RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780996|ref|YP_003065409.1| hypothetical protein CLIBASIA_04485 [Candidatus Liberibacter asiaticus str. psy62] (109 letters) >gnl|CDD|33631 COG3839, MalK, ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]. Length = 338 Score = 30.2 bits (68), Expect = 0.13 Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 6/55 (10%) Query: 11 SGCGKNPVWDSMKGCLNFSSYDDNSGNIDTDESDINTAIAIRKDVARVLQVSYPL 65 SGCGK+ + + G + SG I D D+ ++ +A V Q +Y L Sbjct: 38 SGCGKSTLLRMIAGLE-----EPTSGEILIDGRDVTDLPPEKRGIAMVFQ-NYAL 86 >gnl|CDD|32727 COG2902, COG2902, NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]. Length = 1592 Score = 27.2 bits (60), Expect = 1.1 Identities = 8/31 (25%), Positives = 16/31 (51%) Query: 21 SMKGCLNFSSYDDNSGNIDTDESDINTAIAI 51 ++ G + DNS +D + ++N IA+ Sbjct: 1135 ALAGGRINTDAIDNSAGVDCSDHEVNIKIAL 1165 >gnl|CDD|33953 COG4228, COG4228, Mu-like prophage DNA circulation protein [General function prediction only]. Length = 451 Score = 26.9 bits (59), Expect = 1.2 Identities = 10/52 (19%), Positives = 18/52 (34%), Gaps = 2/52 (3%) Query: 11 SGCG--KNPVWDSMKGCLNFSSYDDNSGNIDTDESDINTAIAIRKDVARVLQ 60 SG G +P + +M +N DD++ IN + + Sbjct: 80 SGAGTLVHPDYGTMNVLINAFERDDSAAEQRVFRFTINATPVFDRTAPEITF 131 >gnl|CDD|34408 COG4799, COG4799, Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]. Length = 526 Score = 26.7 bits (59), Expect = 1.3 Identities = 16/66 (24%), Positives = 23/66 (34%) Query: 33 DNSGNIDTDESDINTAIAIRKDVARVLQVSYPLPAPQEITPRMGNRKTVELLIEIDDQKV 92 SG D D AI + + + L + P P TP +R EL + D Sbjct: 226 RKSGVADLLAEDDEDAIELVRRLLSYLPSNNREPPPVVPTPDEPDRDDEELDSIVPDDPR 285 Query: 93 WLLNVH 98 +V Sbjct: 286 KPYDVR 291 >gnl|CDD|107386 cd06391, PBP1_iGluR_delta_2, N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 are closer related to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq and tumor necrosis factor family that is secreted from cerebellar granule cells. Length = 400 Score = 26.1 bits (57), Expect = 2.0 Identities = 16/73 (21%), Positives = 34/73 (46%), Gaps = 2/73 (2%) Query: 27 NFSSYDDNSGNIDTDESDINTAIAIRKDVARVLQVSYPLPAPQEITPR--MGNRKTVELL 84 N ++D + I+ + SD++ +R+ + R+ + P PQ I+ R GN + L Sbjct: 223 NLVAFDCHWIIINEEISDMDVQELVRRSIGRLTIIRQTFPLPQNISQRCFRGNHRISSSL 282 Query: 85 IEIDDQKVWLLNV 97 + D ++ + Sbjct: 283 CDPKDPFAQMMEI 295 >gnl|CDD|73012 cd03253, ABCC_ATM1_transporter, ATM1 is an ABC transporter that is expressed in the mitochondria. Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.. Length = 236 Score = 25.9 bits (57), Expect = 2.3 Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 7/52 (13%) Query: 11 SGCGKNPVWDSMKGCLNFSSYDDNSGNIDTDESDIN--TAIAIRKDVARVLQ 60 SG GK+ + ++ L F YD +SG+I D DI T ++R+ + V Q Sbjct: 36 SGSGKSTI---LR--LLFRFYDVSSGSILIDGQDIREVTLDSLRRAIGVVPQ 82 >gnl|CDD|36850 KOG1637, KOG1637, KOG1637, Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 560 Score = 26.1 bits (57), Expect = 2.5 Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 3/29 (10%) Query: 3 EDKWYIFYSGCGKNPVWDSMKGCLNFSSY 31 +D +IF C + V + +KGCL+F Y Sbjct: 302 QDDAHIF---CTPDQVKEEIKGCLDFLDY 327 >gnl|CDD|35260 KOG0037, KOG0037, KOG0037, Ca2+-binding protein, EF-Hand protein superfamily [Signal transduction mechanisms]. Length = 221 Score = 24.9 bits (54), Expect = 4.6 Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 2/27 (7%) Query: 18 VWDSMKGCLN-FSSYD-DNSGNIDTDE 42 +W + N F +YD D SG ID+ E Sbjct: 119 LWKYINQWRNVFRTYDRDRSGTIDSSE 145 >gnl|CDD|34862 COG5265, ATM1, ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]. Length = 497 Score = 24.8 bits (54), Expect = 5.0 Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 7/52 (13%) Query: 11 SGCGKNPVWDSMKGCLNFSSYDDNSGNIDTDESDIN--TAIAIRKDVARVLQ 60 SG GK+ + L F YD NSG+I D DI T ++R+ + V Q Sbjct: 298 SGAGKSTILR-----LLFRFYDVNSGSITIDGQDIRDVTQQSLRRAIGIVPQ 344 >gnl|CDD|73060 cd03301, ABC_MalK_N, The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed.. Length = 213 Score = 24.7 bits (54), Expect = 5.6 Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 6/55 (10%) Query: 11 SGCGKNPVWDSMKGCLNFSSYDDNSGNIDTDESDINTAIAIRKDVARVLQVSYPL 65 SGCGK + G + SG I D+ +D+A V Q +Y L Sbjct: 35 SGCGKTTTLRMIAGL-----EEPTSGRIYIGGRDVTDLPPKDRDIAMVFQ-NYAL 83 >gnl|CDD|32824 COG3007, COG3007, Uncharacterized paraquat-inducible protein B [Function unknown]. Length = 398 Score = 24.5 bits (53), Expect = 6.0 Identities = 13/42 (30%), Positives = 21/42 (50%) Query: 36 GNIDTDESDINTAIAIRKDVARVLQVSYPLPAPQEITPRMGN 77 G+ +DE AI++D +V V Y L +P+ P+ G Sbjct: 110 GDAFSDEMKQKVIEAIKQDFGKVDLVVYSLASPRRKHPKTGE 151 >gnl|CDD|39604 KOG4403, KOG4403, KOG4403, Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]. Length = 575 Score = 24.7 bits (53), Expect = 6.5 Identities = 8/13 (61%), Positives = 12/13 (92%) Query: 32 DDNSGNIDTDESD 44 DD++G+ID +ESD Sbjct: 79 DDHNGSIDVEESD 91 >gnl|CDD|173856 cd08491, PBP2_NikA_DppA_OppA_like_12, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 473 Score = 24.3 bits (53), Expect = 7.0 Identities = 6/27 (22%), Positives = 14/27 (51%) Query: 38 IDTDESDINTAIAIRKDVARVLQVSYP 64 ++T E+D+ +IA++ +Y Sbjct: 202 VETGEADLAPSIAVQDATNPDTDFAYL 228 >gnl|CDD|39350 KOG4147, KOG4147, KOG4147, Uncharacterized conserved protein [Function unknown]. Length = 127 Score = 23.8 bits (51), Expect = 9.9 Identities = 8/18 (44%), Positives = 10/18 (55%) Query: 79 KTVELLIEIDDQKVWLLN 96 KT L+I +D WLL Sbjct: 74 KTNNLVINLDHDDRWLLK 91 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 0.417 Gapped Lambda K H 0.267 0.0520 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,356,936 Number of extensions: 59216 Number of successful extensions: 153 Number of sequences better than 10.0: 1 Number of HSP's gapped: 153 Number of HSP's successfully gapped: 14 Length of query: 109 Length of database: 6,263,737 Length adjustment: 75 Effective length of query: 34 Effective length of database: 4,643,062 Effective search space: 157864108 Effective search space used: 157864108 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 (21.7 bits) S2: 51 (23.9 bits)