RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780255|ref|YP_003064668.1| 30S ribosomal protein S3 [Candidatus Liberibacter asiaticus str. psy62] (227 letters) >3i1m_C 30S ribosomal protein S3; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C 3i1q_C 3i1s_C 3i1z_C 3i21_C 2qal_C* 1p6g_C 1p87_C 2aw7_C 2avy_C 2i2u_C 2i2p_C* 2qan_C* 2qb9_C* 2qbb_C* 2qbd_C ... (C:1-109) Length = 109 Score = 139 bits (351), Expect = 4e-34 Identities = 48/109 (44%), Positives = 74/109 (67%) Query: 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERT 60 MGQK++P RLG+ WNS WFA E+ L D K+R+YL L +A V++I+IER Sbjct: 1 MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP 60 Query: 61 HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKP 109 K+ R+ +++ARPG++IGKKG D+EK+RK ++++ +++ EV KP Sbjct: 61 AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKP 109 >2vqe_C 30S ribosomal protein S3; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C* 1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F* 1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C 1xmo_C* 1xmq_C* 1xnq_C* ... (C:1-109) Length = 109 Score = 134 bits (340), Expect = 6e-33 Identities = 47/109 (43%), Positives = 69/109 (63%) Query: 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERT 60 MG KI+PI FRLG+ W SRW+A +Y LL ED +IR L+ L AG+A++ IER Sbjct: 1 MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA 60 Query: 61 HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKP 109 N + V+ A+PG++IG+ G I +R++L+ +T + L+V EV P Sbjct: 61 ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNP 109 >3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (C:1-121) Length = 121 Score = 127 bits (320), Expect = 1e-30 Identities = 35/120 (29%), Positives = 66/120 (55%), Gaps = 11/120 (9%) Query: 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQ--------AGV 52 MGQKINP+ FRLG + S WF++ Y L ED KIR+ ++ ++++ G+ Sbjct: 1 MGQKINPLGFRLGTTQSHYSLWFSQPKNYAEGLQEDQKIRDCIKNYVQKNTKTSSGVEGI 60 Query: 53 AKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRK---KLSNMTNSEIHLSVNEVPKP 109 A+I I++ ++I++ P L+I + +E ++ K N N ++++++ + KP Sbjct: 61 ARIEIQKRIDLIQVIIHMGFPKLLIENRPQGVEDLKINVQKELNCVNRKLNIAITRIAKP 120 >3i1m_C 30S ribosomal protein S3; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C 3i1q_C 3i1s_C 3i1z_C 3i21_C 2qal_C* 1p6g_C 1p87_C 2aw7_C 2avy_C 2i2u_C 2i2p_C* 2qan_C* 2qb9_C* 2qbb_C* 2qbd_C ... (C:110-233) Length = 124 Score = 120 bits (302), Expect = 2e-28 Identities = 63/116 (54%), Positives = 79/116 (68%) Query: 110 EINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYL 169 E++A L+A SI QLERRV+FRRAMKRAVQ+AMR GA G+KV SGRL GAE++RTE Y Sbjct: 1 ELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYR 60 Query: 170 EGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEK 225 EGRVPL TLRA IDY T+ A T YG G+KV++ + + + + K Sbjct: 61 EGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPK 116 >2vqe_C 30S ribosomal protein S3; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C* 1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F* 1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C 1xmo_C* 1xmq_C* 1xnq_C* ... (C:110-239) Length = 130 Score = 118 bits (298), Expect = 5e-28 Identities = 55/116 (47%), Positives = 74/116 (63%) Query: 110 EINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYL 169 ++A L+AQ +A+Q+ERR RRA+K+AVQ M GA G KVI SGR+ GAE +RTE Sbjct: 1 NLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAA 60 Query: 170 EGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEK 225 +GRVPL TLRA+IDYG A+A T YG G+K Y+ L + + + E+ Sbjct: 61 QGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEER 116 >3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (C:122-218) Length = 97 Score = 114 bits (287), Expect = 1e-26 Identities = 40/96 (41%), Positives = 64/96 (66%) Query: 112 NATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEG 171 + ++A+ IA QL+ RV FR+AMK+A++ + G+++ +GR++G E++R E EG Sbjct: 2 DPNILAEFIAGQLKSRVSFRKAMKKAIELTEQADTKGIQIQIAGRIDGKEIARIEWIREG 61 Query: 172 RVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDE 207 RVPLQT+RA IDY T YG GIK+++ + +E Sbjct: 62 RVPLQTIRAKIDYCAYTVRTIYGVLGIKIWIFMGEE 97 >1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Homo sapiens} (A:) Length = 92 Score = 108 bits (273), Expect = 5e-25 Identities = 17/96 (17%), Positives = 36/96 (37%), Gaps = 11/96 (11%) Query: 33 LHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 ++ E+L L + G + + + T II+ + R ++G+KG I ++ + Sbjct: 6 SGFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQ 65 Query: 93 NMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRV 128 PE + L A+ +A + Sbjct: 66 -----------KRFGFPEGSVELYAEKVATRGSGPS 90 >2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_C (c:1-94) Length = 94 Score = 106 bits (267), Expect = 2e-24 Identities = 18/102 (17%), Positives = 41/102 (40%), Gaps = 11/102 (10%) Query: 20 SRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGK 79 + ++ ++ A ++ E+L L + G + + + T II+ + R ++G+ Sbjct: 2 AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61 Query: 80 KGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIA 121 KG I ++ + PE + L A+ +A Sbjct: 62 KGRRIRELTAVVQ-----------KRFGFPEGSVELYAEKVA 92 >2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_C (c:95-243) Length = 149 Score = 99.3 bits (247), Expect = 4e-22 Identities = 25/118 (21%), Positives = 50/118 (42%), Gaps = 3/118 (2%) Query: 111 INATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLE 170 + A A+S+ +L + RRA ++ M GA G +V+ SG+L G + +++ +++ Sbjct: 2 LCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRG-QRAKSMKFVD 60 Query: 171 GRVPL--QTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEKD 226 G + + ++D G GIKV + L + + V + Sbjct: 61 GLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVE 118 >1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} (A:182-284) Length = 103 Score = 46.2 bits (110), Expect = 3e-06 Identities = 17/86 (19%), Positives = 31/86 (36%), Gaps = 13/86 (15%) Query: 29 YGALLHEDLKIREYLQCHLKQAGVAKILIERTHKN------CRIIVYSARP---GLIIGK 79 + E ++ + + + IER N ++ R ++IG Sbjct: 9 QRFMASEIIREKLMRFLGAELPYSVTVEIERFVSNERGGYDINGLILVEREGQKKMVIGN 68 Query: 80 KGTDIEKI----RKKLSNMTNSEIHL 101 KG I+ I RK + M + +HL Sbjct: 69 KGAKIKTIGIEARKDMQEMFEAPVHL 94 >2qs8_A XAA-Pro dipeptidase; amidohydrolase, TIM barrel, protein structure initiative, PSI-2, NYSGXRC, structural genomics; 2.33A {Alteromonas macleodii} (A:159-277) Length = 119 Score = 32.5 bits (74), Expect = 0.047 Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 8/66 (12%) Query: 133 AMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHID----YGTAV 188 + AV+ + GADG+K+ +G + S + + A + YG V Sbjct: 19 EVYAAVRQRYKDGADGIKITVTGGVLSVAKSGQNPQF----TQEEVDAVVSAAKDYGXWV 74 Query: 189 AETAYG 194 A A+G Sbjct: 75 AVHAHG 80 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} (B:1772-1800,B:1916-2006) Length = 120 Score = 32.4 bits (74), Expect = 0.058 Identities = 10/23 (43%), Positives = 12/23 (52%), Gaps = 4/23 (17%) Query: 119 SIAQQLERRVVFRR--AMKRAVQ 139 SI +E VVF R M+ AV Sbjct: 7 SIESLVE--VVFYRGMTMQVAVP 27 >3be7_A Zn-dependent arginine carboxypeptidase; unknown source, amidohydrolase, sargasso SEA, structural genomics, protein structure initiative, PSI; HET: ARG; 2.30A {Unidentified} (A:137-268) Length = 132 Score = 31.9 bits (72), Expect = 0.074 Identities = 15/70 (21%), Positives = 28/70 (40%) Query: 133 AMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETA 192 ++ V+ ++GAD +K A+G + + ++G VA A Sbjct: 31 EARKMVRKNRKYGADLIKFCATGGVMSRNTDVNAKQFTLEEMKAIVDEAHNHGMKVAAHA 90 Query: 193 YGSCGIKVYV 202 +G GIK + Sbjct: 91 HGLIGIKAAI 100 >3feq_A Putative amidohydrolase; unknown source, sargasso SEA, structural genomics, protein structure initiative, PSI; 2.63A {Unidentified} (A:134-273) Length = 140 Score = 31.2 bits (70), Expect = 0.12 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 8/74 (10%) Query: 133 AMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHID----YGTAV 188 ++ AV+ ++ GA +K++ASG + S T+ + +RA +D T V Sbjct: 40 GVRLAVREEIQKGATQIKIMASGGV----ASPTDPIANTQYSEDEIRAIVDEAEAANTYV 95 Query: 189 AETAYGSCGIKVYV 202 AY I V Sbjct: 96 MAHAYTGRAIARAV 109 >2p9b_A Possible prolidase; protein structure initiative II, PSI-2, amidohydrolase, structural genomics; 1.70A {Bifidobacterium longum NCC2705} (A:165-339) Length = 175 Score = 30.8 bits (69), Expect = 0.16 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 6/74 (8%) Query: 133 AMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHID----YGTAV 188 + AV ++ G + +K+ A+G + A+ + ++ RA D YG V Sbjct: 22 EARTAVAQNLKAGVNAIKIAATGGVTDAQEIGEAGSP--QXSVEQXRAICDEAHQYGVIV 79 Query: 189 AETAYGSCGIKVYV 202 A G++ + Sbjct: 80 GAHAQSPEGVRRSL 93 >2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein/RNA complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* (A:) Length = 178 Score = 28.9 bits (63), Expect = 0.63 Identities = 9/26 (34%), Positives = 17/26 (65%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKK 90 ++++ S G IIGK G I +++K+ Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKE 34 >2ghs_A AGR_C_1268P; 15155668, calcium-binding protein, regucalcin, structural genomics, joint center for structural genomics, JCSG; 1.55A {Agrobacterium tumefaciens str} (A:) Length = 326 Score = 28.9 bits (62), Expect = 0.67 Identities = 3/30 (10%), Positives = 7/30 (23%), Gaps = 4/30 (13%) Query: 176 QTLRAHIDYGTAVAETAYG----SCGIKVY 201 + H + A + S + Sbjct: 4 DKIHHHHHHXNAPLSHSRPXXQPSEDKSLA 33 >3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} (A:) Length = 163 Score = 28.0 bits (61), Expect = 1.1 Identities = 8/27 (29%), Positives = 16/27 (59%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKL 91 ++ + + G IIGKKG I+++ + Sbjct: 6 QVFIPAQAVGAIIGKKGQHIKQLSRFA 32 >2gys_A Cytokine receptor common beta chain; dimer of interlocking chains of fibronectin-III domains, four fibronectin-III domains PER chain; HET: NAG FUC BMA NDG; 2.70A {Homo sapiens} (A:1-98) Length = 98 Score = 27.9 bits (62), Expect = 1.3 Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 4/27 (14%) Query: 170 EGRVPLQTLRAHIDYGTAV----AETA 192 E +PLQTLR + DY + + A+T Sbjct: 1 EETIPLQTLRCYNDYTSHITCRWADTQ 27 >2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} (A:) Length = 107 Score = 27.6 bits (61), Expect = 1.6 Identities = 9/45 (20%), Positives = 22/45 (48%), Gaps = 4/45 (8%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKP 109 + + + GL+IG+ G +++ I ++ T + + +S P Sbjct: 10 TFSIPTHKCGLVIGRGGENVKAINQQ----TGAFVEISRQLPPNG 50 >2cxc_A NUSA; transcription termination, RNA binding protein, KH domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix K1} PDB: 2cy1_A (A:1-75) Length = 75 Score = 27.3 bits (61), Expect = 1.7 Identities = 9/55 (16%), Positives = 18/55 (32%), Gaps = 4/55 (7%) Query: 47 LKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHL 101 + + +++ + +V G IG+ G I K L I + Sbjct: 21 ITGVTAYRCIVDEENNRLIFLVSEGEAGRAIGRGGRLI----KLLREALGKNIEV 71 >1wf3_A GTP-binding protein; GTPase, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; HET: GNP; 1.88A {Thermus thermophilus HB8} (A:180-301) Length = 122 Score = 27.3 bits (61), Expect = 1.8 Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 16/54 (29%) Query: 53 AKILIER-THKNCRIIVYSARPGLIIGKKGTDIEKI----RKKLSNMTNSEIHL 101 A + +ER + K ++IG+ G I++I RK+L + +++L Sbjct: 53 AILYVERPSQK-----------AIVIGEGGRKIKEIGQATRKQLEALLGKKVYL 95 >1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} (A:89-174) Length = 86 Score = 27.1 bits (60), Expect = 1.8 Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 4/52 (7%) Query: 58 ERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKP 109 + IV + + GLIIGK G I+ I ++ + + I L N P Sbjct: 12 PGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQ----SGARIELQRNPPPNA 59 >3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome assembly, GTP-binding; HET: GNP; 1.90A {Aquifex aeolicus} (A:191-294) Length = 104 Score = 27.0 bits (60), Expect = 2.2 Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 16/54 (29%) Query: 53 AKILIER-THKNCRIIVYSARPGLIIGKKGTDIEKI----RKKLSNMTNSEIHL 101 +I+++R K +IIGKKG +++I R++L + ++L Sbjct: 52 GEIIVDRENLK-----------PIIIGKKGQRLKEIGKRARQELELILGRPVYL 94 >1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif; 2.00A {Homo sapiens} (A:) Length = 76 Score = 26.3 bits (58), Expect = 3.7 Identities = 10/45 (22%), Positives = 18/45 (40%), Gaps = 4/45 (8%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKP 109 + V G I+GK G + + ++ T + I +S P Sbjct: 6 EMAVPENLVGAILGKGGKTLVEYQEL----TGARIQISKKGEFLP 46 >1b9u_A Protein (ATP synthase); membrane protein; HET: GMA; NMR {Synthetic} (A:) Length = 34 Score = 25.8 bits (57), Expect = 4.7 Identities = 6/11 (54%), Positives = 10/11 (90%) Query: 111 INATLIAQSIA 121 +NAT++ Q+IA Sbjct: 3 LNATILGQAIA 13 >2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Length = 94 Score = 25.9 bits (57), Expect = 4.7 Identities = 9/47 (19%), Positives = 20/47 (42%), Gaps = 4/47 (8%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEI 111 + + +IGK G ++ + K T ++I + + P +I Sbjct: 20 TVAIPKEHHRFVIGKNGEKLQDLELK----TATKIQIPRPDDPSNQI 62 >2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:) Length = 83 Score = 25.9 bits (57), Expect = 5.2 Identities = 10/38 (26%), Positives = 21/38 (55%), Gaps = 4/38 (10%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLS 102 ++ V GL++G KG I++I+++ T++ I Sbjct: 13 QVRVPYRVVGLVVGPKGATIKRIQQR----THTYIVTP 46 >1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} (A:) Length = 71 Score = 25.9 bits (57), Expect = 5.3 Identities = 8/47 (17%), Positives = 16/47 (34%), Gaps = 4/47 (8%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEI 111 I + +IGK G +I +I+ + + + I Sbjct: 8 EINIDHKFHRHLIGKSGANINRIKD----QYKVSVRIPPDSEKSNLI 50 >2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Length = 104 Score = 25.6 bits (56), Expect = 5.3 Identities = 18/102 (17%), Positives = 32/102 (31%), Gaps = 16/102 (15%) Query: 54 KILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEI-- 111 + L + V +IG+KG+ I K+ + IH+ E+ I Sbjct: 9 EALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDE----FEVNIHVPAPELQSDIIAI 64 Query: 112 --------NATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFG 145 A ++L+ R R+ +S G Sbjct: 65 TGLAANLDRAKAGLLERVKELQAEQEDRA--LRSFKSGPSSG 104 >2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I KH domains, fragIle X mental retardation protein, RNA binding protein; 1.90A {Homo sapiens} PDB: 2fmr_A (A:1-64) Length = 64 Score = 25.8 bits (57), Expect = 5.7 Identities = 10/26 (38%), Positives = 14/26 (53%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKK 90 + IV GL IG G +I++ RK Sbjct: 7 QFIVREDLXGLAIGTHGANIQQARKV 32 >1hn0_A Chondroitin ABC lyase I; chondroitinase ABC I, chonroitin digestion, mechanism; 1.90A {Proteus vulgaris} (A:277-434) Length = 158 Score = 25.6 bits (56), Expect = 5.8 Identities = 5/22 (22%), Positives = 7/22 (31%) Query: 23 FARGSEYGALLHEDLKIREYLQ 44 F +GS H R + Sbjct: 102 FVKGSALVTTHHWGYSSRWWYI 123 >2egx_A Putative acetylglutamate kinase; structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.92A {Thermus thermophilus HB8} (A:) Length = 269 Score = 25.3 bits (54), Expect = 6.3 Identities = 15/58 (25%), Positives = 20/58 (34%), Gaps = 2/58 (3%) Query: 107 PKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVK--VIASGRLNGAEL 162 P I + E + + MKR V A+ GVK V A GR+ Sbjct: 201 PDEASLVREIPVERIEDPEYLALAQGRMKRKVMGAVEAVKGGVKRVVFADGRVENPIR 258 >2d9a_A B-MYB, MYB-related protein B; DNA binding, structural genomics, unknown function, NPPSFA; NMR {Mus musculus} (A:) Length = 60 Score = 25.4 bits (56), Expect = 6.6 Identities = 7/33 (21%), Positives = 14/33 (42%), Gaps = 2/33 (6%) Query: 35 EDLKIREYLQCH--LKQAGVAKILIERTHKNCR 65 ED ++R ++ +A RT + C+ Sbjct: 15 EDEQLRALVRQFGQQDWKFLASHFPNRTDQQCQ 47 >2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Length = 95 Score = 25.2 bits (55), Expect = 6.9 Identities = 10/47 (21%), Positives = 16/47 (34%), Gaps = 4/47 (8%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEI 111 + + IIG +G I KI + +I + P P Sbjct: 20 DVPLDHRVHARIIGARGKAIRKIMDE----FKVDIRFPQSGAPDPNC 62 >3gku_A Probable RNA-binding protein; APC21302, structural genomics, PSI-2, protein structure initiative; 2.95A {Clostridium symbiosum atcc 14940} (A:61-140) Length = 80 Score = 25.4 bits (56), Expect = 7.1 Identities = 10/47 (21%), Positives = 18/47 (38%), Gaps = 3/47 (6%) Query: 38 KIREYLQCHLKQAGV---AKILIERTHKNCRIIVYSARPGLIIGKKG 81 K E+L+ + T K + + G++IGK+G Sbjct: 5 KAIEFLEQVFDAXNXAVDISVEYNETEKEXNVNLKGDDXGILIGKRG 51 >2nov_A DNA topoisomerase 4 subunit A; protein, PARC, TOPO IV, GRAM-positive bacteria, quinolone target, DNA binding, DNA cleavage; HET: DNA; 2.67A {Streptococcus pneumoniae} PDB: 3foe_A* 3fof_A* (A:207-341,A:477-496) Length = 155 Score = 25.2 bits (55), Expect = 7.3 Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 8/57 (14%) Query: 48 KQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVN 104 K AG+A++ E RI I KK + E + L T+ +I+ + N Sbjct: 74 KVAGIAEVRDESDRDGLRI--------AIELKKDANTELVLNYLFKYTDLQINYNFN 122 >1d8w_A L-rhamnose isomerase; beta-alpha-8-barrels, aldose-ketose isomerization, hydride shift; 1.60A {Escherichia coli} (A:) Length = 426 Score = 25.2 bits (54), Expect = 7.5 Identities = 6/76 (7%), Positives = 12/76 (15%), Gaps = 5/76 (6%) Query: 125 ERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDY 184 R + K + + + FG L + + Sbjct: 160 SIRQFWIDHCKASRRVSAYFGEQLGTPSVXNIWIPD-----GXKDITVDRLAPRQRLLAA 214 Query: 185 GTAVAETAYGSCGIKV 200 V Sbjct: 215 LDEVISEKLNPAHHID 230 >2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} (A:) Length = 85 Score = 25.2 bits (55), Expect = 7.8 Identities = 9/44 (20%), Positives = 23/44 (52%), Gaps = 4/44 (9%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPK 108 I++ + + GL+IGK G I++++++ ++ L + Sbjct: 17 EIMIPAGKAGLVIGKGGETIKQLQER----AGVKMILIQDGSQN 56 >1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} (A:) Length = 82 Score = 25.2 bits (55), Expect = 7.9 Identities = 10/38 (26%), Positives = 23/38 (60%), Gaps = 4/38 (10%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLS 102 + + + G IIG++G +I +IR+ M+ ++I ++ Sbjct: 9 ELTIPNNLIGCIIGRQGANINEIRQ----MSGAQIKIA 42 >2cxc_A NUSA; transcription termination, RNA binding protein, KH domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix K1} PDB: 2cy1_A (A:76-144) Length = 69 Score = 25.0 bits (55), Expect = 7.9 Identities = 10/53 (18%), Positives = 19/53 (35%), Gaps = 2/53 (3%) Query: 39 IREYLQCHLKQAGVAKILI--ERTHKNCRIIVYSARPGLIIGKKGTDIEKIRK 89 + ++ + I + K I V G IGK G ++++ R Sbjct: 3 LERIVKNLFPGVKIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARL 55 >2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Length = 97 Score = 25.2 bits (55), Expect = 8.0 Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 4/46 (8%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPE 110 + V IIG+KG I +IR + + I + Sbjct: 20 SVTVDPKYHPKIIGRKGAVITQIRLE----HDVNIQFPDKDDGNQP 61 >1gvd_A MYB proto-oncogene protein; transcription, transcription regulation, C-MYB, DNA binding, ION binding, nuclear protein; 1.45A {Mus musculus} (A:) Length = 52 Score = 25.1 bits (55), Expect = 8.5 Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 2/33 (6%) Query: 35 EDLKIREYLQCH--LKQAGVAKILIERTHKNCR 65 ED ++ + +Q + + + +AK L R K CR Sbjct: 10 EDQRLIKLVQKYGPKRWSVIAKHLKGRIGKQCR 42 >2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} (A:1-81) Length = 81 Score = 25.1 bits (55), Expect = 8.6 Identities = 9/44 (20%), Positives = 23/44 (52%), Gaps = 4/44 (9%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPK 108 I++ + + GL+IGK G I++++++ ++ L + Sbjct: 5 EIMIPAGKAGLVIGKGGETIKQLQER----AGVKMILIQDGSQN 44 >2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A (A:1-51) Length = 51 Score = 25.0 bits (55), Expect = 8.9 Identities = 8/33 (24%), Positives = 19/33 (57%), Gaps = 2/33 (6%) Query: 35 EDLKIREYLQCH--LKQAGVAKILIERTHKNCR 65 EDLK+++ + + +++++I R + CR Sbjct: 8 EDLKLQQLVMRYGAKDWIRISQLMITRNPRQCR 40 >1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} (A:) Length = 89 Score = 24.8 bits (54), Expect = 9.5 Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 4/38 (10%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLS 102 ++ + G IIGK G I++IR + + I + Sbjct: 17 QVTIPKDLAGSIIGKGGQRIKQIRH----ESGASIKID 50 >1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} (P:277-344) Length = 68 Score = 25.0 bits (55), Expect = 9.6 Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 1/52 (1%) Query: 39 IREYLQCHLKQAGVAKILI-ERTHKNCRIIVYSARPGLIIGKKGTDIEKIRK 89 ++ + L A V ++ I ++ +K R++V + L IGK G + K Sbjct: 3 PKQLIANALAPATVIEVEILDKENKAARVLVPPTQLSLAIGKGGQNARLAAK 54 >1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} (A:) Length = 82 Score = 24.8 bits (54), Expect = 9.6 Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 4/38 (10%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLS 102 ++ + G IIGK G I++IR + + I + Sbjct: 10 QVTIPKDLAGSIIGKGGQRIKQIRH----ESGASIKID 43 >1guu_A C-MYB, MYB proto-oncogene protein; transcription, transcription regulation, DNA binding, ION bindi proto-oncogene, nuclear protein, activator; 1.6A {Mus musculus} (A:) Length = 52 Score = 24.7 bits (54), Expect = 9.9 Identities = 8/33 (24%), Positives = 16/33 (48%), Gaps = 2/33 (6%) Query: 35 EDLKIREYLQCH--LKQAGVAKILIERTHKNCR 65 ED K+++ ++ + +A L RT C+ Sbjct: 10 EDEKLKKLVEQNGTDDWKVIANYLPNRTDVQCQ 42 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.320 0.134 0.387 Gapped Lambda K H 0.267 0.0664 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 1,698,725 Number of extensions: 73591 Number of successful extensions: 287 Number of sequences better than 10.0: 1 Number of HSP's gapped: 277 Number of HSP's successfully gapped: 78 Length of query: 227 Length of database: 4,956,049 Length adjustment: 85 Effective length of query: 142 Effective length of database: 2,082,624 Effective search space: 295732608 Effective search space used: 295732608 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (24.3 bits)