RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780170|ref|YP_003064583.1| cationic amino acid ABC transporter, periplasmic binding protein [Candidatus Liberibacter asiaticus str. psy62] (342 letters) >gnl|CDD|29040 cd00134, PBPb, Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.. Length = 218 Score = 112 bits (280), Expect = 2e-25 Identities = 59/229 (25%), Positives = 96/229 (41%), Gaps = 14/229 (6%) Query: 36 LKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLALQSK 95 L G F+ ANG+ GFDVD +A++ + K++++ ++ AL+S Sbjct: 1 LTVGTAGTYPPFSFRDANGELTGFDVDLAKAIAKEL---GVKVKFVEVDWDGLITALKSG 57 Query: 96 QIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGTT 155 ++D+++ T R + F Y GQ ++ K I SV L G + VQ G+T Sbjct: 58 KVDLIAAGMTITPERAKQV--DFSDPYYKSGQVILVKKGSPIKSVKDLKGKKVAVQKGST 115 Query: 156 TELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDRPSEHV 215 E Y K + + ++ E AA R DA D AL AL + P E Sbjct: 116 AE----KYLKKALPEAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKH--PPELK 169 Query: 216 ILPDIISKSPLAPAII--QGDTEWYNIVSWTHYAMVTAEEL-GITQKNI 261 I+ I PL + + + E + V+ + EL I++K Sbjct: 170 IVGPSIDLEPLGFGVAVGKDNKELLDAVNKALKELRADGELKKISKKWF 218 >gnl|CDD|31176 COG0834, HisJ, ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]. Length = 275 Score = 103 bits (258), Expect = 6e-23 Identities = 66/260 (25%), Positives = 106/260 (40%), Gaps = 11/260 (4%) Query: 7 VSILCLIILFFTSFSTNASILGDIKKRGFLKCGIN-TGLVGFAEVKA-NGDWKGFDVDFC 64 +++ L+ + A +L IK RG L+ G T F + A G GFDVD Sbjct: 7 LALAALLAALLLAACAAADLLDKIKARGKLRVGTEATYAPPFEFLDAKGGKLVGFDVDLA 66 Query: 65 RALSSAIFDDPSKIQYLPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYF 124 +A++ + D K++++P+ AL++ ++DI+ T R+ + F Y+ Sbjct: 67 KAIAKRLGGDK-KVEFVPVAWDGLIPALKAGKVDIIIAGMTITPERKKKV--DFSDPYYY 123 Query: 125 DGQGFIMHKKK--GISSVSQLSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEI 182 GQ ++ K GI S+ L G + VQ GTT E N K + ++ E Sbjct: 124 SGQVLLVKKDSDIGIKSLEDLKGKKVGVQLGTTDEAEEKAKKPGPNAK--IVAYDSNAEA 181 Query: 183 DAAYRAHRCDAYTGDISALYALKLTNDRPSEHVILPDIISK-SPLAPAIIQG-DTEWYNI 240 A + R DA D + L LKL P +V+L L A+ +G D E Sbjct: 182 LLALKNGRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYLGIALRKGDDPELLEA 241 Query: 241 VSWTHYAMVTAEELGITQKN 260 V+ + L Sbjct: 242 VNKALKELKADGTLQKISDK 261 >gnl|CDD|144186 pfam00497, SBP_bac_3, Bacterial extracellular solute-binding proteins, family 3. Length = 224 Score = 96.2 bits (240), Expect = 1e-20 Identities = 52/211 (24%), Positives = 91/211 (43%), Gaps = 15/211 (7%) Query: 36 LKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLALQSK 95 L+ G + F+ + +G GFDVD +A++ + K++++P++ ALQS Sbjct: 1 LRVGTDADYPPFSYLDEDGKLVGFDVDLAKAIAKRLGV---KVEFVPVSWDGLIPALQSG 57 Query: 96 QIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKK-----KGISSVSQLSGASICV 150 +ID++ T R+ + F Y+ GQ ++ K K I ++ L G + V Sbjct: 58 KIDVIIAGMTITPERKKK--VDFSDPYYYSGQVLVVRKDSPPKIKSIKDLADLKGKKVGV 115 Query: 151 QAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDR 210 Q GTT E L + ++++ E A A R DA D L Sbjct: 116 QKGTTQEDLLKELAP---KGAEIVLYDDQAEALQALAAGRVDAVVADSPVAAY--LIKKN 170 Query: 211 PSEHVILPDIISKSPLAPAIIQGDTEWYNIV 241 P ++++ + +S P A+ +GD E V Sbjct: 171 PGLNLVVGEPLSGEPYGIAVRKGDPELLAAV 201 >gnl|CDD|35943 KOG0724, KOG0724, KOG0724, Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]. Length = 335 Score = 29.5 bits (65), Expect = 1.2 Identities = 16/133 (12%), Positives = 27/133 (20%), Gaps = 13/133 (9%) Query: 159 TLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDRPSEHVILP 218 L D E + Y G + + N R S P Sbjct: 48 ILDDDEPRRTPDSWDKFAEALPLEKRLEDKIE--EYIGLVFDV------NIRESGQKPFP 99 Query: 219 DIISKSPLAPAIIQGDTEWYNIVSWTHYAMVTAEELG-----ITQKNINQVSKDTTNPDV 273 + + W SW Y + + + +N + Sbjct: 100 KYGKSDTSLAEVEEFYNFWPKFKSWRQYPQKDEPDEEDSENRSQSRYSGGTQRGKSNAEE 159 Query: 274 QRFLGIDKSSNIG 286 R G + Sbjct: 160 LRRKGTPVTERER 172 >gnl|CDD|36214 KOG0996, KOG0996, KOG0996, Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning]. Length = 1293 Score = 28.8 bits (64), Expect = 2.0 Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 9/56 (16%) Query: 130 IMHKKKGISSVSQLSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAA 185 + KK ++S LSG G T +LA F H Y P ++EIDAA Sbjct: 1183 VRPPKKSWKNISNLSG-------GEKTLSSLALVFALH--HYKPTPLYVMDEIDAA 1229 >gnl|CDD|146223 pfam03468, XS, XS domain. The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X and SGS3. SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain has recently been predicted to possess an RRM-like RNA-binding domain by fold recognition. Length = 118 Score = 28.1 bits (63), Expect = 3.3 Identities = 14/44 (31%), Positives = 17/44 (38%), Gaps = 9/44 (20%) Query: 23 NASILGDIKKRGFLKCGI-------NTGLVGFAEVKANGDWKGF 59 A + + K GF + G GFA VK DW GF Sbjct: 31 GAKLDDKLSKLGF--NPLKVKPLWNREGHTGFAIVKFAKDWSGF 72 >gnl|CDD|173948 cd08189, Fe-ADH5, Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and belongs to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contains different protein domain. Proteins of this family have not been characterized. Their specific function is unknown. Length = 374 Score = 27.9 bits (63), Expect = 3.6 Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 11/44 (25%) Query: 159 TLADYFKAHNMKYHPIVF---------ERVEEIDAAYRAHRCDA 193 + + + ++Y V+ E VE A YR + CDA Sbjct: 45 KVLEALEGAGIEY--AVYDGVPPDPTIENVEAGLALYRENGCDA 86 >gnl|CDD|173942 cd08183, Fe-ADH2, Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contains different protein domain. Proteins of this family have not been characterized. Their specific function is unknown. They are mainly found in bacteria. Length = 374 Score = 27.1 bits (61), Expect = 6.9 Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 6/40 (15%) Query: 160 LADYFKAHNMKYHPIVFER---VEEIDAA---YRAHRCDA 193 L + +A ++ +V VE +DAA R CD Sbjct: 39 LIEALRAAGIEVTHVVVAGEPSVELVDAAVAEARNAGCDV 78 >gnl|CDD|173951 cd08192, Fe-ADH7, Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. NAD-dependent iron-containing alcohol dehydrogenase-like. Proteins in this family are NAD-dependent alcohol dehydrogenases which are involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. They catalyze the oxidation of beta-hydroxy CoA ester to beta-oxo CoA ester, which then be subject to CoA-dependent thiolysis to yield acetyl-CoA and 6-C8-SPC-CoA. The major laundry surfactant in worldwide use is commercial linear alkylbenzenesulfonate (LAS) which contains 20 congeners of linear alkanes (C10 to C13). LAS is fully biodegradable in oxic environments. Degradation involves microbial communities. Parvibaculum lavamentivorans DS-1T is a representative member of many heterotrophic, LAS-degrading communities, in which it catalyzes the first steps of LAS degradation. Strain DS-1T is a small heterotrophic bacterium able to omega-oxygenate the commercial surfactant linear alkylbenzenesulfonate (LAS) and shorten the side chain by beta-oxidation to yield sulfophenylcarboxylates (SPC). Parvibaculum lavamentivorans utilizes 3-C12-LAS as the sole carbon and energy source, and excretes largely 4-C6-SPC. Length = 370 Score = 27.2 bits (61), Expect = 7.8 Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 7/35 (20%) Query: 184 AAYRAHRCDAYTG-------DISALYALKLTNDRP 211 AAYRA CD D++ AL + P Sbjct: 75 AAYRAGGCDGVIAFGGGSALDLAKAVALMAGHPGP 109 >gnl|CDD|28977 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.. Length = 58 Score = 27.0 bits (60), Expect = 8.2 Identities = 11/45 (24%), Positives = 24/45 (53%), Gaps = 6/45 (13%) Query: 251 AEELGITQKNINQVSKDTTNPDVQRFLGIDKSSNIGEALGLTKDW 295 AE+LG+++ I+++ NP ++ + +ALG++ D Sbjct: 19 AEKLGVSRSTISRIENGKRNPSLETLE------KLAKALGVSLDE 57 >gnl|CDD|144194 pfam00508, PPV_E2_N, E2 (early) protein, N terminal. Length = 201 Score = 26.7 bits (60), Expect = 9.8 Identities = 8/35 (22%), Positives = 16/35 (45%), Gaps = 8/35 (22%) Query: 84 NAKERFLALQSKQIDILSRNTD--------WTLLR 110 ER ALQ + +++ +++ W L+R Sbjct: 2 TLSERLDALQEQLLELYEKDSTDLEDQIEHWKLVR 36 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 0.322 0.138 0.418 Gapped Lambda K H 0.267 0.0747 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,243,682 Number of extensions: 220634 Number of successful extensions: 522 Number of sequences better than 10.0: 1 Number of HSP's gapped: 515 Number of HSP's successfully gapped: 16 Length of query: 342 Length of database: 6,263,737 Length adjustment: 95 Effective length of query: 247 Effective length of database: 4,210,882 Effective search space: 1040087854 Effective search space used: 1040087854 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 (21.9 bits) S2: 58 (26.1 bits)