RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780274|ref|YP_003064687.1| lysophospholipase protein [Candidatus Liberibacter asiaticus str. psy62] (317 letters) >gnl|CDD|32448 COG2267, PldB, Lysophospholipase [Lipid metabolism]. Length = 298 Score = 54.7 bits (131), Expect = 3e-08 Identities = 42/236 (17%), Positives = 87/236 (36%), Gaps = 20/236 (8%) Query: 27 PRAIILACQSIEENIEDYNDFREYFAEENVAVYIYSYR---NTIKTTSDYLRDYPKNTSD 83 P+ +++ + E+ Y + + A VY R + + ++ + Sbjct: 33 PKGVVVLVHGLGEHSGRYEELADDLAARGFDVYALDLRGHGRSPRGQRGHVDSF------ 86 Query: 84 TTIVCDVMKLRTLISEKHGNTSVLLFGYSLGTIIALSTLLKYPQKFSGIALWNLDLCFEK 143 V D+ I+E V L G+S+G +IAL L +YP + G+ L + Sbjct: 87 ADYVDDLDAFVETIAEPDPGLPVFLLGHSMGGLIALLYLARYPPRIDGLVLSS--PALG- 143 Query: 144 YSCMLMTLLLKIEKFFKGSDTPSRLMRHLTTDLWNRNNQNWKNFLKDHSVKKNSQNYILD 203 L +L++ R+ L D + +D + + L Sbjct: 144 ----LGGAILRLILARLALKLLGRIRPKLPVDSNLLEGVLTDDLSRDPAEVAAYEADPLI 199 Query: 204 SNHIPISVWLEFMSMATDISSRGSFNPLSRFIPFCLIGGGN--VSSKIEDLTQTYK 257 P+S W++ +A + + + + +P L+ GG+ V +E L + ++ Sbjct: 200 GVGGPVSRWVDLALLAGRVPAL--RDAPAIALPVLLLQGGDDRVVDNVEGLARFFE 253 >gnl|CDD|36668 KOG1455, KOG1455, KOG1455, Lysophospholipase [Lipid transport and metabolism]. Length = 313 Score = 42.2 bits (99), Expect = 2e-04 Identities = 32/117 (27%), Positives = 47/117 (40%), Gaps = 7/117 (5%) Query: 21 NQTHKTPRAIILACQSI-EENIEDYNDFREYFAEENVAVYIYSYRNTIKTTSDYLRDYPK 79 + PR ++ C E + Y + A+ AVY Y + SD L Y Sbjct: 47 PLSGTEPRGLVFLCHGYGEHSSWRYQSTAKRLAKSGFAVYAIDYEGHGR--SDGLHAYVP 104 Query: 80 NTSDTTIVCDVMKLRTLISEKHGNTSV--LLFGYSLGTIIALSTLLKYPQKFSGIAL 134 + +V DV+ I E+ N + LFG S+G +AL LK P + G L Sbjct: 105 SFDL--VVDDVISFFDSIKEREENKGLPRFLFGESMGGAVALLIALKDPNFWDGAIL 159 >gnl|CDD|30749 COG0400, COG0400, Predicted esterase [General function prediction only]. Length = 207 Score = 37.6 bits (87), Expect = 0.005 Identities = 13/29 (44%), Positives = 17/29 (58%) Query: 106 VLLFGYSLGTIIALSTLLKYPQKFSGIAL 134 ++L G+S G IALS L P F+G L Sbjct: 101 IILIGFSQGANIALSLGLTLPGLFAGAIL 129 >gnl|CDD|30941 COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]. Length = 282 Score = 35.1 bits (78), Expect = 0.023 Identities = 12/38 (31%), Positives = 22/38 (57%) Query: 99 EKHGNTSVLLFGYSLGTIIALSTLLKYPQKFSGIALWN 136 + G V+L G+S+G +AL+ L++P + G+ L Sbjct: 83 DALGLEKVVLVGHSMGGAVALALALRHPDRVRGLVLIG 120 >gnl|CDD|144228 pfam00561, Abhydrolase_1, alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes. Length = 225 Score = 34.8 bits (80), Expect = 0.030 Identities = 13/36 (36%), Positives = 20/36 (55%) Query: 99 EKHGNTSVLLFGYSLGTIIALSTLLKYPQKFSGIAL 134 + G V L G+S+G +IAL+ KYP + + L Sbjct: 36 QALGLDKVNLVGHSMGGLIALAYAAKYPDRVKALVL 71 >gnl|CDD|145406 pfam02230, Abhydrolase_2, Phospholipase/Carboxylesterase. This family consists of both phospholipases and carboxylesterases with broad substrate specificity, and is structurally related to alpha/beta hydrolases pfam00561. Length = 213 Score = 32.7 bits (75), Expect = 0.12 Identities = 12/27 (44%), Positives = 17/27 (62%) Query: 106 VLLFGYSLGTIIALSTLLKYPQKFSGI 132 ++L G+S G +AL T L PQ +GI Sbjct: 104 IILGGFSQGGAVALYTALTLPQPLAGI 130 >gnl|CDD|39380 KOG4178, KOG4178, KOG4178, Soluble epoxide hydrolase [Lipid transport and metabolism]. Length = 322 Score = 31.8 bits (72), Expect = 0.24 Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 1/61 (1%) Query: 76 DYPKNTSDTTIVCDVMKLRTLISEKHGNTSVLLFGYSLGTIIALSTLLKYPQKFSGIALW 135 D P + S+ TI V + L+ + G L G+ G I+A L YP++ G+ Sbjct: 86 DAPPHISEYTIDELVGDIVALL-DHLGLKKAFLVGHDWGAIVAWRLALFYPERVDGLVTL 144 Query: 136 N 136 N Sbjct: 145 N 145 >gnl|CDD|34644 COG5039, COG5039, Exopolysaccharide biosynthesis protein [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]. Length = 339 Score = 31.5 bits (71), Expect = 0.29 Identities = 15/97 (15%), Positives = 30/97 (30%), Gaps = 6/97 (6%) Query: 190 DHSVKKNSQNYILDSNHIPISVWLEFMSMATDISSRGSFNPLSRFIPFCLIGGGNVSSKI 249 DH++ + ++ + + + GGGN+ Sbjct: 45 DHAIAYAEKAFLKQHYGDKVYYEASVKDFSASELIEIKSDIPE--DIIFFTGGGNLG--- 99 Query: 250 EDLTQTYKLTTRLQNEEFYDISLMSLPPTMHSNDPHN 286 DL Y+ F D ++ LP +++ D N Sbjct: 100 -DLYPDYQNFREKIISTFPDYKIIILPQSIYFQDQKN 135 >gnl|CDD|32647 COG2819, COG2819, Predicted hydrolase of the alpha/beta superfamily [General function prediction only]. Length = 264 Score = 31.5 bits (71), Expect = 0.34 Identities = 11/27 (40%), Positives = 14/27 (51%) Query: 108 LFGYSLGTIIALSTLLKYPQKFSGIAL 134 + G+SLG + L LL YP F L Sbjct: 141 IIGHSLGGLFVLFALLTYPDCFGRYGL 167 >gnl|CDD|36667 KOG1454, KOG1454, KOG1454, Predicted hydrolase/acyltransferase (alpha/beta hydrolase superfamily) [General function prediction only]. Length = 326 Score = 30.4 bits (68), Expect = 0.59 Identities = 46/240 (19%), Positives = 73/240 (30%), Gaps = 30/240 (12%) Query: 80 NTSDTTIVCDVMKLRTLIS---EKHGNTSVLLFGYSLGTIIALSTLLKYPQKFSGIALWN 136 + + + +L LI ++ V L G+SLG I+AL YP+ + L + Sbjct: 101 SPLPRGPLYTLRELVELIRRFVKEVFVEPVSLVGHSLGGIVALKAAAYYPETVDSLVLLD 160 Query: 137 LDLCFEKY--SCMLMTLLLKIEKFFKGSDTPSRLMRHLTTDLWNRNNQNWKNFLKDHSVK 194 L L Y + L ++KF + L L + + Sbjct: 161 L-LGPPVYSTPKGIKGLRRLLDKFLSALELLIPLSLTEPVRLVSE-GLLRCLKVVYTDPS 218 Query: 195 KNSQNYIL-----DSNHIPISVWLEFMSMATDISSRGSFNPLS-----RFIPFCLIGGGN 244 + + + H L N LS P +I G Sbjct: 219 RLLEKLLHLLSRPVKEHFHRDARLSLFL----ELLGFDENLLSLIKKIWKCPVLIIWGD- 273 Query: 245 VSSKIEDLTQTYKLTTRLQNEEFYDISLMSLPPTMHSNDPHNVFPPPAIKKLRNWIVNSY 304 +I L +L +L N E +I P H PH P LR++I Sbjct: 274 -KDQIVPLELAEELKKKLPNAELVEI-----PGAGH--LPHLERPEEVAALLRSFIARLR 325 >gnl|CDD|35887 KOG0668, KOG0668, KOG0668, Casein kinase II, alpha subunit [Signal transduction mechanisms, Cell cycle control, cell division, chromosome partitioning, Transcription]. Length = 338 Score = 29.9 bits (67), Expect = 0.87 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 7/49 (14%) Query: 122 LLKYPQKFSGIALWNLDLCFEKYSCMLMTLLLKIEKFFKGSDTPSRLMR 170 L+ Y + +W+L CML +++ + E FF G D +L++ Sbjct: 204 LVDYQMYDYSLDMWSL-------GCMLASMIFRKEPFFHGHDNYDQLVK 245 >gnl|CDD|144380 pfam00756, Esterase, Putative esterase. This family contains Esterase D. However it is not clear if all members of the family have the same function. This family is related to the pfam00135 family. Length = 243 Score = 29.3 bits (66), Expect = 1.3 Identities = 10/23 (43%), Positives = 13/23 (56%) Query: 108 LFGYSLGTIIALSTLLKYPQKFS 130 L G S+G + AL L YP +F Sbjct: 115 LAGQSMGGLGALYLALHYPDRFG 137 >gnl|CDD|163683 cd07945, DRE_TIM_CMS, Leptospira interrogans citramalate synthase (CMS) and related proteins, N-terminal catalytic TIM barrel domain. Citramalate synthase (CMS) catalyzes the conversion of pyruvate and acetyl-CoA to (R)-citramalate in the first dedicated step of the citramalate pathway. Citramalate is only found in Leptospira interrogans and a few other microorganisms. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM". Length = 280 Score = 29.3 bits (66), Expect = 1.7 Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 14/72 (19%) Query: 18 HSYNQTHKTPRAIILACQSIEENIEDYNDFREYFAEEN---VAVYIYSYRNTIKTTSDYL 74 H Q KTP EE+ D + EY A +N V +Y+ + N ++ + DY+ Sbjct: 101 HCTEQLRKTP----------EEHFADIREVIEY-AIKNGIEVNIYLEDWSNGMRDSPDYV 149 Query: 75 RDYPKNTSDTTI 86 SD I Sbjct: 150 FQLVDFLSDLPI 161 >gnl|CDD|32528 COG2382, Fes, Enterochelin esterase and related enzymes [Inorganic ion transport and metabolism]. Length = 299 Score = 28.0 bits (62), Expect = 3.2 Identities = 9/27 (33%), Positives = 18/27 (66%) Query: 107 LLFGYSLGTIIALSTLLKYPQKFSGIA 133 +L G SLG +++L L++P++F + Sbjct: 180 VLAGDSLGGLVSLYAGLRHPERFGHVL 206 >gnl|CDD|34934 COG5368, COG5368, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 451 Score = 27.7 bits (61), Expect = 3.9 Identities = 12/40 (30%), Positives = 18/40 (45%) Query: 145 SCMLMTLLLKIEKFFKGSDTPSRLMRHLTTDLWNRNNQNW 184 + +LM LL +F G D +R DL+ R + W Sbjct: 126 TALLMAGLLCARAYFDGQDEDEIEIRQSAADLYERVDWAW 165 >gnl|CDD|35263 KOG0040, KOG0040, KOG0040, Ca2+-binding actin-bundling protein (spectrin), alpha chain (EF-Hand protein superfamily) [Cytoskeleton]. Length = 2399 Score = 27.7 bits (61), Expect = 4.9 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 5/76 (6%) Query: 1 MSQKTFLTEDETIHKSVHSYNQTHKTPRAIILACQSIEENIEDYNDFREYFAEENVAVYI 60 + + F ED + + S NQ ++ +A +++ED ++Y A+ N A Sbjct: 851 VEEGHFAAED--VRSRLKSLNQNWESLKA---KASQRRQDLEDSLQAQQYLADANEAESW 905 Query: 61 YSYRNTIKTTSDYLRD 76 + I ++DY +D Sbjct: 906 MREKEPIVGSTDYGKD 921 >gnl|CDD|39592 KOG4391, KOG4391, KOG4391, Predicted alpha/beta hydrolase BEM46 [General function prediction only]. Length = 300 Score = 27.3 bits (60), Expect = 5.2 Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 6/82 (7%) Query: 55 NVAVYIYSYRNTIKTTSDYLRDYPKNTSDTTIVCDVMKLRTLISEKHGNTSVLLFGYSLG 114 + V I SYR K+ + K S+ + D + R + + T ++LFG SLG Sbjct: 106 KMNVLIVSYRGYGKSEGSPSEEGLKLDSEAVL--DYLMTRPDLDK----TKIVLFGRSLG 159 Query: 115 TIIALSTLLKYPQKFSGIALWN 136 +A+ K + S I + N Sbjct: 160 GAVAIHLASKNSDRISAIIVEN 181 >gnl|CDD|114026 pfam05277, DUF726, Protein of unknown function (DUF726). This family consists of several uncharacterized eukaryotic proteins. Length = 343 Score = 27.4 bits (61), Expect = 5.5 Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%) Query: 95 TLISEKHGNTSVLLFGYSLGTIIALSTLLK-YPQKFSGI 132 LIS G V L G+SLG + LL+ +K G+ Sbjct: 209 ALISRNLGVRPVTLIGFSLGARVIFYCLLELAKRKAYGL 247 >gnl|CDD|133313 cd04113, Rab4, Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 161 Score = 27.2 bits (61), Expect = 5.9 Identities = 6/15 (40%), Positives = 10/15 (66%) Query: 221 DISSRGSFNPLSRFI 235 DI++R SF L ++ Sbjct: 81 DITNRTSFEALPTWL 95 >gnl|CDD|36343 KOG1128, KOG1128, KOG1128, Uncharacterized conserved protein, contains TPR repeats [General function prediction only]. Length = 777 Score = 27.3 bits (60), Expect = 5.9 Identities = 14/80 (17%), Positives = 29/80 (36%), Gaps = 11/80 (13%) Query: 150 TLLLKIEKFFKGSDTPSRLMRHLTTDLWNRNNQNWKNFLKDH-SVKKNSQNYILD----- 203 L++EK R +T + N + W N + +KK + + Sbjct: 527 CAALQLEKEQAAVKA---FHRCVTLEPDNA--EAWNNLSTAYIRLKKKKRAFRKLKEALK 581 Query: 204 SNHIPISVWLEFMSMATDIS 223 N+ +W +M ++ D+ Sbjct: 582 CNYQHWQIWENYMLVSVDVG 601 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 0.319 0.134 0.403 Gapped Lambda K H 0.267 0.0672 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,938,869 Number of extensions: 203094 Number of successful extensions: 556 Number of sequences better than 10.0: 1 Number of HSP's gapped: 556 Number of HSP's successfully gapped: 29 Length of query: 317 Length of database: 6,263,737 Length adjustment: 94 Effective length of query: 223 Effective length of database: 4,232,491 Effective search space: 943845493 Effective search space used: 943845493 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 (21.8 bits) S2: 57 (25.9 bits)