.1 d.104.1.1 PDB: 1kmm_A*
1kmn_A* 2el9_A*
Length = 423
Score = 29.1 bits (66), Expect = 2.5
Identities = 20/77 (25%), Positives = 29/77 (37%), Gaps = 29/77 (37%)
Query: 155 LSSKNPVLQN-------ITDYLIEEASAEEEELLGKSEENTEETEQVDPNVLRVLDRL-I 206
L SKNP +Q + DYL EE+ + ++L+ I
Sbjct: 207 LDSKNPEVQALLNDAPALGDYLDEESREHFAG------------------LCKLLESAGI 248
Query: 207 LYL---RIVHSVDYYNH 220
Y R+V +DYYN
Sbjct: 249 AYTVNQRLVRGLDYYNR 265
>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 = 27.7 bits (62), Expect = 2.6
Identities = 11/82 (13%), Positives = 31/82 (37%), Gaps = 6/82 (7%)
Query: 20 GESKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRYSGFLRVA--IADPQPDR-RWF 76
G S + P + ++F+RNL+ + + + +++ G L+ + P + +
Sbjct: 1 GSSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQF-GDLKYVRVVLHPDTEHSKGC 59
Query: 77 RRGWVTFRRDVDIKEICWNLNN 98
+ F ++ +
Sbjct: 60 --AFAQFMTQEAAQKCLAAASL 79
>3qbr_A SJA, sjchgc06286 protein; helical bundle, BCL-2-like fold,
apoptosis; HET: NHE; 2.60A {Schistosoma japonicum}
Length = 179
Score = 28.4 bits (62), Expect = 2.7
Identities = 13/59 (22%), Positives = 24/59 (40%)
Query: 147 AQQPMSYTLSSKNPVLQNITDYLIEEASAEEEELLGKSEENTEETEQVDPNVLRVLDRL 205
+Q PMS T + +L+ A+ ++ + L +NT PN ++ L
Sbjct: 7 SQDPMSNTADFRLQTSTLCHSFLLASANKQDTDYLTDLLDNTNIDLTCVPNGQEIIHSL 65
>1qe0_A Histidyl-tRNA synthetase; class II tRNA synthetase, beta sheet,
ligase; 2.70A {Staphylococcus aureus} SCOP: c.51.1.1
d.104.1.1
Length = 420
Score = 28.7 bits (65), Expect = 2.8
Identities = 21/77 (27%), Positives = 27/77 (35%), Gaps = 29/77 (37%)
Query: 155 LSSKNPVLQ-------NITDYLIEEASAEEEELLGKSEENTEETEQVDPNVLRVLDRL-I 206
L K + ITD+L EE+ A E+ V LD L I
Sbjct: 206 LDCKVDRDKEAIKTAPRITDFLNEESKAYYEQ------------------VKAYLDDLGI 247
Query: 207 LYL---RIVHSVDYYNH 220
Y +V +DYY H
Sbjct: 248 PYTEDPNLVRGLDYYTH 264
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 27.3 bits (61), Expect = 2.9
Identities = 14/71 (19%), Positives = 25/71 (35%), Gaps = 5/71 (7%)
Query: 36 SIFLRNLAPTITKAEVENLCKRYSGFLRVAIADPQPDRRWFRRGWVTFRRDVDIKEICWN 95
+++ NL K E+E Y V IA + F +V F D ++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIA---RNPPGF--AFVEFEDPRDAEDAVRG 56
Query: 96 LNNIRLRDCEL 106
L+ + +
Sbjct: 57 LDGKVICGSRV 67
>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 = 27.4 bits (61), Expect = 3.1
Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 20 GESKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRYSGFLRVAIADPQPDRR 74
G S + P S+I+++ L ++T ++ + K+ G +++ QP
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQC-GVVKMNKRTGQPMIH 54
>4e51_A Histidine--tRNA ligase; seattle structural genomics center for
infectious disease, S aminoacylation, tRNA activation,
charged tRNA; HET: HIS; 2.65A {Burkholderia
thailandensis}
Length = 467
Score = 28.8 bits (65), Expect = 3.1
Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 29/77 (37%)
Query: 155 LSSKNPVLQN-------ITDYLIEEASAEEEELLGKSEENTEETEQVDPNVLRVLDRL-I 206
L +KNP LQ + D+L + + A E + R+L +
Sbjct: 235 LDTKNPALQEIVRNAPKLIDFLGDVSRAHFEG------------------LQRLLKANNV 276
Query: 207 LYL---RIVHSVDYYNH 220
+ R+V +DYYN
Sbjct: 277 PFTINPRLVRGLDYYNL 293
>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 = 28.0 bits (63), Expect = 3.6
Identities = 20/107 (18%), Positives = 40/107 (37%), Gaps = 7/107 (6%)
Query: 22 SKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRYSGFLRVAIADPQPDR-RWFRRGW 80
S + + +F+ NL P + AE++ +A+ D + R F G+
Sbjct: 2 SHMVEGSESTTPFN-LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKF--GY 58
Query: 81 VTFRRDVDIKEICWNLNNIRLRDCELGAIVNRDLSRRVRTVSGLTSL 127
V F + E L +++ E+ + + R + V +L
Sbjct: 59 VDF-ESAEDLEKALELTGLKVFGNEI--KLEKPKGRDSKKVRAARTL 102
>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 = 27.6 bits (60), Expect = 3.7
Identities = 7/22 (31%), Positives = 10/22 (45%), Gaps = 3/22 (13%)
Query: 126 SLKPVVQFDMKLSLWTDGQEPA 147
+LK + L L+ D PA
Sbjct: 21 ALK---KLQASLKLYADDSAPA 39
>1h4v_B Histidyl-tRNA synthetase; class IIA aminoacyl-tRNA synthetase, ATP
+ L-histidine tRNA(His)-> AMP + PPI +
L-histidyl-tRNA(His); 2.4A {Thermus thermophilus} SCOP:
c.51.1.1 d.104.1.1 PDB: 1ady_A* 1adj_A
Length = 421
Score = 27.9 bits (63), Expect = 4.7
Identities = 21/79 (26%), Positives = 29/79 (36%), Gaps = 31/79 (39%)
Query: 155 LSSKNPVLQ---------NITDYLIEEASAEEEELLGKSEENTEETEQVDPNVLRVLDRL 205
L SK+ Q + D+L EEA A +E V R L+RL
Sbjct: 206 LDSKSERDQALLKELGVRPMLDFLGEEARAHLKE------------------VERHLERL 247
Query: 206 -ILYL---RIVHSVDYYNH 220
+ Y +V +DYY
Sbjct: 248 SVPYELEPALVRGLDYYVR 266
>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 = 26.4 bits (59), Expect = 4.9
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 34 TSSIFLRNLAPTITKAEVENLCKRY 58
+ +F+RNL+ T ++ ++E L Y
Sbjct: 8 SGRLFVRNLSYTSSEEDLEKLFSAY 32
>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 = 26.6 bits (59), Expect = 5.5
Identities = 9/42 (21%), Positives = 13/42 (30%), Gaps = 3/42 (7%)
Query: 18 NGGESKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRYS 59
+ G S N P + LR L +K E+
Sbjct: 2 SSGSSGNSPDTA---NDGFVRLRGLPFGCSKEEIVQFFSGLE 40
>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 = 27.1 bits (60), Expect = 6.1
Identities = 14/80 (17%), Positives = 33/80 (41%), Gaps = 4/80 (5%)
Query: 24 NEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRYSGFLRVAIA-DPQPDR-RWFRRGWV 81
NE + L ++ ++++ NL+ T+ ++ L + ++ + D F +V
Sbjct: 29 NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGF--CFV 86
Query: 82 TFRRDVDIKEICWNLNNIRL 101
+ D + +N RL
Sbjct: 87 EYYSRADAENAMRYINGTRL 106
>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 = 26.4 bits (59), Expect = 8.9
Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 4/80 (5%)
Query: 27 PPRALHRTSSIFLRNLAPTITKAEVENLCKRYSGFLRVAIA-DPQPDR-RWFRRGWVTFR 84
P A R +++++ L T+T+ E+E L +Y + I D R G++ F
Sbjct: 81 PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGV--GFIRFD 138
Query: 85 RDVDIKEICWNLNNIRLRDC 104
+ ++ +E LN +
Sbjct: 139 KRIEAEEAIKGLNGQKPSGA 158
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
0.316 0.133 0.391
Gapped
Lambda K H
0.267 0.0747 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,197,909
Number of extensions: 308229
Number of successful extensions: 972
Number of sequences better than 10.0: 1
Number of HSP's gapped: 962
Number of HSP's successfully gapped: 45
Length of query: 339
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 245
Effective length of database: 4,077,219
Effective search space: 998918655
Effective search space used: 998918655
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: 41 (21.6 bits)
S2: 58 (26.1 bits)