RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781067|ref|YP_003065480.1| elongation factor P [Candidatus Liberibacter asiaticus str. psy62] (189 letters) >gnl|CDD|179058 PRK00529, PRK00529, elongation factor P; Validated. Length = 186 Score = 246 bits (630), Expect = 3e-66 Identities = 70/186 (37%), Positives = 109/186 (58%) Query: 3 KVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQV 62 + A+ +RKG V+++DG+ Y+VL ++ PGKG + +++ + G V ++ ++V Sbjct: 1 MISANDLRKGLVIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLLTGSVVEKTFKAGDKV 60 Query: 63 ERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVA 122 ERA VE + Q+LY D +G+ FM+ ETY+Q+ V + +GD + +EGMEV ++ + G Sbjct: 61 ERADVERREMQYLYNDGDGYVFMDTETYEQIEVPADQVGDAAKFLKEGMEVTVVFYNGEP 120 Query: 123 LSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNS 182 +SVE+P V V +TEP KG T + KPA L VP IN G+ I + T Sbjct: 121 ISVELPNFVELEVTETEPGVKGDTASGGTKPATLETGAVVQVPLFINEGEKIKVDTRTGE 180 Query: 183 YVERVK 188 YVER K Sbjct: 181 YVERAK 186 >gnl|CDD|161673 TIGR00038, efp, translation elongation factor P. function: involved in peptide bond synthesis. stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity). The trusted cutoff of this model is set high enough to exclude members of TIGR02178, an EFP-like protein of certain Gammaproteobacteria. Length = 184 Score = 219 bits (560), Expect = 5e-58 Identities = 65/182 (35%), Positives = 108/182 (59%) Query: 6 ASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVERA 65 A+ +RKG V+++DG+ Y+VL ++ PGKG +V+++ + G + +R+ E+VE+A Sbjct: 3 ANDLRKGLVIELDGEPYVVLEFEHVKPGKGQAFVRVKLKNLLTGKVLEKTFRSGEKVEKA 62 Query: 66 FVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSV 125 VE++ Q+LY+D + + FM+ ETY+Q+ + ++++GD + +E MEV + + G + V Sbjct: 63 DVEEREMQYLYKDGDSYVFMDTETYEQIELPKDLLGDAAKFLKENMEVSVTFYNGEPIGV 122 Query: 126 EVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVE 185 E+P V V +TEP KG T + KPA L VP I G+ I + T YVE Sbjct: 123 ELPNFVELEVTETEPGVKGDTASGGTKPATLETGAVVQVPLFIEEGEKIKVDTRTGEYVE 182 Query: 186 RV 187 R Sbjct: 183 RA 184 >gnl|CDD|179863 PRK04542, PRK04542, elongation factor P; Provisional. Length = 189 Score = 105 bits (264), Expect = 8e-24 Identities = 52/184 (28%), Positives = 100/184 (54%), Gaps = 3/184 (1%) Query: 6 ASAVRKGNVLDVDGKLYIVLVAKNFHPGK--GTPITQVEMRRISDGVKVSNRWRTTEQVE 63 A+ ++KG V++ +GKL +V P G + ++ + G+KV R++ + ++ Sbjct: 4 ANEIKKGMVVEYNGKLLLVKDIDRQSPSGRGGATLYKMRFYDVRTGLKVEERFKGDDILD 63 Query: 64 RAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGME-VKLLIHEGVA 122 + + F Y D + + FM+ E Y T ++ I D+ ++ EGM +++L +G Sbjct: 64 TVDLTRRPVTFSYIDGDEYVFMDNEDYTPYTFKKDQIEDELLFIPEGMPGMQVLTVDGQP 123 Query: 123 LSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNS 182 +++E+P+ V +++T PS KG + +A KPA LS + VP +I+ G+ I I TE+ Sbjct: 124 VALELPQTVDLEIVETAPSIKGASASARTKPATLSTGLVIQVPEYISTGEKIRINTEERK 183 Query: 183 YVER 186 ++ R Sbjct: 184 FMGR 187 >gnl|CDD|183522 PRK12426, PRK12426, elongation factor P; Provisional. Length = 185 Score = 98.4 bits (245), Expect = 9e-22 Identities = 45/184 (24%), Positives = 91/184 (49%) Query: 4 VIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVE 63 V++S + G + LY V+ KG +V ++ V V ++ ++V+ Sbjct: 2 VLSSQLSVGMFISTKDGLYKVVSVSKVTGPKGETFIKVSLQAADSDVVVERNFKAGQEVK 61 Query: 64 RAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVAL 123 A E + ++LY + + + F++ YD++ + +E++ D ++ + G+ V L+++G Sbjct: 62 EAQFEPRNLEYLYLEGDEYLFLDLGNYDKIYIPKEIMKDNFLFLKAGVTVSALVYDGTVF 121 Query: 124 SVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSY 183 SVE+P + V T+ +++ K A+L + VPP + IGD I + T Y Sbjct: 122 SVELPHFLELMVSKTDFPGDSLSLSGGAKKALLETGVEVLVPPFVEIGDVIKVDTRTCEY 181 Query: 184 VERV 187 ++RV Sbjct: 182 IQRV 185 >gnl|CDD|131233 TIGR02178, yeiP, elongation factor P-like protein YeiP. This model represents the family of Escherichia coli protein YeiP, a close homolog of elongation factor P (TIGR00038) and probably itself a translation factor. Member of this family are found only in some Gammaproteobacteria, including E. coli and Vibrio cholerae. Length = 186 Score = 96.1 bits (239), Expect = 5e-21 Identities = 48/184 (26%), Positives = 98/184 (53%), Gaps = 3/184 (1%) Query: 6 ASAVRKGNVLDVDGKLYIVLVAKNFHPGK--GTPITQVEMRRISDGVKVSNRWRTTEQVE 63 AS ++KG++++ +GK ++ + P G + M + G KV R++ + ++ Sbjct: 2 ASEMKKGSIVEYNGKTLLIKDIQRSSPQGRGGNVRYKFRMYDVPTGSKVEERFKADDMLD 61 Query: 64 RAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGME-VKLLIHEGVA 122 + + F Y+D E + FM+ E Y T ++ I D+ ++ EG+ + + + +G Sbjct: 62 TVELLRREASFSYKDGEEYVFMDEEDYTPYTFDKDAIEDELLFISEGLSGMYVQLIDGSP 121 Query: 123 LSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNS 182 +++E+P+HVV +++T P KG + + KPA L + VP +I G+ I+I T + + Sbjct: 122 VALELPQHVVLEIVETPPEIKGASASKRPKPAKLITGLVVQVPEYITTGERILINTTERA 181 Query: 183 YVER 186 ++ R Sbjct: 182 FMGR 185 >gnl|CDD|173042 PRK14578, PRK14578, elongation factor P; Provisional. Length = 187 Score = 93.7 bits (233), Expect = 2e-20 Identities = 56/182 (30%), Positives = 93/182 (51%), Gaps = 2/182 (1%) Query: 7 SAVRKGNVLDVDGKLYIVLVAKNFHPGK--GTPITQVEMRRISDGVKVSNRWRTTEQVER 64 S +KG V+ +DG ++L P + + + R + G + +R+ ++VE Sbjct: 5 SDFKKGLVIQLDGAPCLLLDVTFQSPSARGANTMVKTKYRNLLTGQVLEKTFRSGDKVEE 64 Query: 65 AFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALS 124 A E + QFLY D + FM+ ETY+Q + E+ + +G EV+L + +G ++ Sbjct: 65 ADFERHKGQFLYADGDRGVFMDLETYEQFEMEEDAFSAIAPFLLDGTEVQLGLFQGRMVN 124 Query: 125 VEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYV 184 V++P V TV DT P K T TA K A+L +R VPP++ G+ I + T D ++ Sbjct: 125 VDLPMTVELTVTDTAPVMKNATATAQTKEAVLETGLRLQVPPYLESGEKIKVDTRDGRFI 184 Query: 185 ER 186 R Sbjct: 185 SR 186 >gnl|CDD|150075 pfam09285, Elong-fact-P_C, Elongation factor P, C-terminal. Members of this family of nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology. Length = 56 Score = 75.6 bits (187), Expect = 7e-15 Identities = 21/56 (37%), Positives = 27/56 (48%) Query: 131 VVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVER 186 V V++TEP KG T ++ KPA L VP I G+ I + T YV R Sbjct: 1 VELEVVETEPGVKGDTASSGTKPATLETGAEVQVPLFIEEGEKIKVDTRTGEYVSR 56 >gnl|CDD|129074 smart00841, Elong-fact-P_C, Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970. Length = 56 Score = 74.8 bits (185), Expect = 1e-14 Identities = 23/56 (41%), Positives = 26/56 (46%) Query: 131 VVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVER 186 V V +TEP KG T + KPA L VP IN GD I + T YV R Sbjct: 1 VELEVTETEPGVKGDTASGGTKPATLETGAVVQVPLFINEGDKIKVDTRTGEYVSR 56 >gnl|CDD|149330 pfam08207, EFP_N, Elongation factor P (EF-P) KOW-like domain. Length = 58 Score = 60.5 bits (148), Expect = 3e-10 Identities = 18/57 (31%), Positives = 37/57 (64%) Query: 6 ASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQV 62 AS ++KG V+++DG+ Y+VL ++ PGKG + +++ + G KV +++ ++V Sbjct: 2 ASDLKKGLVIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLRTGAKVEKTFKSGDKV 58 >gnl|CDD|129148 TIGR00037, eIF_5A, translation initiation factor eIF-5A. Observed in eukaryotes and archaea. Length = 130 Score = 31.3 bits (71), Expect = 0.14 Identities = 31/113 (27%), Positives = 53/113 (46%), Gaps = 7/113 (6%) Query: 7 SAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTEQVERA 65 SA+R G + +DG+ ++ PGK G +V I G K+ +T +VE Sbjct: 10 SALRVGGYVVIDGRPCKIVDISTSKPGKHGHAKARVVAIGIFTGKKLEFVSPSTSKVEVP 69 Query: 66 FVEDQRFQFLYQDQEGFHFMNPETY--DQVTVSEEVIGDQKVYFQEGMEVKLL 116 V+ + +Q L M+ +TY D++ + EE +GD + G EV+ + Sbjct: 70 IVDRREYQVLAIMGGMVQLMDLDTYETDELPIPEE-LGDS---LEPGFEVEYI 118 >gnl|CDD|181436 PRK08462, PRK08462, biotin carboxylase; Validated. Length = 445 Score = 28.9 bits (65), Expect = 0.85 Identities = 15/32 (46%), Positives = 17/32 (53%), Gaps = 2/32 (6%) Query: 72 FQFLYQDQEGFHFMNPETYDQV--TVSEEVIG 101 F+FL F+FM T QV TVSE V G Sbjct: 276 FEFLLDSNLDFYFMEMNTRLQVEHTVSEMVSG 307 >gnl|CDD|184330 PRK13794, PRK13794, hypothetical protein; Provisional. Length = 479 Score = 28.5 bits (64), Expect = 1.1 Identities = 23/99 (23%), Positives = 34/99 (34%), Gaps = 20/99 (20%) Query: 96 SEEVIGDQKV----YFQEGM---EVKLLIHEGVALSVEVPRHVVFTVIDTEPSS---KGQ 145 EE+I D V + E ++ EG + + V D P KG Sbjct: 84 MEEIIVDGAVVGIIRYNEKKHRWKIIPRP-EGARRLIPTAKKKFIVVKDDVPKFIRNKGA 142 Query: 146 TVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYV 184 +V P + I GDD++IL E+ V Sbjct: 143 SVLR---PGVAE------ASEDIEEGDDVIILDENGDVV 172 >gnl|CDD|180406 PRK06111, PRK06111, acetyl-CoA carboxylase biotin carboxylase subunit; Validated. Length = 450 Score = 28.5 bits (64), Expect = 1.2 Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 11/64 (17%) Query: 72 FQFLYQDQEGFHFMNPETYDQVT--VSEEVIGDQKVYFQEGMEVKLLIHEGVALSV---E 126 +FL +Q+ F+F+ T QV V+EE+ G V E +L I G LS + Sbjct: 274 IEFLVDEQKNFYFLEMNTRLQVEHPVTEEITGIDLV------EQQLRIAAGEKLSFTQDD 327 Query: 127 VPRH 130 + R Sbjct: 328 IKRS 331 >gnl|CDD|102207 PRK06145, PRK06145, acyl-CoA synthetase; Validated. Length = 497 Score = 28.3 bits (63), Expect = 1.3 Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 2/52 (3%) Query: 56 WRTTEQVERAFVED--QRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKV 105 W+ E+ AF D + Y D+EGF ++ D + E I +V Sbjct: 360 WKDPEKTAEAFYGDWFRSGDVGYLDEEGFLYLTDRKKDMIISGGENIASSEV 411 >gnl|CDD|129605 TIGR00514, accC, acetyl-CoA carboxylase, biotin carboxylase subunit. This model represents the biotin carboxylase subunit found usually as a component of acetyl-CoA carboxylase. Acetyl-CoA carboxylase is designated EC 6.4.1.2 and this component, biotin carboxylase, has its own designation, EC 6.3.4.14. Homologous domains are found in eukaryotic forms of acetyl-CoA carboxylase and in a number of other carboxylases (e.g. pyruvate carboxylase), but seed members and trusted cutoff are selected so as to exclude these. In some systems, the biotin carboxyl carrier protein and this protein (biotin carboxylase) may be shared by different carboxyltransferases. However, this model is not intended to identify the biotin carboxylase domain of propionyl-coA carboxylase. The model should hit the full length of proteins, except for chloroplast transit peptides in plants. If it hits a domain only of a longer protein, there may be a problem with the identification. Length = 449 Score = 27.8 bits (62), Expect = 1.8 Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 2/32 (6%) Query: 72 FQFLYQDQEGFHFMNPETYDQV--TVSEEVIG 101 +FL F+FM T QV V+E + G Sbjct: 274 VEFLLDKNGEFYFMEMNTRIQVEHPVTEMITG 305 >gnl|CDD|181492 PRK08591, PRK08591, acetyl-CoA carboxylase biotin carboxylase subunit; Validated. Length = 451 Score = 27.1 bits (61), Expect = 2.7 Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 2/32 (6%) Query: 72 FQFLYQDQEGFHFMNPETYDQV--TVSEEVIG 101 +FLY+ F+F+ T QV V+E + G Sbjct: 274 IEFLYEKNGEFYFIEMNTRIQVEHPVTEMITG 305 >gnl|CDD|185215 PRK15315, PRK15315, outer membrane protein RatA; Provisional. Length = 1865 Score = 26.9 bits (59), Expect = 2.9 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 10/73 (13%) Query: 78 DQEGFHFMNPETYDQVTVSEEVIGDQKVYFQE----GME--VKLLIHEGVALSVEVPRHV 131 D EG +PE Y VT +V G + + G+E +++++ + +VE+P V Sbjct: 533 DSEGMSASSPEHYTGVT---DVNGQAHLTLKHNSGLGVETPIRIVMPDDEGGNVELPFSV 589 Query: 132 VFTVIDTEPSSKG 144 +FTV+ T P G Sbjct: 590 IFTVV-TSPDVDG 601 >gnl|CDD|132676 TIGR03637, cas1_YPEST, CRISPR-associated endonuclease Cas1, YPEST subtype. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 protein particular to the YPEST subtype of CRISPR/Cas system. Length = 307 Score = 25.9 bits (57), Expect = 6.7 Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 1/21 (4%) Query: 33 GKGTPITQVEMRRISD-GVKV 52 G GT ITQ MR ++ GV V Sbjct: 50 GTGTSITQAAMRELAKAGVMV 70 >gnl|CDD|178660 PLN03113, PLN03113, DNA ligase 1; Provisional. Length = 744 Score = 25.7 bits (56), Expect = 8.1 Identities = 10/25 (40%), Positives = 16/25 (64%) Query: 144 GQTVTASYKPAILSNDIRTTVPPHI 168 GQT+ A+ A + N+ +T PP+I Sbjct: 298 GQTLLAALGQAAVYNEEHSTPPPNI 322 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.318 0.135 0.381 Gapped Lambda K H 0.267 0.0649 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,056,477 Number of extensions: 186333 Number of successful extensions: 380 Number of sequences better than 10.0: 1 Number of HSP's gapped: 376 Number of HSP's successfully gapped: 32 Length of query: 189 Length of database: 5,994,473 Length adjustment: 88 Effective length of query: 101 Effective length of database: 4,092,969 Effective search space: 413389869 Effective search space used: 413389869 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 (21.7 bits) S2: 54 (24.7 bits)