RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780713|ref|YP_003065126.1| 16S rRNA-processing protein [Candidatus Liberibacter asiaticus str. psy62] (190 letters) >gnl|CDD|31149 COG0806, RimM, RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]. Length = 174 Score = 125 bits (316), Expect = 6e-30 Identities = 57/176 (32%), Positives = 88/176 (50%), Gaps = 8/176 (4%) Query: 1 MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRY--VLYSNDNRELRILKM---YR 55 M K + L+L+ I +THG+ GEV + S+ + P L Y L E + L + + Sbjct: 1 MTKPENLLLVGKIVSTHGIRGEVRVKSFTDFPESLFDYGPWLLLKPGGEWQELTVESVRK 60 Query: 56 KNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKY 115 I F GID+ ++A L+ +++ R + ELEEDEF+ DL +E G+ Sbjct: 61 HKNLLILKFKGIDDRNAAEALKGYEIFVDRSEL--PELEEDEFYYHDLIGLEVVTEDGEL 118 Query: 116 WGQVCGVYNFGAGSILEIKN-TMEKTFLIPFTKFAVLEVNLQENKILIDPIAAGLN 170 G+V + GA +L +K +K LIPF V EV+L+ KI +DP L+ Sbjct: 119 LGKVTEILETGANDVLVVKAKGGKKERLIPFVDAVVKEVDLEAKKIEVDPDEGLLD 174 >gnl|CDD|145113 pfam01782, RimM, RimM N-terminal domain. The RimM protein is essential for efficient processing of 16S rRNA. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes. This N-terminal domain is found associated with a PRC-barrel domain. Length = 84 Score = 61.0 bits (149), Expect = 2e-10 Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 5/84 (5%) Query: 9 LMATIGTTHGLNGEVYIDSYANNPIDL----NRYVLYSNDN-RELRILKMYRKNKRFIAT 63 L+ I THGL GEV + S+ + P + ++L + L + + K I Sbjct: 1 LVGKIVGTHGLKGEVKVKSFTDFPEAIFDYGPWFLLKKKGEWKPLTVESVRLHKKGLIVK 60 Query: 64 FSGIDNIHSASELRDLKLYAKRQD 87 F G+D+ +A L+ +LY R D Sbjct: 61 FEGVDDRDAAEALKGAELYVPRSD 84 >gnl|CDD|147440 pfam05239, PRC, PRC-barrel domain. The PRC-barrel is an all beta barrel domain found in photosystem reaction centre subunit H of the purple bacteria and RNA metabolism proteins of the RimM group. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the carboxyl terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain. Length = 77 Score = 45.7 bits (109), Expect = 7e-06 Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 9/79 (11%) Query: 95 EDEFFNTDLEEMETFDRQGKYWGQVCGVY-NFGAGSILEIK-----NTMEKTFLIPFTKF 148 EDEF+ +DL +E + G+ G+V V + G G +L + +K LIPFTK Sbjct: 1 EDEFYASDLIGLEVYTEDGEKLGKVKDVVIDEGEGDVLYLVVSVGGFLGDKEVLIPFTK- 59 Query: 149 AVLEVNLQENKILIDPIAA 167 LEV+L +++I++D Sbjct: 60 --LEVDLGKDRIIVDAPKE 76 >gnl|CDD|147584 pfam05478, Prominin, Prominin. The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration. Length = 809 Score = 30.0 bits (68), Expect = 0.40 Identities = 20/95 (21%), Positives = 37/95 (38%), Gaps = 14/95 (14%) Query: 27 SYANNPIDLNRYVLYSNDNRELRI-------LKMYRKNKRFIATFSGIDNIHSASELRDL 79 + P +LN L + EL+I + +N + T ++N + +EL D+ Sbjct: 506 QVLDTPGNLNPGYLNLSGTLELKINLTISEVYRDCEQN-EPLYTVLQLNNSYDLNELLDI 564 Query: 80 KLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGK 114 K Y D+ELE +L + + + Sbjct: 565 KQYTPEI---DQELES---LKVNLSTITLLTPEAR 593 >gnl|CDD|37205 KOG1994, KOG1994, KOG1994, Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]. Length = 268 Score = 28.1 bits (62), Expect = 1.6 Identities = 20/93 (21%), Positives = 34/93 (36%), Gaps = 3/93 (3%) Query: 43 NDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDL-KLYAKRQDFKDEELEE--DEFF 99 ND + ++ M R++ G S L+ + + KD EL E +E Sbjct: 165 NDEDKKNMIPMVRESLEASPALKGEKGFGRPSTLKKCETSIIESRITKDTELAELEEEII 224 Query: 100 NTDLEEMETFDRQGKYWGQVCGVYNFGAGSILE 132 L ++ F R Y+ CG+ + E Sbjct: 225 EERLTKINIFLRSEHYYCFFCGIKYKDEEDLYE 257 >gnl|CDD|36928 KOG1716, KOG1716, KOG1716, Dual specificity phosphatase [Defense mechanisms]. Length = 285 Score = 26.7 bits (58), Expect = 3.8 Identities = 8/39 (20%), Positives = 17/39 (43%) Query: 65 SGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDL 103 GI ++ + S + K Q K + ++ +TD+ Sbjct: 99 LGITHVLNVSSSCPNPRFLKEQGIKYLRIPVEDNPSTDI 137 >gnl|CDD|143429 cd07111, ALDH_F16, Aldehyde dehydrogenase family 16A1-like. Uncharacterized aldehyde dehydrogenase family 16 member A1 (ALDH16A1) and other related sequences are present in this CD. The active site cysteine and glutamate residues are not conserved in the human ALDH16A1 protein sequence. Length = 480 Score = 26.6 bits (59), Expect = 4.8 Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 9/54 (16%) Query: 49 RILKMYRKNKRFIATFSGIDNIHSASELRDLKL---------YAKRQDFKDEEL 93 RI + +K++R A +DN E RD + +A D EL Sbjct: 89 RIARHIQKHQRLFAVLESLDNGKPIRESRDCDIPLVARHFYHHAGWAQLLDTEL 142 >gnl|CDD|38012 KOG2801, KOG2801, KOG2801, Probable Rab-GAPs [Intracellular trafficking, secretion, and vesicular transport]. Length = 559 Score = 25.8 bits (56), Expect = 7.7 Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 1/34 (2%) Query: 85 RQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQ 118 + D ++L E T+L+E++ RQG YW Q Sbjct: 14 KMDAAIQDLGPKELSCTELQELKQLARQG-YWAQ 46 >gnl|CDD|35665 KOG0444, KOG0444, KOG0444, Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]. Length = 1255 Score = 25.8 bits (56), Expect = 8.0 Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 2/24 (8%) Query: 91 EELEEDEFFNTDLEEMETFDRQGK 114 E+L E+ +N DLE ME+F +GK Sbjct: 885 EQLMEE--WNYDLELMESFVLEGK 906 >gnl|CDD|37149 KOG1938, KOG1938, KOG1938, Protein with predicted involvement in meiosis (GSG1) [Cell cycle control, cell division, chromosome partitioning]. Length = 960 Score = 25.8 bits (56), Expect = 8.5 Identities = 11/44 (25%), Positives = 14/44 (31%) Query: 32 PIDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGIDNIHSASE 75 D +LYS D+ E + K F D HS Sbjct: 161 APDNTLGILYSFDSGEFQTRKGADLLFMFGHPNLAFDAYHSTKR 204 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 0.318 0.137 0.392 Gapped Lambda K H 0.267 0.0695 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,295,805 Number of extensions: 119136 Number of successful extensions: 310 Number of sequences better than 10.0: 1 Number of HSP's gapped: 305 Number of HSP's successfully gapped: 21 Length of query: 190 Length of database: 6,263,737 Length adjustment: 88 Effective length of query: 102 Effective length of database: 4,362,145 Effective search space: 444938790 Effective search space used: 444938790 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 (24.6 bits)