RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780448|ref|YP_003064861.1| hypothetical protein CLIBASIA_01665 [Candidatus Liberibacter asiaticus str. psy62] (311 letters) >gnl|CDD|119324 cd06582, TM_PBP1_LivH_like, Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH 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 LivH forms a heterodimer with another TM, LivM, to generate the transmembrane pore. LivM 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 = 272 Score = 30.5 bits (70), Expect = 0.60 Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 9/50 (18%) Query: 29 LLAIPAAYLGKVLFGLV---------RGSSIATKIATTGIATVVQEATVM 69 LA+ A L L G++ RG+ + T + T G ++ + ++ Sbjct: 52 WLALLLALLVAALLGVLLERLVLRPLRGAPLLTLLITFGGLLILLQGLLL 101 >gnl|CDD|32727 COG2902, COG2902, NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]. Length = 1592 Score = 28.8 bits (64), Expect = 1.9 Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 14/94 (14%) Query: 217 EKVQLISSYAHEHIFCKPFTKDLLNLANKNIYQLSNPRYSYQ-FNTLKDKTIS----FVA 271 + ++LI+++ H HIF P DL + + PR S+ ++ IS V+ Sbjct: 984 KHIRLIAAFDHRHIFIDP-NPDLAVSFAERKRLFALPRSSWSDYDA---SKISKGGGVVS 1039 Query: 272 KEEGLVTYLNGSLHRNYGIKAEGILSRNAPPELH 305 + +T + GI AP EL Sbjct: 1040 RSAKAITLSPEVIAAL-GIDKT----ELAPNELI 1068 >gnl|CDD|33905 COG4158, COG4158, Predicted ABC-type sugar transport system, permease component [General function prediction only]. Length = 329 Score = 27.6 bits (61), Expect = 4.7 Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 5/49 (10%) Query: 23 IVSDVALLAIPAAYLGKVLFGLVRGSSIATK-----IATTGIATVVQEA 66 ++ A L+IPAA L +L GL G +A I T G T ++ A Sbjct: 98 LMPGWAALSIPAALLAGLLLGLFNGLLVAYAGLPPFIVTLGTYTALRGA 146 >gnl|CDD|33750 COG3969, COG3969, Predicted phosphoadenosine phosphosulfate sulfotransferase [General function prediction only]. Length = 407 Score = 27.6 bits (61), Expect = 4.8 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 1/57 (1%) Query: 241 NLANKNIYQLSNPRYSYQFNTLKDKTISFV-AKEEGLVTYLNGSLHRNYGIKAEGIL 296 ++N+ + + R + FNT +SF K+ GL+ +L + R G +L Sbjct: 6 IYLDENVLEAAIERLEWIFNTFPRVCVSFSGGKDSGLMLHLVAEVARENGRDKISVL 62 >gnl|CDD|37214 KOG2003, KOG2003, KOG2003, TPR repeat-containing protein [General function prediction only]. Length = 840 Score = 27.4 bits (60), Expect = 4.8 Identities = 37/175 (21%), Positives = 73/175 (41%), Gaps = 20/175 (11%) Query: 68 VMTKTTQEGALLAKEGIEATHIMEGGSTAIKSESVGAKELISASQNSQTVTQTGNIS--- 124 V K + A A + A ++GG ++ L N+ +T GNI+ Sbjct: 444 VFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNIDRYNAAALTNKGNIAFAN 503 Query: 125 -DATKASSTIKDAQSIDRS--QAIFQ-----------KMPLEEYPRLQKIGINYFRDFKL 170 D KA+ K+A + D S +A+F L+ + +L I +N L Sbjct: 504 GDLDKAAEFYKEALNNDASCTEALFNIGLTAEALGNLDEALDCFLKLHAILLNNAE--VL 561 Query: 171 LGTNKVYKNLLDASRATEFIIDGKKINIDSAQNMLAELNKIFPKDFEKVQLISSY 225 + +Y+ L D ++A E ++ + I + +L++L ++ ++ +K Q + Sbjct: 562 VQIANIYELLEDPAQAIELLMQANSL-IPNDPAILSKLADLYDQEGDKSQAFQCH 615 >gnl|CDD|145974 pfam03116, NQR2_RnfD_RnfE, NQR2, RnfD, RnfE family. This family of bacterial proteins includes a sodium-translocating NADH-ubiquinone oxidoreductase (i.e. a respiration linked sodium pump). In Vibrio cholerae, it negatively regulates the expression of virulence factors through inhibiting (by an unknown mechanism) the transcription of the transcriptional activator ToxT. The family also includes proteins involved in nitrogen fixation, RnfD and RnfE. The similarity of these proteins to NADH-ubiquinone oxidoreductases was previously noted. Length = 319 Score = 27.4 bits (62), Expect = 5.1 Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 4/39 (10%) Query: 15 NYGWGALGIVSDVALLAIPAAYLGKVLFGLVRGSSIATK 53 +G AL ++ L+A+ A L + LF +R + K Sbjct: 37 FFGLQALPVI----LVAVVVALLWEALFLKLRKRPVTFK 71 >gnl|CDD|114185 pfam05445, Pox_ser-thr_kin, Poxvirus serine/threonine protein kinase. Length = 434 Score = 27.4 bits (61), Expect = 5.3 Identities = 30/87 (34%), Positives = 41/87 (47%), Gaps = 15/87 (17%) Query: 161 GINYFRDFKLLGTNKVYKNLLDASRATEFIIDGKKINID--SAQNMLAELNKIFPKDFEK 218 GINY KLL +YK +L + I+DG+ +NI S + ML N+ KD EK Sbjct: 149 GINY----KLLFLIILYKRVLHMLLLIKQILDGQPLNITYLSFKKMLKIFNER--KDSEK 202 Query: 219 -VQLISSYAHEHIFCKPFTKDLLNLAN 244 V+L S F K +N+ N Sbjct: 203 FVKLFSY------FYPKVVKSNINVIN 223 >gnl|CDD|111458 pfam02561, FliS, Flagellar protein FliS. FliS is coded for by the FliD operon and is transcribed in conjunction with FliD and FliT, however this protein has no known function. Length = 122 Score = 27.0 bits (60), Expect = 6.1 Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 11/59 (18%) Query: 178 KNLLDASRATEFI----IDGKKINIDSAQNMLAELNKIFPKDFEK-----VQLISSYAH 227 K + RA EFI I+ K NI AQN++ EL D EK L++ Y + Sbjct: 28 KAIKALVRAAEFIENEDIEKKNENISKAQNIITELRSTL--DEEKGGEIAQNLLAIYTY 84 >gnl|CDD|185679 cd02064, FAD_synthetase_N, FAD synthetase, N-terminal domain of the bifunctional enzyme. FAD synthetase_N. N-terminal domain of the bifunctional riboflavin biosynthesis protein riboflavin kinase/FAD synthetase. These enzymes have both ATP:riboflavin 5'-phosphotransferase and ATP:FMN-adenylyltransferase activities. The N-terminal domain is believed to play a role in the adenylylation reaction of FAD synthetases. The C-terminal domain is thought to have kinase activity. FAD synthetase is present among all kingdoms of life. However, the bifunctional enzyme is not found in mammals, which use separate enzymes for FMN and FAD formation. Length = 180 Score = 27.1 bits (61), Expect = 6.8 Identities = 8/27 (29%), Positives = 17/27 (62%) Query: 217 EKVQLISSYAHEHIFCKPFTKDLLNLA 243 EK++L+ S +++ PF K+ +L+ Sbjct: 60 EKLELLESLGVDYLLVLPFDKEFASLS 86 >gnl|CDD|144323 pfam00681, Plectin, Plectin repeat. This family includes repeats from plectin, desmoplakin, envoplakin and bullous pemphigoid antigen. Length = 45 Score = 27.0 bits (61), Expect = 6.9 Identities = 10/27 (37%), Positives = 17/27 (62%), Gaps = 3/27 (11%) Query: 178 KNLLDASRATEFIID---GKKINIDSA 201 LL+A AT IID G++++++ A Sbjct: 1 LRLLEAQAATGGIIDPETGERLSVEEA 27 >gnl|CDD|147208 pfam04925, SHQ1, SHQ1 protein. S. cerevisiae SHQ1 protein is required for SnoRNAs of the box H/ACA Quantitative accumulation (unpublished). Length = 186 Score = 26.8 bits (60), Expect = 8.2 Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 9/47 (19%) Query: 246 NIYQLSNPRYSY--QFNTLKDKTISFVAKEEGLVTYLNGSLHRNYGI 290 I +LS P+ S+ F+ +KD I+F+ + +TY L+RN+ + Sbjct: 68 TIGKLS-PQLSWLDSFSNVKDALIAFIRR---ALTY---PLYRNFDL 107 >gnl|CDD|32710 COG2884, FtsE, Predicted ATPase involved in cell division [Cell division and chromosome partitioning]. Length = 223 Score = 26.7 bits (59), Expect = 8.5 Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 2/33 (6%) Query: 148 KMPLEEYPRL-QKIGINYFRDFKLLGTNKVYKN 179 ++ E P L ++IG+ F+DF+LL VY+N Sbjct: 68 RLKGREIPFLRRQIGV-VFQDFRLLPDRTVYEN 99 >gnl|CDD|146010 pfam03172, Sp100, Sp100 domain. The function of this domain is unknown. It is about 105 amino acid residues in length and is predicted to be predominantly alpha helical. This domain is usually found at the amino terminus of protein that contain a SAND domain pfam01342. Length = 104 Score = 26.5 bits (59), Expect = 8.7 Identities = 10/17 (58%), Positives = 13/17 (76%) Query: 144 AIFQKMPLEEYPRLQKI 160 A+F + LEEYP LQ+I Sbjct: 78 ALFSDVNLEEYPDLQEI 94 >gnl|CDD|39770 KOG4570, KOG4570, KOG4570, Uncharacterized conserved protein [Function unknown]. Length = 418 Score = 26.6 bits (58), Expect = 9.9 Identities = 11/43 (25%), Positives = 19/43 (44%) Query: 35 AYLGKVLFGLVRGSSIATKIATTGIATVVQEATVMTKTTQEGA 77 YLG+VL + + ++ A V A + T+ +GA Sbjct: 254 GYLGRVLQVMEKEAASPEDSKACREALDVLAAVLKALTSADGA 296 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 0.131 0.362 Gapped Lambda K H 0.267 0.0753 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,364,680 Number of extensions: 166184 Number of successful extensions: 409 Number of sequences better than 10.0: 1 Number of HSP's gapped: 409 Number of HSP's successfully gapped: 25 Length of query: 311 Length of database: 6,263,737 Length adjustment: 94 Effective length of query: 217 Effective length of database: 4,232,491 Effective search space: 918450547 Effective search space used: 918450547 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: 57 (25.7 bits)