RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780357|ref|YP_003064770.1| hypothetical protein CLIBASIA_01210 [Candidatus Liberibacter asiaticus str. psy62] (394 letters) >gnl|CDD|183185 PRK11539, PRK11539, ComEC family competence protein; Provisional. Length = 755 Score = 42.7 bits (101), Expect = 2e-04 Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 4/50 (8%) Query: 104 FHCIPVYGLIANILAIPILSFVVIPAGLIAILLMILSLDNIPFGVMAWGL 153 FH I + L AN+ A+P++SF+ +P L+A++L +L P W L Sbjct: 384 FHGISLTSLPANLWAVPLVSFITVPLILLALVLHLLP----PLEQGLWFL 429 >gnl|CDD|161839 TIGR00361, ComEC_Rec2, DNA internalization-related competence protein ComEC/Rec2. The role for this protein in species that are not naturally transformable is unknown. Length = 662 Score = 41.4 bits (97), Expect = 4e-04 Identities = 23/66 (34%), Positives = 38/66 (57%), Gaps = 6/66 (9%) Query: 100 LIKHFHCIPVYGLIANILAIPILSFVVIPAGLIAILLMILSLDNIPFGVM--AWGLDIII 157 + HFH + AN+LA+P +F ++P L A+LL+ LS FG + +W D++I Sbjct: 312 QLYHFHGFSLISFPANMLAVPFYTFCIVPLILAAVLLLSLS---GSFGRLQGSW-FDLLI 367 Query: 158 HIAHRI 163 +A R+ Sbjct: 368 SLALRL 373 >gnl|CDD|180955 PRK07390, PRK07390, NAD(P)H-quinone oxidoreductase subunit F; Validated. Length = 613 Score = 33.3 bits (77), Expect = 0.10 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 7/49 (14%) Query: 99 FLIKHFHCIPVYGLIANILAIPILSFVVI------PAGLIAILLMILSL 141 FL++ IP+YGLI +L++P S +I PA + +L+ +L+ Sbjct: 4 FLLQTSWLIPLYGLIGALLSLP-WSPGIIRRTGPRPAAYLNLLMTLLAF 51 >gnl|CDD|162399 TIGR01525, ATPase-IB_hvy, heavy metal translocating P-type ATPase. This alignment encompasses two equivalog models for the copper and cadmium-type heavy metal transporting P-type ATPases (TIGR01511 and TIGR01512) as well as those species which score ambiguously between both models. For more comments and references, see the files on TIGR01511 and 01512. Length = 556 Score = 32.6 bits (75), Expect = 0.17 Identities = 11/32 (34%), Positives = 20/32 (62%) Query: 109 VYGLIANILAIPILSFVVIPAGLIAILLMILS 140 + L N++AIP+ + ++P L+A+LL S Sbjct: 514 AWALGYNLVAIPLAAGGLLPLWLLAVLLHEGS 545 >gnl|CDD|178242 PLN02635, PLN02635, disproportionating enzyme. Length = 538 Score = 28.6 bits (64), Expect = 2.7 Identities = 20/59 (33%), Positives = 25/59 (42%), Gaps = 12/59 (20%) Query: 336 RDINTKLCNVSLLITPEILQKQGSLEITIIPPSNDNDKVKF---------IIKSAIENL 385 +D N C +LLI+ E L K G LE +P KV F +I A E L Sbjct: 89 QDAN---CGNTLLISLEELVKDGLLEEDELPEPVPVGKVDFSAVAELKDPLIAKAAERL 144 >gnl|CDD|131015 TIGR01960, ndhF3_CO2, NAD(P)H dehydrogenase, subunit NdhF3 family. This family represents a subfamily of NAD(P)H dehydrogenase subunit 5, or ndhF. It is restricted to two paralogs in each completed cyanobacterial genome, in which several subtypes of ndhF are found. Included in this family is NdhF3, shown to play a role in high-affinity CO2 uptake in Synechococcus sp. PCC7002. In all cases, neighboring genes include a paralog of ndhD but do include other NAD(P)H dehydrogenase subunits. Instead, genes related to C02 uptake tend to be found nearby. Length = 606 Score = 28.5 bits (64), Expect = 2.8 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 7/49 (14%) Query: 99 FLIKHFHCIPVYGLIANILAIPILSFVVI------PAGLIAILLMILSL 141 L++ +P YGLI +L++P S + PAG +L+ ++ Sbjct: 4 SLLETSWLVPFYGLIGALLSLP-WSPGITRQTGPRPAGYFNLLMTFVAF 51 >gnl|CDD|148126 pfam06325, PrmA, Ribosomal protein L11 methyltransferase (PrmA). This family consists of several Ribosomal protein L11 methyltransferase (EC:2.1.1.-) sequences. Length = 294 Score = 27.6 bits (62), Expect = 5.9 Identities = 13/60 (21%), Positives = 21/60 (35%), Gaps = 14/60 (23%) Query: 81 LNEIRANIGTYGSASASIFLIKHFHCIPVYGLIANILAIPILSFV------VIPAGLIAI 134 LN + A + Y ++ANILA P++ V P G + + Sbjct: 205 LNGVEAQLEVYLPGDLPE--------GKADVVVANILADPLIELAPDIYALVKPGGYLIL 256 >gnl|CDD|161838 TIGR00360, ComEC_N-term, ComEC/Rec2-related protein. The related model ComEC_Rec2 (TIGR00361) describes a set of proteins of ~ 700-800 residues, one each from a number of different species, of which most can become competent for natural transformation with exogenous DNA. The best-studied examples are ComEC from Bacillus subtilis and Rec-2 from Haemophilus influenzae, where the protein appears to form part of the DNA import structure. This model represents a region found in full-length ComEC/Rec2 and shorter homologs of unknown function from large number of additional bacterial species, most of which are not known to become competent for transformation (an exception is Helicobacter pylori). Length = 171 Score = 27.3 bits (61), Expect = 6.5 Identities = 12/29 (41%), Positives = 21/29 (72%) Query: 100 LIKHFHCIPVYGLIANILAIPILSFVVIP 128 L+ FH + ++AN+LAIP+ SF+++P Sbjct: 142 LLYLFHGLSPISVLANLLAIPLYSFLLLP 170 >gnl|CDD|129873 TIGR00791, gntP, gluconate transporter. This family includes known gluconate transporters of E. coli and Bacillus species as well as an idonate transporter from E. coli. Length = 440 Score = 26.9 bits (60), Expect = 8.7 Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 4/60 (6%) Query: 105 HCIPVYGLIANILAI----PILSFVVIPAGLIAILLMILSLDNIPFGVMAWGLDIIIHIA 160 C G IA IL I V+I +G+ + ++S NI +MAW + I+ IA Sbjct: 292 SCGSAIGSIAMILLIIGGGGAFKQVLIDSGVGDYIAELMSGMNISPILMAWLIAAILRIA 351 >gnl|CDD|162101 TIGR00911, 2A0308, L-type amino acid transporter. Length = 501 Score = 27.0 bits (60), Expect = 8.9 Identities = 25/115 (21%), Positives = 51/115 (44%), Gaps = 11/115 (9%) Query: 113 IANILAIPILSFVVI-----------PAGLIAILLMILSLDNIPFGVMAWGLDIIIHIAH 161 IA I+++PI++F+ + P L+A L + + GVM+W + ++ ++ Sbjct: 270 IAIIISMPIVTFIYVLTNIAYFTVLSPEELLASLAVAVDFGERLLGVMSWAMPALVGLSC 329 Query: 162 RISVAHNEFCIGRIPETSFVTIVVEFLLMVFCKTNIRHIGSIMIGITIIILFTFP 216 SV + F R+ + LL + + + S++I T+ +L F Sbjct: 330 FGSVNGSLFSSSRLFFVGGREGHLPSLLSMIHVKRLTPLPSLLIVCTLTLLMLFS 384 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 0.325 0.141 0.425 Gapped Lambda K H 0.267 0.0680 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 6,439,016 Number of extensions: 420374 Number of successful extensions: 1247 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1246 Number of HSP's successfully gapped: 41 Length of query: 394 Length of database: 5,994,473 Length adjustment: 95 Effective length of query: 299 Effective length of database: 3,941,713 Effective search space: 1178572187 Effective search space used: 1178572187 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 58 (26.2 bits)