RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780470|ref|YP_003064883.1| translation initiation factor IF-1 [Candidatus Liberibacter asiaticus str. psy62] (110 letters) >1hr0_W Translation initiation factor; ribosomal subunit, ribosome, IF1; 3.20A {Escherichia coli} (W:) Length = 71 Score = 83.9 bits (208), Expect = 8e-18 Identities = 36/107 (33%), Positives = 49/107 (45%), Gaps = 40/107 (37%) Query: 3 KEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPI 62 +++T+ G+V+E LPNA FRVKL Sbjct: 3 EKDTIRTEGVVTEALPNATFRVKL------------------------------------ 26 Query: 63 SYLDN-AVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR 108 D+ ++AY +G+MR H IRI GD+V V + PYD TR RI YR Sbjct: 27 ---DSGPEILAYISGKMRMHYIRILPGDRVVVEITPYDPTRGRIVYR 70 >1ah9_A IF1, initiation factor 1; ribosome binding, protein-RNA interaction, OB fold; NMR {Escherichia coli} (A:) Length = 71 Score = 81.2 bits (201), Expect = 4e-17 Identities = 34/108 (31%), Positives = 48/108 (44%), Gaps = 38/108 (35%) Query: 3 KEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPI 62 KE+ +E G V E LPN FRV+L Sbjct: 2 KEDNIEMQGTVLETLPNTMFRVEL------------------------------------ 25 Query: 63 SYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110 + VV A+ +G+MRK+ IRI GDKV V + PYD+++ RI +R + Sbjct: 26 --ENGHVVTAHISGKMRKNYIRILTGDKVTVELTPYDLSKGRIVFRSR 71 >3i4o_A Translation initiation factor IF-1; cytoplasm, protein biosynthesis; 1.47A {Mycobacterium tuberculosis} (A:) Length = 79 Score = 79.7 bits (197), Expect = 1e-16 Identities = 34/111 (30%), Positives = 51/111 (45%), Gaps = 39/111 (35%) Query: 1 MPKEE-TLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGV 59 M K++ +E G V E LPNA FR++L Sbjct: 7 MAKKDGAIEVEGRVVEPLPNAMFRIEL--------------------------------- 33 Query: 60 DPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110 + V+A+ +G+MR+H IRI D+V V ++PYD++R RI YR+K Sbjct: 34 -----ENGHKVLAHISGKMRQHYIRILPEDRVVVELSPYDLSRGRIVYRYK 79 >1jt8_A EIF-1A, probable translation initiation factor 1A; beta barrel, translation factor; NMR {Methanocaldococcus jannaschii} (A:) Length = 102 Score = 56.7 bits (137), Expect = 1e-09 Identities = 20/111 (18%), Positives = 35/111 (31%), Gaps = 40/111 (36%) Query: 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60 +P++E E GI+ ++L + RV+ Sbjct: 14 IPRKEENEILGIIEQMLGASRVRVRC---------------------------------- 39 Query: 61 PISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDM-TRARITYRFK 110 LD + GR++ RI + GD V V + I +R+ Sbjct: 40 ----LDGKTRLGRIPGRLKN-RIWVREGDVVIVKPWEVQGDQKCDIIWRYT 85 >1d7q_A Translation initiation factor 1A; OB-fold, beta-barrel, RNA-binding protein; NMR {Homo sapiens} (A:) Length = 143 Score = 56.8 bits (137), Expect = 1e-09 Identities = 13/110 (11%), Positives = 31/110 (28%), Gaps = 39/110 (35%) Query: 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60 + +E + V ++L N Sbjct: 25 LVFKEDGQEYAQVIKMLGNGRLEAMCF--------------------------------- 51 Query: 61 PISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110 D + + G++RK ++ I+ D + V + Y +A + ++ Sbjct: 52 -----DGVKRLCHIRGKLRK-KVWINTSDIILVGLRDYQDNKADVILKYN 95 >2oqk_A Putative translation initiation factor EIF-1A; malaria, eukaryotic initiation factor (EIF), SGC, structural genomics; 1.80A {Cryptosporidium parvum iowa II} (A:) Length = 117 Score = 56.3 bits (136), Expect = 1e-09 Identities = 14/110 (12%), Positives = 31/110 (28%), Gaps = 39/110 (35%) Query: 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60 + +E + G V L N Sbjct: 26 LVFKEEGQEYGQVQRXLGNGRLDAYCF--------------------------------- 52 Query: 61 PISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110 D + + G+ RK ++ ++ GD V V++ + ++ I ++ Sbjct: 53 -----DGQKRLCHIRGKXRK-KVWVNPGDIVLVSLRDFQDSKGDIILKYT 96 >1n6u_A Interferon-alpha/beta receptor beta chain; immunoglobulin fold, fibronectin fold, two-domain structure, immune system; NMR {Homo sapiens} (A:106-212) Length = 107 Score = 27.5 bits (61), Expect = 0.64 Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 2/55 (3%) Query: 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESG 55 + + F+ I+ +L+PN N+ V + D A K S +K G ES Sbjct: 53 IKGNMSGNFTYIIDKLIPNTNYCVSVYLEHSDEQAVIK--SPLKCTLLPPGQESE 105 >2z1d_A Hydrogenase expression/formation protein HYPD; [NIFE] hydrogenase maturation, [4Fe-4S] cluster, thiol redox; HET: CSW; 2.07A {Thermococcus kodakarensis KOD1} (A:69-192,A:261-346) Length = 210 Score = 27.0 bits (60), Expect = 0.99 Identities = 7/35 (20%), Positives = 14/35 (40%) Query: 59 VDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKV 93 + P+ + +I A + I + GD K+ Sbjct: 2 ITPVEDIVAMQLIMRKAREEGEEIILTTFGDMYKI 36 >3eno_A Putative O-sialoglycoprotein endopeptidase; hydrolase, metal-binding, metalloprotease, protease, zinc, keops complex, ATPase, metal ION binding; 3.02A {Thermoplasma acidophilum} (A:1-126,A:288-334) Length = 173 Score = 26.9 bits (59), Expect = 1.1 Identities = 9/24 (37%), Positives = 15/24 (62%) Query: 66 DNAVVIAYTAGRMRKHRIRISLGD 89 DN ++IA A M K +R+S+ + Sbjct: 129 DNGIMIAQAALLMYKSGVRMSVEE 152 >2ivn_A O-sialoglycoprotein endopeptidase; UP1 keops complex, Fe/Zn dependent nucleotide phosphatase, metalloprotease, hypothetical protein, zinc; HET: ANP; 1.65A {Pyrococcus abyssi} PDB: 2ivo_A 2ivp_A* (A:1-118,A:283-330) Length = 166 Score = 26.5 bits (58), Expect = 1.2 Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 4/44 (9%) Query: 66 DNAVVIAYTAGRMRKHRIRISLGDKVKVAMNP-YDMTRARITYR 108 DN +IAYT RM K I L + + + I + Sbjct: 121 DNGAMIAYTGLRMYKAGISFRLEE---TIVKQKFRTDEVEIVWH 161 >3en9_A Glycoprotease, O-sialoglycoprotein endopeptidase/protein kinase; endopeptidase activity, protein kinase activity; HET: TBR; 2.67A {Methanocaldococcus jannaschii} PDB: 3enh_A* 2vwb_A* (A:1-125,A:287-326) Length = 165 Score = 26.4 bits (58), Expect = 1.4 Identities = 8/24 (33%), Positives = 13/24 (54%) Query: 66 DNAVVIAYTAGRMRKHRIRISLGD 89 DN +IA+ M K+ +SL + Sbjct: 128 DNGAMIAWLGLLMHKNGRWMSLDE 151 >1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ ATPase, DNA polymerase; HET: ATG ADP; 2.85A {Saccharomyces cerevisiae} (A:395-516) Length = 122 Score = 26.3 bits (58), Expect = 1.7 Identities = 8/35 (22%), Positives = 15/35 (42%), Gaps = 4/35 (11%) Query: 30 DDDSSADCKLDSKVKSNFSESGSESGNDGVDPISY 64 D ++ K+ + VKS F + N P++ Sbjct: 90 DVTTAIIKKIPATVKSGF----TRKYNSMTHPVAI 120 >2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae} (B:81-218) Length = 138 Score = 25.3 bits (55), Expect = 2.7 Identities = 5/58 (8%), Positives = 17/58 (29%), Gaps = 5/58 (8%) Query: 53 ESGNDGVDPISYLDNAVV-----IAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARI 105 +D P + L A+ + ++ + +K++ + + Sbjct: 23 GIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFVDVKP 80 >3csq_A Morphogenesis protein 1; hydrolase, infection, late protein; 1.80A {Bacteriophage phi-29} (A:166-334) Length = 169 Score = 25.5 bits (55), Expect = 2.8 Identities = 6/70 (8%), Positives = 15/70 (21%), Gaps = 3/70 (4%) Query: 41 SKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGR---MRKHRIRISLGDKVKVAMNP 97 + + S S G +D + + A ++ +V Sbjct: 11 INISQGENGSFSHKGTLCIDFVGKTEKYPYYAPCDCTCVWRGDASAYLAWTSDKEVMCAD 70 Query: 98 YDMTRARITY 107 + Sbjct: 71 GSVRYITWVN 80 >1gji_A C-REL protein, C-REL proto-oncogene protein; NF-KB/DNA complex, transcription factor, C-REL homodimer, transcription/DNA complex; 2.85A {Gallus gallus} (A:1-175) Length = 175 Score = 25.2 bits (55), Expect = 3.4 Identities = 13/99 (13%), Positives = 32/99 (32%), Gaps = 10/99 (10%) Query: 18 PNANFRVKLITNDDD--------SSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAV 69 R L+T ++ DC+ E S + I + Sbjct: 50 GKVKIRTTLVTKNEPYKPHPHDLVGKDCRDGYYEAEFGPERRVLSFQN--LGIQCVKKKD 107 Query: 70 VIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR 108 + + R+ K ++ ++ ++ YD+ R+ ++ Sbjct: 108 LKESISLRISKKINPFNVPEEQLHNIDEYDLNVVRLCFQ 146 >1foe_A T-lymphoma invasion and metastasis inducing protein 1; DBL homology domain, pleckstrin homology domain, GTPase, guanine nucleotide exchange factor; 2.80A {Mus musculus} (A:212-377) Length = 166 Score = 24.8 bits (54), Expect = 4.7 Identities = 8/28 (28%), Positives = 10/28 (35%) Query: 37 CKLDSKVKSNFSESGSESGNDGVDPISY 64 K SK K S S + DP + Sbjct: 64 YKDGSKQKKKLVGSHRLSIYEEWDPFRF 91 >2qhr_L 13F6-1-2 FAB fragment V lambda X light chain; immunologlobulin fold, antibody-peptide complex, immune system/viral protein complex; 2.00A {Mus musculus} PDB: 3ffd_B (L:1-118) Length = 118 Score = 24.2 bits (53), Expect = 6.7 Identities = 4/25 (16%), Positives = 6/25 (24%) Query: 32 DSSADCKLDSKVKSNFSESGSESGN 56 + FS S S + Sbjct: 51 KKDGSHSTGDGIPDRFSGSSSGADR 75 >1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} (A:1-75) Length = 75 Score = 23.9 bits (52), Expect = 7.1 Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 2/48 (4%) Query: 59 VDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARIT 106 V S + V+ G RK++I +GD V + + Sbjct: 25 VLDESEDSDKVIQCRGRGIFRKNKITPLVGDYVVY--QAENDKEGYLM 70 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 0.315 0.132 0.365 Gapped Lambda K H 0.267 0.0714 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 784,950 Number of extensions: 30103 Number of successful extensions: 105 Number of sequences better than 10.0: 1 Number of HSP's gapped: 101 Number of HSP's successfully gapped: 35 Length of query: 110 Length of database: 4,956,049 Length adjustment: 65 Effective length of query: 45 Effective length of database: 2,758,724 Effective search space: 124142580 Effective search space used: 124142580 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 (21.5 bits) S2: 50 (23.1 bits)