RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781112|ref|YP_003065525.1| putative amino acid-binding periplasmic ABC transporter protein [Candidatus Liberibacter asiaticus str. psy62] (274 letters) >gnl|CDD|144186 pfam00497, SBP_bac_3, Bacterial extracellular solute-binding proteins, family 3. Length = 224 Score = 181 bits (462), Expect = 2e-46 Identities = 80/229 (34%), Positives = 117/229 (51%), Gaps = 13/229 (5%) Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102 LRVGTD YPP S+ D G+L GFD+DL K +A RL +KVEF + GLI L + + Sbjct: 1 LRVGTDADYPPFSYL--DEDGKLVGFDVDLAKAIAKRLGVKVEFVPVSWDGLIPALQSGK 58 Query: 103 YDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVRSD----QQDIRSFKDLTDKTVAQILG 157 DV++ + ITPER+KK DFS PY +LVVR D + I+ DL K V G Sbjct: 59 IDVIIAGMTITPERKKKVDFSDPYYYSGQVLVVRKDSPPKIKSIKDLADLKGKKVGVQKG 118 Query: 158 TDLSRFAKELKSH---LVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFK 214 T KEL +V + ++LQ L + R DA + +++ P L Sbjct: 119 TTQEDLLKELAPKGAEIVLYDDQAEALQALAAGRVDAVVADSPVAAYLIKKNP---GLNL 175 Query: 215 IADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDK 263 + +RKG+ +L ++N+ L + DGT K+++++F K Sbjct: 176 VVGEPLSGEPYGIAVRKGDPELLAAVNKALAELKADGTLAKLYEKWFGK 224 >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 = 144 bits (365), Expect = 2e-35 Identities = 79/224 (35%), Positives = 120/224 (53%), Gaps = 11/224 (4%) Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102 L VGT G YPP SF D GELTGFD+DL K +A L +KV+F E GLIT L + + Sbjct: 1 LTVGTAGTYPPFSFR--DANGELTGFDVDLAKAIAKELGVKVKFVEVDWDGLITALKSGK 58 Query: 103 YDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS 161 D++ + ITPER K+ DFS PY +++V+ I+S KDL K VA G+ Sbjct: 59 VDLIAAGMTITPERAKQVDFSDPYYKSGQVILVKKG-SPIKSVKDLKGKKVAVQKGSTAE 117 Query: 162 RFAKEL--KSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRM 219 ++ K+ ++ +V + ++L L + R DA ++ +I L++ P + KI Sbjct: 118 KYLKKALPEAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKHPPE---LKIVGPS 174 Query: 220 KDNSAVAFMM--RKGNNKLTRSINEILCAIHLDGTYKKIFDRYF 261 D + F + K N +L ++N+ L + DG KKI ++F Sbjct: 175 IDLEPLGFGVAVGKDNKELLDAVNKALKELRADGELKKISKKWF 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 = 137 bits (344), Expect = 4e-33 Identities = 77/244 (31%), Positives = 117/244 (47%), Gaps = 9/244 (3%) Query: 36 RTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLN--LKVEFFETAVSG 93 + + + LRVGT+ Y P G+L GFD+DL K +A RL KVEF A G Sbjct: 29 KIKARGKLRVGTEATYAPPFEFLDAKGGKLVGFDVDLAKAIAKRLGGDKKVEFVPVAWDG 88 Query: 94 LITGLDTNRYDVLV-NVAITPERQKKYDFSIPYI-AHRVLLVVRSDQQDIRSFKDLTDKT 151 LI L + D+++ + ITPER+KK DFS PY + +VLLV + I+S +DL K Sbjct: 89 LIPALKAGKVDIIIAGMTITPERKKKVDFSDPYYYSGQVLLVKKDSDIGIKSLEDLKGKK 148 Query: 152 VAQILGTDLSRFAKELK----SHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRP 207 V LGT K K + +V + ++L L + R DA + + Sbjct: 149 VGVQLGTTDEAEEKAKKPGPNAKIVAYDSNAEALLALKNGRADAVVSDSAVLAGLKLLKK 208 Query: 208 HDGNLFKIADRMKDNSAVAFMMRKGNNK-LTRSINEILCAIHLDGTYKKIFDRYFDKNII 266 + G + + +RKG++ L ++N+ L + DGT +KI D++F + Sbjct: 209 NPGLYVLLVFPGLSVEYLGIALRKGDDPELLEAVNKALKELKADGTLQKISDKWFGPDDY 268 Query: 267 SSVP 270 S P Sbjct: 269 SKAP 272 >gnl|CDD|34243 COG4623, COG4623, Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]. Length = 473 Score = 45.7 bits (108), Expect = 1e-05 Identities = 56/241 (23%), Positives = 88/241 (36%), Gaps = 41/241 (17%) Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFF-ETAVSGLITGLDTN 101 LRV T I P S+ + +G TG + +L K A L +K++ + L LD Sbjct: 25 LRVST--INSPLSYF--EDKGGPTGLEYELAKAFADYLGVKLKIIPADNIDQLFDALDNG 80 Query: 102 RYDVLV-NVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDL 160 D+ + ER K + Y + LV R Q RS L + + G+ Sbjct: 81 NADLAAAGLLYNSERLKNFQPGPTYYSVSQQLVYRKGQYRPRSLGQLKGRQITVAKGSAH 140 Query: 161 SRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNL-FKIAD-- 217 K LK E L+ K D + D L +G L + IAD Sbjct: 141 VEDLKLLK---------ETKYPELIWKVDDKLGVED------LLEMVAEGKLDYTIADSV 185 Query: 218 ------RMKDNSAVAF-----------MMRKGNNKLTRSINEILCAIHLDGTYKKIFDRY 260 R+ AVAF + R ++ L+ ++ + L DG ++ ++Y Sbjct: 186 EISLFQRVHPELAVAFDLTDEQPVAWYLPRDDDSTLSAALLDFLNEAKEDGLLARLEEKY 245 Query: 261 F 261 Sbjct: 246 L 246 >gnl|CDD|36270 KOG1052, KOG1052, KOG1052, Glutamate-gated kainate-type ion channel receptor subunit GluR5 and related subunits [Inorganic ion transport and metabolism, Amino acid transport and metabolism, Signal transduction mechanisms]. Length = 656 Score = 42.8 bits (100), Expect = 1e-04 Identities = 29/88 (32%), Positives = 43/88 (48%), Gaps = 11/88 (12%) Query: 61 GRGELTGFDIDLIKEVAHRLNLKVEFFETA-----------VSGLITGLDTNRYDVLVNV 109 G + GF+IDL++ +A RLN E GL+ L DV ++ Sbjct: 240 GNDRIEGFEIDLLQALAKRLNFSYEIIFVPDGSGSRDPNGNWDGLVGQLVDGEADVGADI 299 Query: 110 AITPERQKKYDFSIPYIAHRVLLVVRSD 137 ITPER K DF+IPY+ ++++VR Sbjct: 300 TITPERSKYVDFTIPYLQFGIVIIVRKP 327 >gnl|CDD|39641 KOG4440, KOG4440, KOG4440, NMDA selective glutamate-gated ion channel receptor subunit GRIN1 [Inorganic ion transport and metabolism, Amino acid transport and metabolism, Signal transduction mechanisms]. Length = 993 Score = 34.7 bits (79), Expect = 0.027 Identities = 19/95 (20%), Positives = 41/95 (43%), Gaps = 21/95 (22%) Query: 67 GFDIDLIKEVAHRLNLKVEFFETA--------------------VSGLITGLDTNRYDVL 106 GF IDL+ +++ +N + A +G+I L + + D++ Sbjct: 464 GFCIDLLIKLSRTMNFTYDVHLVADGKFGTQERVNNSSETNKKEWNGMIGELLSGQADMI 523 Query: 107 VN-VAITPERQKKYDFSIPYIAHRVLLVVRSDQQD 140 V + I PER + +FS P+ + ++ + + + Sbjct: 524 VAPLTINPERAQYIEFSKPFKYQGITILEKKEIRR 558 >gnl|CDD|146045 pfam03219, TLC, TLC ATP/ADP transporter. Length = 491 Score = 33.4 bits (77), Expect = 0.070 Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 2/27 (7%) Query: 10 KIFFSKYLFFAPFFILFSYYFVIYPFR 36 K+F+ FF FF LF+ FV+YP R Sbjct: 90 KVFYIIISFFLVFFALFA--FVLYPNR 114 >gnl|CDD|36271 KOG1053, KOG1053, KOG1053, Glutamate-gated NMDA-type ion channel receptor subunit GRIN2A and related subunits [Inorganic ion transport and metabolism, Amino acid transport and metabolism, Signal transduction mechanisms]. Length = 1258 Score = 32.3 bits (73), Expect = 0.13 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 13/84 (15%) Query: 67 GFDIDLIKEVAHRLNLKVEFF-----------ETAVSGLITGLDTNRYDVLV-NVAITPE 114 GF ID++K++A + + + +G+I + R D+ V ++ I E Sbjct: 467 GFCIDILKKLARDVKFTYDLYLVTNGKHGKKINGVWNGMIGEVVYQRADMAVGSLTINEE 526 Query: 115 RQKKYDFSIPYIAHRV-LLVVRSD 137 R + DFS+P++ + ++V RS+ Sbjct: 527 RSEVVDFSVPFVETGISVMVARSN 550 >gnl|CDD|39916 KOG4718, KOG4718, KOG4718, Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]. Length = 235 Score = 30.7 bits (69), Expect = 0.47 Identities = 22/120 (18%), Positives = 38/120 (31%), Gaps = 20/120 (16%) Query: 52 PPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLVNVAI 111 P + H G + D I E+ L + + + +D Y V VN+A Sbjct: 29 PLCANHVTTKPGSKEAIE-DFINEINDTL----HNLDQLIKRIKYPVDGREYLVYVNLAA 83 Query: 112 TPERQKKYDFS----------IPYIA-----HRVLLVVRSDQQDIRSFKDLTDKTVAQIL 156 TP+ + F+ + I H +D K L + ++L Sbjct: 84 TPDSKMATGFTANEIELFRKALEKIMSSEDCHIASSTAYNDIVLQAKSKPLKKSRIEELL 143 >gnl|CDD|33015 COG3202, COG3202, ATP/ADP translocase [Energy production and conversion]. Length = 509 Score = 30.2 bits (68), Expect = 0.59 Identities = 13/28 (46%), Positives = 18/28 (64%), Gaps = 2/28 (7%) Query: 9 RKIFFSKYLFFAPFFILFSYYFVIYPFR 36 K+F+ FF FF LF+ FVIYP++ Sbjct: 92 EKVFYIILGFFLGFFALFA--FVIYPYK 117 >gnl|CDD|36272 KOG1054, KOG1054, KOG1054, Glutamate-gated AMPA-type ion channel receptor subunit GluR2 and related subunits [Inorganic ion transport and metabolism, Amino acid transport and metabolism, Signal transduction mechanisms]. Length = 897 Score = 30.0 bits (67), Expect = 0.74 Identities = 25/104 (24%), Positives = 51/104 (49%), Gaps = 17/104 (16%) Query: 60 DGRGELTGFDIDLIKEVAHRLNLKVEFF------------ETAV-SGLITGLDTNRYDVL 106 +G G+ +DL E+A + +K + F +T + +G++ L R D+ Sbjct: 440 EGNERYEGYCVDLAAEIAKHIGIKYKLFIVGDGKYGARDADTKIWNGMVGELVYGRADIA 499 Query: 107 V-NVAITPERQKKYDFSIPYIAHRVLLVVRSDQQD---IRSFKD 146 V + IT R++ DFS P+++ + ++++ Q+ + SF D Sbjct: 500 VAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLD 543 >gnl|CDD|144535 pfam00977, His_biosynth, Histidine biosynthesis protein. Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalysed by eight enzymes. The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold. In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel. This family belong to the common phosphate binding site TIM barrel family. Length = 229 Score = 28.6 bits (65), Expect = 1.8 Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 13/48 (27%) Query: 63 GELTGFDIDLIKEVAHRLNLKV-------------EFFETAVSGLITG 97 G L+G D++L +E+A +N+ V E F V G+I G Sbjct: 173 GTLSGPDLELTRELAEAVNIPVIASGGVGSLEDLKELFSEGVDGVIAG 220 >gnl|CDD|36001 KOG0782, KOG0782, KOG0782, Predicted diacylglycerol kinase [Signal transduction mechanisms]. Length = 1004 Score = 28.1 bits (62), Expect = 2.9 Identities = 12/35 (34%), Positives = 15/35 (42%) Query: 142 RSFKDLTDKTVAQILGTDLSRFAKELKSHLVFSHN 176 RS KDL G DL+ +ELK + N Sbjct: 567 RSSKDLCKHITVVCDGVDLTPKIQELKLQCIVFLN 601 >gnl|CDD|73393 cd04731, HisF, The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4- carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria.. Length = 243 Score = 27.7 bits (62), Expect = 3.4 Identities = 9/25 (36%), Positives = 16/25 (64%) Query: 60 DGRGELTGFDIDLIKEVAHRLNLKV 84 D G G+D++LI+ V+ +N+ V Sbjct: 172 DRDGTKKGYDLELIRAVSSAVNIPV 196 >gnl|CDD|29486 cd02862, NorE_like, NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of nitric oxide reductase (NOR). Based on this and on its similarity to subunit III of cytochrome c oxidase (CcO) and ubiquinol oxidase, NorE has been speculated to be a subunit of NOR.. Length = 186 Score = 27.5 bits (61), Expect = 4.4 Identities = 8/22 (36%), Positives = 12/22 (54%) Query: 13 FSKYLFFAPFFILFSYYFVIYP 34 S+ L F FI ++ Y +YP Sbjct: 18 LSELLAFGALFIAYAVYRALYP 39 >gnl|CDD|107292 cd06297, PBP1_LacI_like_12, Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding. Length = 269 Score = 27.5 bits (61), Expect = 4.5 Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 2/51 (3%) Query: 85 EFFETAVSGLITGLDTNRYDVLVNVAITPERQKKY--DFSIPYIAHRVLLV 133 EF+ + G+ L RYD+ + ++ R K+Y ++ Y+ +LL Sbjct: 12 EFYRRLLEGIEGALLEQRYDLALFPLLSLARLKRYLESTTLAYLTDGLLLA 62 >gnl|CDD|34614 COG5009, MrcA, Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]. Length = 797 Score = 27.2 bits (60), Expect = 5.6 Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 2/30 (6%) Query: 236 LTRSINEILCAIHLDGTYKK--IFDRYFDK 263 L R I E L AI ++ + K I + Y +K Sbjct: 138 LERKIKEALLAIRIEQSLSKDEILELYLNK 167 >gnl|CDD|39466 KOG4265, KOG4265, KOG4265, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]. Length = 349 Score = 26.9 bits (59), Expect = 6.5 Identities = 19/98 (19%), Positives = 32/98 (32%), Gaps = 14/98 (14%) Query: 12 FFSKYLFFAPFFILFSYYFVIYPFRTEDQS-ALRVGTDGIYPPHSFHAQDGRGEL----- 65 F L +LF F E+ L + P + H + G G+L Sbjct: 141 FTFDALAQGAITVLF--------FAKEEVLCGLVLLVPDELPSITVHFEKGLGQLFLQPS 192 Query: 66 TGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNRY 103 TG D ++ L+L + ++S + D Sbjct: 193 TGIDFSVMSIDDLSLSLDRRVYPLSISAEVQPSDVVES 230 >gnl|CDD|144928 pfam01515, PTA_PTB, Phosphate acetyl/butaryl transferase. This family contains both phosphate acetyltransferase and phosphate butaryltransferase. These enzymes catalyse the transfer of an acetyl or butaryl group to orthophosphate. Length = 319 Score = 26.5 bits (59), Expect = 9.2 Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 1/29 (3%) Query: 202 FLERRPHDGNLFKIADR-MKDNSAVAFMM 229 F E R H G +IA ++D + A M+ Sbjct: 83 FYELRKHKGMTPEIAREIVRDPTYFAAML 111 >gnl|CDD|173767 cd08227, PK_STRAD_alpha, Pseudokinase domain of STE20-related kinase adapter protein alpha. Protein Kinase family, STE20-related kinase adapter protein (STRAD) alpha subfamily, pseudokinase domain. The STRAD alpha subfamily is part of a larger superfamily that includes the catalytic domains of serine/threonine kinases (STKs), protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. STRAD forms a complex with the scaffolding protein MO25, and the STK, LKB1, resulting in the activation of the kinase. In the complex, LKB1 phosphorylates and activates adenosine monophosphate-activated protein kinases (AMPKs), which regulate cell energy metabolism and cell polarity. LKB1 is a tumor suppressor linked to the rare inherited disease, Peutz-Jeghers syndrome, which is characterized by a predisposition to benign polyps and hyperpigmentation of the buccal mucosa. There are two forms of STRAD, alpha and beta, that complex with LKB1 and MO25. The structure of STRAD-alpha is available and shows that this protein binds ATP, has an ordered activation loop, and adopts a closed conformation typical of fully active protein kinases. It does not possess activity due to nonconservative substitutions of essential catalytic residues. ATP binding enhances the affinity of STRAD for MO25. The conformation of STRAD-alpha, stabilized through ATP and MO25, may be needed to activate LKB1. A mutation which results in a truncation of a C-terminal part of the human STRAD-alpha pseudokinase domain and disrupts its association with LKB1, leads to PMSE (polyhydramnios, megalencephaly, symptomatic epilepsy) syndrome. Several splice variants of STRAD-alpha exist which exhibit different effects on the localization and activation of LKB1. Length = 327 Score = 26.1 bits (57), Expect = 9.8 Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 1/36 (2%) Query: 175 HNF-EQSLQLLLSKRTDATMIPDIPFFNFLERRPHD 209 H+F EQ LQ R A+ + + FF ++RR + Sbjct: 284 HHFVEQCLQRNPDARPSASTLLNHSFFKQIKRRASE 319 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 0.327 0.142 0.417 Gapped Lambda K H 0.267 0.0764 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,426,716 Number of extensions: 182060 Number of successful extensions: 825 Number of sequences better than 10.0: 1 Number of HSP's gapped: 806 Number of HSP's successfully gapped: 34 Length of query: 274 Length of database: 6,263,737 Length adjustment: 92 Effective length of query: 182 Effective length of database: 4,275,709 Effective search space: 778179038 Effective search space used: 778179038 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 57 (25.7 bits)