RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780728|ref|YP_003065141.1| pilus assembly protein [Candidatus Liberibacter asiaticus str. psy62] (263 letters) >gnl|CDD|33540 COG3745, CpaB, Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]. Length = 276 Score = 157 bits (397), Expect = 4e-39 Identities = 88/259 (33%), Positives = 131/259 (50%), Gaps = 7/259 (2%) Query: 1 MKLTRLMGIVVSGVFALVAGIIAMRLVSPHHVQTEEVITENPAKFINVLISKGDLAVGMV 60 M+ RL+ ++V+ A +AG++A + V VL++ DL VG Sbjct: 1 MRPKRLIILIVALAAAGLAGVLAASIWLAPAVPATAEPVAPGKPTKPVLVAAVDLPVGQR 60 Query: 61 VTPNILEWVAFPEENVFDGFIDDVHQPNAMQELDGVLVRVPILKGDPIRLEKLVDRGNGG 120 ++ + L W +P ++V G I + P+A+ L G +VRVPI G+P+ KL G Sbjct: 61 LSADQLRWQPWPADSVPAGAISRENAPDALTGLAGRIVRVPIGAGEPVLPSKLSGPGTRT 120 Query: 121 LSSLLPKGKRAATMDISISSAVGGMIKPNDHVDVVMVRSLSER----KPTVTVVLSNIRV 176 LSS+LP GKRA + + VGG + P D VDV++ + VL NIRV Sbjct: 121 LSSVLPPGKRAVAIRVDEVVGVGGFVLPGDRVDVILTVRKDDAGADSSKLAETVLPNIRV 180 Query: 177 IAIDHNIDSDE--RVLVGSTATLELTPMQAKALVAAQSVAKLSLVLRSIADLNPSSSEDS 234 +A+D I E +VG TATLE+TP QA+ L AQ + LSL LRS+AD + + Sbjct: 181 LAVDQTISEREDGSPVVGRTATLEVTPDQAEKLTLAQQMGTLSLALRSVADAQEPDTGAA 240 Query: 235 DVWDVQEEGK-EIQIIKAG 252 + + +Q+IK G Sbjct: 241 TGLLLGDPVAATVQLIKGG 259 >gnl|CDD|73256 cd01302, Cyclic_amidohydrolases, Cyclic amidohydrolases, including hydantoinase, dihydropyrimidinase, allantoinase, and dihydroorotase, are involved in the metabolism of pyrimidines and purines, sharing the property of hydrolyzing the cyclic amide bond of each substrate to the corresponding N-carbamyl amino acids. Allantoinases catalyze the degradation of purines, while dihydropyrimidinases and hydantoinases, a microbial counterpart of dihydropyrimidinase, are involved in pyrimidine degradation. Dihydroorotase participates in the de novo synthesis of pyrimidines.. Length = 337 Score = 28.7 bits (64), Expect = 1.6 Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 7/45 (15%) Query: 36 EVITENPAKFINVLISKGDLAVG-----MVVTPNILEWVAFPEEN 75 E+++ENPA+ L KG +AVG ++V P EW EE Sbjct: 274 EILSENPARIFG-LYPKGTIAVGYDADLVIVDPKK-EWKVTAEEI 316 >gnl|CDD|119323 cd06581, TM_PBP1_LivM_like, Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of branched-chain amino acids (AAs). These types of transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP, which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. E. coli LivM forms a heterodimer with another TM, LivH, to generate the transmembrane pore. LivH is not included in this subgroup. The LIV-1/LS transporter is comprised of two TMs (LivM and LivH), two ABCs (LivG and LivF), and one of two alternative PBPs, LivJ (LIV-BP) or LivK (LS-BP). In addition to transporting branched-chain AAs including leucine, isoleucine and valine, the E. coli LIV-1/LS transporter is involved in the uptake of the aromatic AA, phenylalanine.. Length = 268 Score = 28.6 bits (65), Expect = 1.8 Identities = 7/21 (33%), Positives = 13/21 (61%) Query: 6 LMGIVVSGVFALVAGIIAMRL 26 L +V+ + L+ G+ A+RL Sbjct: 52 LAAGLVAALVGLLLGLPALRL 72 >gnl|CDD|37955 KOG2744, KOG2744, KOG2744, DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription]. Length = 512 Score = 28.1 bits (62), Expect = 2.2 Identities = 9/37 (24%), Positives = 20/37 (54%), Gaps = 2/37 (5%) Query: 77 FDGFIDDVHQPNAMQELDGVLVRVPILKGDPIRLEKL 113 + F++D+ + M++ + +PI+ G P+ L L Sbjct: 164 SEEFMEDLRRF--MKKRGTKVKSIPIIGGQPLDLHWL 198 >gnl|CDD|33350 COG3548, COG3548, Predicted integral membrane protein [Function unknown]. Length = 197 Score = 27.5 bits (61), Expect = 4.3 Identities = 11/51 (21%), Positives = 20/51 (39%), Gaps = 1/51 (1%) Query: 1 MKLTRLMGIVVSGVFALVAGIIAMRLVSPHHVQTEEVITENPAKFINVLIS 51 M RL VFA++ I+ + + P + + E + I +S Sbjct: 10 MGKGRLEAFT-DAVFAIIMTIMVLEIKVPKGGGRLQALAELLSSLIIYALS 59 >gnl|CDD|32643 COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport and metabolism]. Length = 394 Score = 26.7 bits (59), Expect = 5.9 Identities = 11/30 (36%), Positives = 15/30 (50%) Query: 3 LTRLMGIVVSGVFALVAGIIAMRLVSPHHV 32 L R + + GVF +A +A RLV P Sbjct: 106 LARALAGLAHGVFWSIAAALAARLVPPGKR 135 >gnl|CDD|176912 cd08903, START_STARD5-like, Lipid-binding START domain of mammalian STARD5 and related proteins. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD5, and related domains. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD5 is ubiquitously expressed, with highest levels in liver and kidney. STARD5 functions in the kidney within the proximal tubule cells where it is associated with the Endoplasmic Reticulum (ER), and may participate in ER-associated cholesterol transport. It binds cholesterol and 25-hydroxycholesterol. Expression of the gene encoding STARD5 is increased by ER stress, and its mRNA and protein levels are elevated in a type I diabetic mouse model of human diabetic nephropathy. Length = 208 Score = 26.7 bits (59), Expect = 6.2 Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 5/33 (15%) Query: 131 AATMDISIS-----SAVGGMIKPNDHVDVVMVR 158 A + D+S+ SA +I P D VDVV+V+ Sbjct: 88 AISDDVSVCRTVTPSAAMKIISPRDFVDVVLVK 120 >gnl|CDD|147331 pfam05099, TerB, Tellurite resistance protein TerB. This family contains the TerB tellurite resistance proteins from a a number of bacteria. Length = 140 Score = 26.8 bits (60), Expect = 6.4 Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 2/39 (5%) Query: 174 IRVIAIDHNIDSDERVLVGS--TATLELTPMQAKALVAA 210 V D +D +ER + + L P +A AL+ Sbjct: 31 AEVAKADGQVDEEERQAIRRLLRSRFGLDPEEAAALIEL 69 >gnl|CDD|145132 pfam01808, AICARFT_IMPCHas, AICARFT/IMPCHase bienzyme. This is a family of bifunctional enzymes catalysing the last two steps in de novo purine biosynthesis. The bifunctional enzyme is found in both prokaryotes and eukaryotes. The second last step is catalysed by 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase EC:2.1.2.3 (AICARFT), this enzyme catalyses the formylation of AICAR with 10-formyl-tetrahydrofolate to yield FAICAR and tetrahydrofolate. The last step is catalysed by IMP (Inosine monophosphate) cyclohydrolase EC:3.5.4.10 (IMPCHase), cyclizing FAICAR (5-formylaminoimidazole-4-carboxamide ribonucleotide) to IMP. Length = 315 Score = 26.6 bits (59), Expect = 7.5 Identities = 12/23 (52%), Positives = 15/23 (65%) Query: 140 SAVGGMIKPNDHVDVVMVRSLSE 162 SA GG+I ND VDV + +SE Sbjct: 169 SAFGGIIALNDEVDVETAKEISE 191 >gnl|CDD|36133 KOG0915, KOG0915, KOG0915, Uncharacterized conserved protein [Function unknown]. Length = 1702 Score = 26.5 bits (58), Expect = 8.0 Identities = 22/129 (17%), Positives = 43/129 (33%), Gaps = 10/129 (7%) Query: 10 VVSGVFALVAGIIAMRLVSPHHVQ----TEEVITENPAKFIN----VLISKG-DLAVGMV 60 VV V ++ + R+ S H VQ + + + + + G D A V Sbjct: 43 VVRQVLEILTHVNK-RVKSQHEVQLPVLALLKLYAAQSTMVRNFAIIYVEMGFDRAPPKV 101 Query: 61 VTPNILEWVAFPEENVFDGFIDDVHQPNAMQELDGVLVRVPILKGDPIRLEKLVDRGNGG 120 V P + E ++ + + I + + +L+ P +G + N Sbjct: 102 VGPCLAEKISPDVSHKYRSLITSQDKDLILDFCLHLLLYQPSSQGQGSSPGLSPFQVNRI 161 Query: 121 LSSLLPKGK 129 + KG Sbjct: 162 IGEFALKGD 170 >gnl|CDD|31205 COG1001, AdeC, Adenine deaminase [Nucleotide transport and metabolism]. Length = 584 Score = 26.3 bits (58), Expect = 9.3 Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 2/35 (5%) Query: 144 GMIKPNDHVDVVMVRSLSERKPTVTVVLSNIRVIA 178 G+I P D+V++ L R VT VL RV+A Sbjct: 326 GLIAPGRRADLVILEDL--RNFKVTSVLIKGRVVA 358 >gnl|CDD|176969 CHL00028, clpP, ATP-dependent Clp protease proteolytic subunit. Length = 200 Score = 26.0 bits (58), Expect = 9.8 Identities = 10/25 (40%), Positives = 12/25 (48%), Gaps = 1/25 (4%) Query: 7 MGIVVS-GVFALVAGIIAMRLVSPH 30 +G+ S F L G I RL PH Sbjct: 96 LGLAASMASFILAGGEITKRLAFPH 120 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 0.317 0.135 0.370 Gapped Lambda K H 0.267 0.0788 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,993,263 Number of extensions: 155806 Number of successful extensions: 452 Number of sequences better than 10.0: 1 Number of HSP's gapped: 450 Number of HSP's successfully gapped: 26 Length of query: 263 Length of database: 6,263,737 Length adjustment: 92 Effective length of query: 171 Effective length of database: 4,275,709 Effective search space: 731146239 Effective search space used: 731146239 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 (21.6 bits) S2: 56 (25.2 bits)