RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780957|ref|YP_003065370.1| dihydrofolate reductase protein [Candidatus Liberibacter asiaticus str. psy62] (176 letters) >gnl|CDD|182714 PRK10769, folA, dihydrofolate reductase; Provisional. Length = 159 Score = 126 bits (317), Expect = 4e-30 Identities = 55/138 (39%), Positives = 78/138 (56%), Gaps = 6/138 (4%) Query: 6 IILIAAITRNNVIGSCGGMPWKISSDLKRFKSLTTGNPVVMGYRTFQSIGRLLPGRTNII 65 I LIAA+ + VIG MPW + +DL FK T PV+MG T++SIGR LPGR NI+ Sbjct: 2 ISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIV 61 Query: 66 ITRDNTRRASVNPEAVLASSILDSLDLASKTGSKKIFIIGGGEIYAQTISLAHTLYITHI 125 I + + + S+ ++L A +I +IGGG +Y Q + A LY+THI Sbjct: 62 I----SSQPGTDDRVTWVKSVDEALAAAGD--VPEIMVIGGGRVYEQFLPKAQRLYLTHI 115 Query: 126 EKEIEGDVFFPSIDSNIW 143 + E+EGD FP + + W Sbjct: 116 DAEVEGDTHFPDYEPDEW 133 >gnl|CDD|185491 PTZ00164, PTZ00164, bifunctional dihydrofolate reductase-thymidylate synthase; Provisional. Length = 514 Score = 109 bits (275), Expect = 3e-25 Identities = 57/191 (29%), Positives = 91/191 (47%), Gaps = 29/191 (15%) Query: 1 MTRPEIILIAAITRNNVIGSCGGMPWKISSDLKRFKSLTT-------------GNPVVMG 47 + + ++ A+T IG +PW I D+K F +TT N V+MG Sbjct: 5 SSLKDFSIVVAVTLKRGIGIGNSLPWHIPEDMKFFSKITTYVREEKYEKSPKKQNAVIMG 64 Query: 48 YRTFQSIG---RLLPGRTNIIITRDNTRRASVNPEAVLASSILDSL-DLASKTGSKKIFI 103 +T++SI R L R N++++R +P ++ S+ D+L LA +KIFI Sbjct: 65 RKTWESIPKKFRPLKNRINVVLSR-TLTEEEADPGVLVFGSLEDALRLLAEDLSIEKIFI 123 Query: 104 IGGGEIYAQTIS--LAHTLYITHIEKEIEGDVFFPSIDSN---IWKKQEKEIITSAGEGD 158 IGG +Y + +S L +Y+T + E E DVFFP I + + + T + G Sbjct: 124 IGGASVYREALSANLLDKIYLTRVNSEYECDVFFPKIPESFFIVAIVSQ----TFSTNGT 179 Query: 159 DYPTRFVIYDR 169 Y FVIY++ Sbjct: 180 SY--DFVIYEK 188 >gnl|CDD|100572 PRK00478, scpA, segregation and condensation protein A/unknown domain fusion protein; Provisional. Length = 505 Score = 63.4 bits (154), Expect = 3e-11 Identities = 41/130 (31%), Positives = 65/130 (50%), Gaps = 3/130 (2%) Query: 6 IILIAAITRNNVIGSCGGMPWKISSDLKRFKSLTTGNPVVMGYRTFQSIGRLLPGRTNII 65 I LI N I +PWKI +L F TT + +VMGY TFQ++ ++L + NI+ Sbjct: 2 IKLIWCEDLNFGIAKNNQIPWKIDEELNHFHQTTTNHTIVMGYNTFQAMNKILANQANIV 61 Query: 66 ITRDNTRRASVNPEAVLASSILDSLDLASKTGSKKIFIIGGGEIYAQTISLAHTLYITHI 125 I++ + R N E + + + L S + +FIIGG + Q I A L I+ + Sbjct: 62 ISKKHQRELKNNNELFVFNDLKKLLIDFS---NVDLFIIGGKKTIEQFIKYADQLIISKL 118 Query: 126 EKEIEGDVFF 135 + + D+F Sbjct: 119 NADYKCDLFV 128 >gnl|CDD|163534 TIGR03822, AblA_like_2, lysine-2,3-aminomutase-related protein. Members of this protein form a distinctive clade, homologous to lysine-2,3-aminomutase (of Bacillus, Clostridium, and methanogenic archaea) and likely similar in function. Members of this family are found in Rhodopseudomonas, Caulobacter crescentus, Bradyrhizobium, etc. Length = 321 Score = 29.7 bits (67), Expect = 0.38 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 1/59 (1%) Query: 38 LTTGNPVVMGYRTFQSIGRLLPGRTNIIITRDNTRRASVNPEAVLASSILDSLDLASKT 96 LT G+P+V+ R I L ++ I R +TR +P V +++ +L + KT Sbjct: 142 LTGGDPLVLSPRRLGDIMARLAAIDHVKIVRFHTRVPVADPARVTP-ALIAALKTSGKT 199 >gnl|CDD|179700 PRK03995, PRK03995, hypothetical protein; Provisional. Length = 267 Score = 28.8 bits (65), Expect = 0.77 Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 6/55 (10%) Query: 76 VNPEAV--LASSILDSLDLASKTGSKKIFIIGGGEIYA--QT-ISLAHTLYITHI 125 N A LA ++++ LD K IGGG YA T ++L HI Sbjct: 157 KNERAGEILAEAVIEVLDSIEYEKFKPAIGIGGGH-YAPKFTKLALESEYCFGHI 210 >gnl|CDD|132448 TIGR03407, urea_ABC_UrtA, urea ABC transporter, urea binding protein. Members of this protein family are ABC transporter substrate-binding proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. Members of this protein family tend to have the twin-arginine signal for Sec-independent transport across the plasma membrane. Length = 359 Score = 27.7 bits (62), Expect = 1.7 Identities = 18/81 (22%), Positives = 41/81 (50%), Gaps = 9/81 (11%) Query: 86 ILDSLD-LASKTGSKKIFIIGGGEIYAQTISLAHTLYITHIEKEIEGDVFFP-------S 137 I+ ++D L SK G+K+ F++G ++ +T + Y+ + + G+ + P + Sbjct: 121 IIPAVDYLLSKKGAKRFFLLGSDYVFPRTANKIIKAYLKSLGGTVVGEDYTPLGHTDFQT 180 Query: 138 IDSNIWKKQEKEIITSAGEGD 158 I + I K + +++ + GD Sbjct: 181 IINKI-KAFKPDVVFNTLNGD 200 >gnl|CDD|178012 PLN02387, PLN02387, long-chain-fatty-acid-CoA ligase family protein. Length = 696 Score = 27.4 bits (61), Expect = 1.8 Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 2/28 (7%) Query: 21 CGGMPWKISSDLKRFKSLTTGNPVVMGY 48 GG P +S D +RF ++ G P+ GY Sbjct: 427 SGGAP--LSGDTQRFINICLGAPIGQGY 452 >gnl|CDD|179315 PRK01642, cls, cardiolipin synthetase; Reviewed. Length = 483 Score = 27.4 bits (62), Expect = 2.1 Identities = 9/45 (20%), Positives = 16/45 (35%), Gaps = 1/45 (2%) Query: 52 QSIGRLLPGRTNIIITRDNTRRASVNPEAVLASSILDSLDLASKT 96 + RL I + N R N + +I+ ++LA Sbjct: 98 APLFRLCERLQGIPGLKGNQLRLLTNGDETFQ-AIIRDIELARHY 141 >gnl|CDD|131341 TIGR02288, PaaN_2, phenylacetic acid degradation protein paaN. This family includes sequences from Burkholderia, Bordetella, Streptomyces. Other PaaN enzymes are represented by a separate model, TIGR02278. Length = 551 Score = 27.2 bits (60), Expect = 2.4 Identities = 22/67 (32%), Positives = 29/67 (43%), Gaps = 8/67 (11%) Query: 17 VIGSCGGMP-WKISSDLKRFKSLTTGNPVVMGYRTFQSIGRLLPGRTNIIITRDNTRRAS 75 VIG C P W L F SL TGNPV++ G +LP + + R+ A Sbjct: 199 VIG-CSTFPTWNTYPGL--FASLATGNPVLVKPHP----GAILPLALTVQVAREVLGEAG 251 Query: 76 VNPEAVL 82 +P V Sbjct: 252 FDPNLVT 258 >gnl|CDD|180667 PRK06718, PRK06718, precorrin-2 dehydrogenase; Reviewed. Length = 202 Score = 26.9 bits (60), Expect = 3.1 Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 12/56 (21%) Query: 99 KKIFIIGGGEIYAQTISLAHTL--YITHIEKEIEGDVFFPSIDSNIWKK-QEKEII 151 K++ I+GGG++ + TL Y HI V P + N+ K +E +I Sbjct: 11 KRVVIVGGGKVAGRRAI---TLLKYGAHIV------VISPELTENLVKLVEEGKIR 57 >gnl|CDD|178003 PLN02375, PLN02375, molybderin biosynthesis protein CNX3. Length = 270 Score = 26.6 bits (58), Expect = 3.6 Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 6/71 (8%) Query: 65 IITRDNTRRASVNPEAVLASSILDSLDLASKTGS------KKIFIIGGGEIYAQTISLAH 118 + ++DN++R ++ V+ + L LA++ G KI I G + + I L H Sbjct: 130 VSSKDNSKRTALACCKVILGKRVFDLVLANQMGKGDVLGVAKIAGINGAKQTSSLIPLCH 189 Query: 119 TLYITHIEKEI 129 + +TH+ ++ Sbjct: 190 NIALTHVRVDL 200 >gnl|CDD|161881 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a histidyl-tRNA synthetase in every completed genome. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and actually serve as regulatory subunits for an enzyme of histidine biosynthesis. They were excluded from the seed alignment and score much lower than do single copy histidyl-tRNA synthetases of other genomes not included in the seed alignment. These putative second copies of HisS score below the trusted cutoff. The regulatory protein kinase GCN2 of Saccharomyces cerevisiae (YDR283c), and related proteins from other species designated eIF-2 alpha kinase, have a domain closely related to histidyl-tRNA synthetase that may serve to detect and respond to uncharged tRNA(his), an indicator of amino acid starvation; these regulatory proteins are not orthologous and so score below the noise cutoff. Length = 397 Score = 26.3 bits (59), Expect = 4.3 Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 3/49 (6%) Query: 68 RDNTRRASVNPEAVLASSILDSLDLASKTGSKKIFIIGGGEIYAQTISL 116 R R V+ + L A K G++ I+G E+ T++L Sbjct: 346 RKAGIRVEVDLGG---RKLKKQLKYADKLGARFAVILGEDELANGTVTL 391 >gnl|CDD|184767 PRK14611, PRK14611, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional. Length = 275 Score = 25.9 bits (57), Expect = 5.4 Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 5/69 (7%) Query: 91 DLASKTGSKKIFIIGGGEIYAQTISLAHTLYITHIEKEIEGDVFFPSIDSN---IWKKQE 147 +LAS + F + GG + I I +EI + +P+I S+ ++ K Sbjct: 124 ELASSISADAPFFLKGGFALGRGIGDKLEFLEKPISREIT--LVYPNIKSSTGRVYSKVT 181 Query: 148 KEIITSAGE 156 K+I+T+ + Sbjct: 182 KQILTNKED 190 >gnl|CDD|153005 pfam12571, DUF3751, Tail fiber protein. This domain family is found in bacteria and viruses, and is approximately 160 amino acids in length. There are two completely conserved residues (K and W) that may be functionally important. Length = 159 Score = 25.8 bits (57), Expect = 5.8 Identities = 11/32 (34%), Positives = 17/32 (53%) Query: 58 LPGRTNIIITRDNTRRASVNPEAVLASSILDS 89 LP I+ + T+ VN AV+ S +LD+ Sbjct: 10 LPAEAQIVHRQAVTQYGYVNENAVVYSVVLDT 41 >gnl|CDD|149852 pfam08915, tRNA-Thr_ED, Archaea-specific editing domain of threonyl-tRNA synthetase. Archaea-specific editing domain of threonyl-tRNA synthetase, with marked structural similarity to D-amino acids deacylases found in eubacteria and eukaryotes. This domain can bind D-amino acids, and ensures high fidelity during translation. It is especially responsible for removing incorrectly attached serine from tRNA-Thr. The domain forms a fold that can be be defined as two layers of beta-sheets (a three-stranded sheet and a five-stranded sheet), with two alpha-helices located adjacent to the five-stranded sheet. Length = 137 Score = 25.6 bits (57), Expect = 6.6 Identities = 8/27 (29%), Positives = 16/27 (59%) Query: 77 NPEAVLASSILDSLDLASKTGSKKIFI 103 NPE V+ + + L +ASK + ++ + Sbjct: 50 NPEEVIEKAAEEILKVASKVKATRVVL 76 >gnl|CDD|161756 TIGR00194, uvrC, excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments. Length = 574 Score = 25.4 bits (56), Expect = 7.2 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 11/74 (14%) Query: 1 MTRPEIILIAAITRNNVIGSC----GGMPWKISSDLKRFKSLTTGNPVVMGYRTFQSIGR 56 + R EI I+ I + +GS G P K S S+T G+ + ++ Sbjct: 381 IKRIEIFDISHIDGSQTVGSMVVFEDGKPLKASYRRYNINSITGGD-------DYAAMRE 433 Query: 57 LLPGRTNIIITRDN 70 +L R + I ++N Sbjct: 434 VLRRRYSSIQKKNN 447 >gnl|CDD|181618 PRK09038, PRK09038, flagellar motor protein MotD; Reviewed. Length = 281 Score = 25.4 bits (56), Expect = 8.1 Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 7/44 (15%) Query: 44 VVMGYRTFQSI-------GRLLPGRTNIIITRDNTRRASVNPEA 80 +GY FQ + GR R ++I R+ R S+ P Sbjct: 211 AAVGYGEFQPVADNDTAEGRARNRRVVLVILRNLDVRRSLTPVG 254 >gnl|CDD|178418 PLN02823, PLN02823, spermine synthase. Length = 336 Score = 25.0 bits (55), Expect = 9.8 Identities = 8/17 (47%), Positives = 10/17 (58%) Query: 92 LASKTGSKKIFIIGGGE 108 L K +FI+GGGE Sbjct: 98 LLHHPNPKTVFIMGGGE 114 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 0.319 0.137 0.396 Gapped Lambda K H 0.267 0.0663 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,904,236 Number of extensions: 175726 Number of successful extensions: 335 Number of sequences better than 10.0: 1 Number of HSP's gapped: 330 Number of HSP's successfully gapped: 25 Length of query: 176 Length of database: 5,994,473 Length adjustment: 87 Effective length of query: 89 Effective length of database: 4,114,577 Effective search space: 366197353 Effective search space used: 366197353 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (24.7 bits)