RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 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|88417 cd04451, S1_IF1, S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of the mRNA.. Length = 64 Score = 73.6 bits (181), Expect = 1e-14 Identities = 36/102 (35%), Positives = 51/102 (50%), Gaps = 38/102 (37%) Query: 7 LEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLD 66 +E G+V+E LPNA FRV+L E+G E Sbjct: 1 IEMEGVVTEALPNAMFRVEL----------------------ENGHE------------- 25 Query: 67 NAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR 108 V+A+ +G+MR + IRI GD+VKV ++PYD+T+ RI YR Sbjct: 26 ---VLAHISGKMRMNYIRILPGDRVKVELSPYDLTKGRIVYR 64 >gnl|CDD|176953 CHL00010, infA, translation initiation factor 1. Length = 78 Score = 73.1 bits (180), Expect = 2e-14 Identities = 36/111 (32%), Positives = 52/111 (46%), Gaps = 40/111 (36%) Query: 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60 M KE +E G+V+E LPN FRV+L Sbjct: 1 MKKENKIEMEGLVTESLPNGMFRVRL---------------------------------- 26 Query: 61 PISYLDN-AVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110 DN V+ Y +G++R++ IRI GD+VKV ++PYD+T+ RI YR + Sbjct: 27 -----DNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLR 72 >gnl|CDD|30710 COG0361, InfA, Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]. Length = 75 Score = 72.5 bits (178), Expect = 2e-14 Identities = 35/110 (31%), Positives = 50/110 (45%), Gaps = 38/110 (34%) Query: 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60 M K + +E G V E+LPN FRV+L Sbjct: 1 MAKPDEIEMEGTVIEMLPNGRFRVEL---------------------------------- 26 Query: 61 PISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110 + +A+ +G+MRK+RIRI GD V V ++PYD+T+ RI YR+K Sbjct: 27 ----ENGHERLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVYRYK 72 >gnl|CDD|110196 pfam01176, eIF-1a, Translation initiation factor 1A / IF-1. This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1. Length = 65 Score = 55.2 bits (134), Expect = 4e-09 Identities = 29/101 (28%), Positives = 38/101 (37%), Gaps = 39/101 (38%) Query: 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDN 67 E G V+E+L N F V+L DG Sbjct: 4 EMIGQVTEMLGNGRFEVEL-----------------------------EDGH-------- 26 Query: 68 AVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR 108 +A+ G+ RK RI I GD V V ++PYD + RI YR Sbjct: 27 -ERLAHIPGKRRK-RIWILRGDFVLVELSPYDKVKGRIIYR 65 >gnl|CDD|30879 COG0533, QRI7, Metal-dependent proteases with possible chaperone activity [Posttranslational modification, protein turnover, chaperones]. Length = 342 Score = 27.1 bits (60), Expect = 1.1 Identities = 10/24 (41%), Positives = 11/24 (45%) Query: 66 DNAVVIAYTAGRMRKHRIRISLGD 89 DNA +IAY K IS D Sbjct: 302 DNAAMIAYAGLLRYKAGRFISPLD 325 >gnl|CDD|119407 cd02696, MurNAc-LAA, N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino acids in certain cell wall glycopeptides. These proteins are Zn-dependent peptidases with highly conserved residues involved in cation co-ordination. MurNAc-LAA in this family is one of several peptidoglycan hydrolases (PGHs) found in bacterial and bacteriophage or prophage genomes that are involved in the degradation of the peptidoglycan. In Escherichia coli, there are five MurNAc-LAAs present: AmiA, AmiB, AmiC and AmiD that are periplasmic, and AmpD that is cytoplasmic. Three of these (AmiA, AmiB and AmiC) belong to this family, the other two (AmiD and AmpD) do not. E. coli AmiA, AmiB and AmiC play an important role in cleaving the septum to release daughter cells after cell division. In general, bacterial MurNAc-LAAs are members of the bacterial autolytic system and carry a signal peptide in their N-termini that allows their transport across the cytoplasmic membrane. However, the bacteriophage MurNAc-LAAs are endolysins since these phage-encoded enzymes break down bacterial peptidoglycan at the terminal stage of the phage reproduction cycle. As opposed to autolysins, almost all endolysins have no signal peptides and their translocation through the cytoplasmic membrane is thought to proceed with the help of phage-encoded holin proteins. The amidase catalytic module is fused to another functional module (cell wall binding module or CWBM) either at the N- or C-terminus, which is responsible for high affinity binding of the protein to the cell wall.. Length = 172 Score = 27.1 bits (61), Expect = 1.2 Identities = 9/30 (30%), Positives = 16/30 (53%) Query: 3 KEETLEFSGIVSELLPNANFRVKLITNDDD 32 K+ L + +++LL A +V L +DD Sbjct: 24 KDINLAIALKLAKLLEAAGAKVVLTRDDDT 53 >gnl|CDD|88466 cd05791, S1_CSL4, S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".. Length = 92 Score = 26.3 bits (58), Expect = 1.8 Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 2/48 (4%) Query: 62 ISYLDNAVVIAYTAGRMRKHRIRISLGDKVKV--AMNPYDMTRARITY 107 I + + G +RK IR + DKV++ P D+ RA++ Sbjct: 26 ILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVIS 73 >gnl|CDD|144931 pfam01520, Amidase_3, N-acetylmuramoyl-L-alanine amidase. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls. Length = 172 Score = 26.0 bits (58), Expect = 2.1 Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 1/36 (2%) Query: 3 KEETLEFSGIVSELLPNANFRVKLITNDDDSSADCK 38 K+ L+ + +++LL A V L T DDDS Sbjct: 23 KDLNLDIALRLAKLLEAAGVEVVL-TRDDDSFVSLS 57 >gnl|CDD|107371 cd06376, PBP1_mGluR_groupIII, Ligand-binding domain of the group III metabotropic glutamate receptor. Ligand-binding domain of the group III metabotropic glutamate receptor, a family which contains mGlu4R, mGluR6R, mGluR7, and mGluR8; all of which inhibit adenylyl cyclase. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes. Length = 463 Score = 25.2 bits (55), Expect = 4.5 Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 2/34 (5%) Query: 1 MPKE-ETLEFSGIVSELLPNANFR-VKLITNDDD 32 +P+E EF I+ LL N R V + N+DD Sbjct: 210 IPREPRPGEFDKIIKRLLETPNARAVIIFANEDD 243 >gnl|CDD|173846 cd01157, MCAD, Medium chain acyl-CoA dehydrogenase. MCADs are mitochondrial beta-oxidation enzymes, which catalyze the alpha,beta dehydrogenation of the corresponding medium chain acyl-CoA by FAD, which becomes reduced. The reduced form of MCAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. MCAD is a homotetramer. Length = 378 Score = 24.9 bits (54), Expect = 4.6 Identities = 11/33 (33%), Positives = 16/33 (48%) Query: 70 VIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTR 102 I + R+ K + I G K+AM +D TR Sbjct: 209 GITFEDVRVPKENVLIGEGAGFKIAMGAFDKTR 241 >gnl|CDD|143211 cd05734, Ig7_DSCAM, Seventh immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM). Ig7_DSCAM: the seventh immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM). DSCAM is a cell adhesion molecule expressed largely in the developing nervous system. The gene encoding DSCAM is located at human chromosome 21q22, the locus associated with the mental retardation phenotype of Down Syndrome. DSCAM is predicted to be the largest member of the IG superfamily. It has been demonstrated that DSCAM can mediate cation-independent homophilic intercellular adhesion. Length = 79 Score = 24.5 bits (53), Expect = 7.0 Identities = 10/36 (27%), Positives = 20/36 (55%) Query: 15 ELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSES 50 +LL N + +K + +D CK+ + V ++ S+S Sbjct: 39 QLLSNGSLLIKHVLEEDSGYYLCKVSNDVGADASKS 74 >gnl|CDD|36570 KOG1356, KOG1356, KOG1356, Putative transcription factor 5qNCA, contains JmjC domain [Transcription]. Length = 889 Score = 24.2 bits (52), Expect = 7.5 Identities = 11/63 (17%), Positives = 22/63 (34%), Gaps = 4/63 (6%) Query: 30 DDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVV----IAYTAGRMRKHRIRI 85 D+S C+ + F++ G + P Y A+ I+ + R+ + Sbjct: 131 KDESPVFCRFYEFRRLQFTKKGVLRVQGFLSPDQYDPEAISLWGPISGSDSRLDTETAKY 190 Query: 86 SLG 88 L Sbjct: 191 ILA 193 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.315 0.132 0.365 Gapped Lambda K H 0.267 0.0768 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,211,932 Number of extensions: 52385 Number of successful extensions: 128 Number of sequences better than 10.0: 1 Number of HSP's gapped: 127 Number of HSP's successfully gapped: 19 Length of query: 110 Length of database: 6,263,737 Length adjustment: 76 Effective length of query: 34 Effective length of database: 4,621,453 Effective search space: 157129402 Effective search space used: 157129402 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: 51 (23.3 bits)