RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780470|ref|YP_003064883.1| translation initiation factor IF-1 [Candidatus Liberibacter asiaticus str. psy62] (110 letters) >gnl|CDD|178954 PRK00276, infA, translation initiation factor IF-1; Validated. Length = 72 Score = 105 bits (264), Expect = 3e-24 Identities = 42/110 (38%), Positives = 55/110 (50%), Gaps = 38/110 (34%) Query: 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60 M KE+ +E G V E LPNA FRV+L E+G E Sbjct: 1 MAKEDVIEMEGTVVEALPNAMFRVEL----------------------ENGHE------- 31 Query: 61 PISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110 V+A+ +G+MRK+ IRI GDKV V ++PYD+T+ RITYR K Sbjct: 32 ---------VLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITYRHK 72 >gnl|CDD|183529 PRK12442, PRK12442, translation initiation factor IF-1; Reviewed. Length = 87 Score = 81.8 bits (202), Expect = 3e-17 Identities = 41/110 (37%), Positives = 54/110 (49%), Gaps = 38/110 (34%) Query: 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60 M KEE +E GIV E+LP++ FRV L E+G Sbjct: 1 MAKEELIELDGIVDEVLPDSRFRVTL--------------------------ENG----- 29 Query: 61 PISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110 V AY +GRMRKHRIRI GD+V + ++PYD+T+ RI +R K Sbjct: 30 -------VEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFRHK 72 >gnl|CDD|129120 TIGR00008, infA, translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575). Length = 68 Score = 73.9 bits (182), Expect = 8e-15 Identities = 39/106 (36%), Positives = 51/106 (48%), Gaps = 38/106 (35%) Query: 3 KEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPI 62 KE+ +E G V+E LPNA FRV+L N Sbjct: 1 KEDKIEMEGKVTESLPNAMFRVEL-ENGH------------------------------- 28 Query: 63 SYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR 108 V+A+ +G++R H IRI GDKVKV ++PYD+TR RITYR Sbjct: 29 ------EVLAHISGKIRMHYIRILPGDKVKVELSPYDLTRGRITYR 68 >gnl|CDD|163434 TIGR03722, arch_KAE1, universal archaeal protein Kae1. This family represents the archaeal protein Kae1. Its partner Bud32 is fused with it in about half of the known archaeal genomes. The pair, which appears universal in the archaea, corresponds to EKC/KEOPS complex in eukaryotes. A recent characterization of the member from Pyrococcus abyssi, as an iron-binding, atypical DNA-binding protein with an apurinic lyase activity, challenges the common annotation of close homologs as O-sialoglycoprotein endopeptidase. The latter annotation is based on a characterized protein from the bacterium Pasteurella haemolytica. Length = 322 Score = 30.3 bits (69), Expect = 0.10 Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%) Query: 61 PISYL-DNAVVIAYTAGRMRKHRIRISLGD 89 P Y DN +IAYT M KH + I + + Sbjct: 277 PPEYAGDNGAMIAYTGLLMYKHGVTIPVEE 306 >gnl|CDD|181985 PRK09605, PRK09605, bifunctional UGMP family protein/serine/threonine protein kinase; Validated. Length = 535 Score = 29.1 bits (66), Expect = 0.28 Identities = 7/24 (29%), Positives = 11/24 (45%) Query: 66 DNAVVIAYTAGRMRKHRIRISLGD 89 DN +IA+ M K + + D Sbjct: 286 DNGAMIAWLGLLMYKAGDTLDIED 309 >gnl|CDD|184878 PRK14878, PRK14878, UGMP family protein; Provisional. Length = 323 Score = 28.7 bits (65), Expect = 0.35 Identities = 9/24 (37%), Positives = 12/24 (50%) Query: 66 DNAVVIAYTAGRMRKHRIRISLGD 89 DN +IAYT KH + I + Sbjct: 282 DNGAMIAYTGLLAYKHGVTIPPEE 305 >gnl|CDD|180392 PRK06084, PRK06084, O-acetylhomoserine aminocarboxypropyltransferase; Validated. Length = 425 Score = 26.0 bits (57), Expect = 2.2 Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 1/46 (2%) Query: 12 IVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSES-GSESGN 56 +++ LP + +DD ++ + +D + K+ F ES G+ +GN Sbjct: 113 LLAHTLPRIGIETRFAAHDDIAALEALIDERTKAVFCESIGNPAGN 158 >gnl|CDD|162066 TIGR00845, caca, sodium/calcium exchanger 1. This model is specific for the eukaryotic sodium ion/calcium ion exchangers of the Caca family. Length = 928 Score = 25.9 bits (57), Expect = 2.3 Identities = 8/26 (30%), Positives = 14/26 (53%) Query: 4 EETLEFSGIVSELLPNANFRVKLITN 29 EE+ EF V +L+ N + + T+ Sbjct: 672 EESYEFKSTVDKLIKKTNLALVVGTH 697 >gnl|CDD|179708 PRK04012, PRK04012, translation initiation factor IF-1A; Provisional. Length = 100 Score = 25.3 bits (56), Expect = 3.2 Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 1/34 (2%) Query: 76 GRMRKHRIRISLGDKVKVAMNPYDMTRARITYRF 109 G+M+K R+ I GD V VA + +A I +R+ Sbjct: 52 GKMKK-RMWIREGDVVIVAPWDFQDEKADIIWRY 84 >gnl|CDD|181528 PRK08661, PRK08661, prolyl-tRNA synthetase; Provisional. Length = 477 Score = 25.5 bits (57), Expect = 3.4 Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 3/31 (9%) Query: 3 KEETLEFSGIVSELLPNANFRVKLITNDDDS 33 KEE LE++ ++E L A RVKL DD S Sbjct: 302 KEEVLEYAKELAEELKKAGIRVKL---DDRS 329 >gnl|CDD|182796 PRK10871, nlpD, lipoprotein NlpD; Provisional. Length = 319 Score = 25.2 bits (55), Expect = 4.1 Identities = 17/38 (44%), Positives = 20/38 (52%), Gaps = 3/38 (7%) Query: 40 DSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGR 77 D KV NFS SE GN G+D I+ +IA GR Sbjct: 205 DGKVIENFS--ASEGGNKGID-IAGSKGQAIIATADGR 239 >gnl|CDD|162469 TIGR01657, P-ATPase-V, P-type ATPase of unknown pump specificity (type V). These P-type ATPases form a distinct clade but the substrate of their pumping activity has yet to be determined. This clade has been designated type V in. Length = 1054 Score = 25.0 bits (55), Expect = 4.6 Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 17/97 (17%) Query: 3 KEETLEFSGIVSELLPNANFRVKLITNDDDSSA-----DCKLDSK----VKSNFSESGSE 53 K +T E V + L A+ R +IT D+ +A +C + + + + S Sbjct: 658 KPDTKE----VIKELKRASIRTVMITGDNPLTAVHVARECGIVNPSNTLILAEAEPPESG 713 Query: 54 SGN----DGVDPISYLDNAVVIAYTAGRMRKHRIRIS 86 N + +D I + V I Y G+ + S Sbjct: 714 KPNQIKFEVIDSIPFASTQVEIPYPLGQDSVEDLLAS 750 >gnl|CDD|162275 TIGR01263, 4HPPD, 4-hydroxyphenylpyruvate dioxygenase. This protein oxidizes 4-hydroxyphenylpyruvate, a tyrosine and phenylalanine catabolite, to homogentisate. Homogentisate can undergo a further non-enzymatic oxidation and polymerization into brown pigments that protect some bacterial species from light. A similar process occurs spontaneously in blood and is hemolytic (see PubMed:8000039). In some bacterial species, this enzyme has been studied as a hemolysin. Length = 353 Score = 24.6 bits (54), Expect = 5.4 Identities = 8/29 (27%), Positives = 17/29 (58%) Query: 8 EFSGIVSELLPNANFRVKLITNDDDSSAD 36 E+S + S ++ + + +VK+ N+ S D Sbjct: 195 EYSALNSIVMASPDGKVKIPLNEPASGKD 223 >gnl|CDD|163429 TIGR03717, R_switched_YjbE, integral membrane protein, YjbE family. Rfam model RF00080 describes a structured RNA element called the yybP-ykoY leader, or SraF, which may precede one or several genes in a genome. Members of this highly hydrophobic protein family commonly are preceded by a yybP-ykoY leader, which may serve as a riboswitch. From the larger group of TerC homologs (pfam03741), this subfamily contains protein YjbE from Bacillus subtilis. A transport function is proposed. Length = 176 Score = 24.8 bits (55), Expect = 5.5 Identities = 9/16 (56%), Positives = 10/16 (62%) Query: 66 DNAVVIAYTAGRMRKH 81 DNAVVIA A + H Sbjct: 15 DNAVVIALAARNLPAH 30 >gnl|CDD|152593 pfam12158, DUF3592, Protein of unknown function (DUF3592). This family of proteins is functionally uncharacterized.This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 150 and 242 amino acids in length. Length = 134 Score = 24.7 bits (54), Expect = 5.6 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 9/50 (18%) Query: 69 VVIAYTA--GRMRKHRIRIS-------LGDKVKVAMNPYDMTRARITYRF 109 V+ + GR + R +G++V V +P + +ARI R Sbjct: 60 PVVEFRYDDGRRIRFRSGSGSNPPGYRVGERVPVYYDPDNPEQARIDRRG 109 >gnl|CDD|165300 PHA02999, PHA02999, Hypothetical protein; Provisional. Length = 382 Score = 24.3 bits (53), Expect = 6.5 Identities = 9/18 (50%), Positives = 14/18 (77%) Query: 92 KVAMNPYDMTRARITYRF 109 KV++NPY MT++ + Y F Sbjct: 170 KVSVNPYSMTKSLMNYMF 187 >gnl|CDD|181794 PRK09355, PRK09355, hydroxyethylthiazole kinase; Validated. Length = 263 Score = 24.4 bits (54), Expect = 6.8 Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 4/39 (10%) Query: 43 VKSNFSE----SGSESGNDGVDPISYLDNAVVIAYTAGR 77 ++ N SE +G + GVD +AV IA A + Sbjct: 116 IRGNASEIAALAGEAAETKGVDSTDGSADAVEIAKAAAK 154 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 0.315 0.132 0.365 Gapped Lambda K H 0.267 0.0757 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,698,218 Number of extensions: 90843 Number of successful extensions: 185 Number of sequences better than 10.0: 1 Number of HSP's gapped: 185 Number of HSP's successfully gapped: 32 Length of query: 110 Length of database: 5,994,473 Length adjustment: 76 Effective length of query: 34 Effective length of database: 4,352,265 Effective search space: 147977010 Effective search space used: 147977010 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 (23.0 bits)