RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780689|ref|YP_003065102.1| flagellar motor switch protein G [Candidatus Liberibacter asiaticus str. psy62] (345 letters) >gnl|CDD|31725 COG1536, FliG, Flagellar motor switch protein [Cell motility and secretion]. Length = 339 Score = 186 bits (474), Expect = 7e-48 Identities = 85/325 (26%), Positives = 163/325 (50%), Gaps = 4/325 (1%) Query: 21 SLTQKDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQ 80 LT +KA +LLA+ ++++ ++L+H + E++ + L +SPEE E +++EFE Sbjct: 10 PLTGTEKAAILLLALGEEIAAEVLKHLSPEEIQRLSTEMATLKTVSPEEKEQVLEEFEEL 69 Query: 81 FIAGIGLTENSKNIESILEEGLEQNELEKLLNKSDISQENNNSIWDHLKETDPGVIADFL 140 F G+ + + L E E + L + S +D L++ DP +AD + Sbjct: 70 FTEQAGINKGADEYARELLEKALGEEKAESLLERITGSAIQTSPFDLLRKLDPSQLADLI 129 Query: 141 SKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIMKRTVNLPKISPYIQKTIEKCI--- 197 EHPQT A +LS +PP A +L P ++ AD++KR L +SP +E + Sbjct: 130 KNEHPQTIALILSYLPPDQAAEILSTLPEELRADVVKRIATLEGVSPEALAELENVLEKK 189 Query: 198 VEMLPQSNSNTSTGPEKVANLINELEKPQVDKLLTSLQEVSKEAFDKVRPKVFLFDDLIT 257 ++ L + + G + A ++N L++ +L SL+E E ++++ K+F+F+D++ Sbjct: 190 LQSLVNEDYSKLGGIKAAAEILNLLDRGTEKTILESLEEEDPELAEEIKEKMFVFEDIVL 249 Query: 258 LSSHDLSIVFNNISLEVLGKALHGTSIETQNAILHCLSNRQRKIIEENIVLNDSSIAPRE 317 L + + + E L AL G S E + IL +S R ++++E + + + Sbjct: 250 LDDRSIQRLLREVDKEDLAIALKGASEELREKILSNMSKRAAEMLKEELE-FLGPVRLSD 308 Query: 318 VAMARRSIVQEAISLLKTNKIELSN 342 V A+++I+ L ++ +I + Sbjct: 309 VETAQKAILNIVRRLAESGEIVIKR 333 >gnl|CDD|145059 pfam01706, FliG_C, FliG C-terminal domain. FliG is a component of the flageller rotor, present in about 25 copies per flagellum. This domain functions specifically in motor rotation. Length = 110 Score = 71.4 bits (176), Expect = 4e-13 Identities = 31/110 (28%), Positives = 55/110 (50%), Gaps = 1/110 (0%) Query: 231 LTSLQEVSKEAFDKVRPKVFLFDDLITLSSHDLSIVFNNISLEVLGKALHGTSIETQNAI 290 L +L+E E +++R +F F+DL+ L D+ + + +VL AL G S E + I Sbjct: 1 LEALEERDPELAEEIRKLMFTFEDLVRLDDRDIQRLLREVDKDVLALALKGASEELREKI 60 Query: 291 LHCLSNRQRKIIEENIVLNDSSIAPREVAMARRSIVQEAISLLKTNKIEL 340 L +S R +++ E + + +V A++ IV L + +IEL Sbjct: 61 LSNMSKRAAEMLREELEALG-PVRLSDVEAAQKEIVAIVRELAEEGEIEL 109 >gnl|CDD|32420 COG2239, MgtE, Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]. Length = 451 Score = 33.3 bits (76), Expect = 0.11 Identities = 24/127 (18%), Positives = 52/127 (40%), Gaps = 11/127 (8%) Query: 117 SQENNNSIWDHLKETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIM 176 + ++ D L++ D V+ L++ HP A +L +P V P + A++ Sbjct: 5 QLLDIENLIDLLEDKDLSVLRKLLARLHPADVAEILEELPGRERVVVWRLLPKEDAAEV- 63 Query: 177 KRTVNLPKISPYIQKTIEKCIVEMLPQSNSNTSTG--PEKVANLINELEKPQVDKLLTSL 234 L ++ +++ I I + + + + A+L++EL D+LL+ L Sbjct: 64 -----LGELDDEVREEI---IEALSDEELAAAIEELDIDDAADLLDELPDEVRDELLSLL 115 Query: 235 QEVSKEA 241 + Sbjct: 116 DPEERAR 122 >gnl|CDD|36330 KOG1114, KOG1114, KOG1114, Tripeptidyl peptidase II [Posttranslational modification, protein turnover, chaperones]. Length = 1304 Score = 32.6 bits (74), Expect = 0.18 Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 5/71 (7%) Query: 68 EELEDIIDEFESQFIAGIGLTENSKNIESILEE-----GLEQNELEKLLNKSDISQENNN 122 EE + I + + +++ + E K + L + L KL+ KSD +E N Sbjct: 1072 EECAEAIRDLQVSWLSKLADEEAEKIYNYLKSSYPDYLPLLEVRLAKLMQKSDAVKETNK 1131 Query: 123 SIWDHLKETDP 133 I + L D Sbjct: 1132 KIEEILSAADS 1142 >gnl|CDD|37150 KOG1939, KOG1939, KOG1939, Oxoprolinase [Amino acid transport and metabolism]. Length = 1247 Score = 30.3 bits (68), Expect = 0.74 Identities = 37/155 (23%), Positives = 67/155 (43%), Gaps = 24/155 (15%) Query: 191 KTIEKCIVEMLPQSNSNTSTGPEKVANLINELEKPQVDKLLTSLQEVSKEAFDKVRPKVF 250 + + I ++ Q +N G + V +LI E V + +Q ++ A ++ KV Sbjct: 906 RNLSDNISDLKAQIAANHK-GIQLVTSLIEEYGLDVVQAYMKHIQNNAELAVREMLKKVG 964 Query: 251 LFDDLITLSSHDLSIVFNNISLEVL-----GKAL---HGTSIE-----------TQNAIL 291 TLS+ D + I L+V G+A+ GT E T +A++ Sbjct: 965 RRVLEKTLSAEDFMDDGSPIKLKVTIDPEKGEAIFDFTGTGPEVYGNCNAPEAVTYSAVI 1024 Query: 292 HCLSNRQRKIIEENIVLNDSSIAPREVAMARRSIV 326 +CL R ++ E+I LN +AP ++ + S + Sbjct: 1025 YCL----RCLVNEDIPLNQGCLAPIQIKIPAGSFL 1055 >gnl|CDD|146204 pfam03448, MgtE_N, MgtE intracellular N domain. This domain is found at the N-terminus of eubacterial magnesium transporters of the MgtE family pfam01769. This domain is an intracellular domain that has an alpha-helical structure. The crystal structure of the MgtE transporter shows two of 5 magnesium ions are in the interface between the N domain and the CBS domains. In the absence of magnesium there is a large shift between the N and CBS domains. Length = 102 Score = 29.4 bits (67), Expect = 1.6 Identities = 23/105 (21%), Positives = 45/105 (42%), Gaps = 13/105 (12%) Query: 144 HPQTTAYVLSMMPPSIGASVLLRFPNKIHADIMKRTVNLPKISPYIQKTIEKCIVEMLPQ 203 HP A +L +PP ++L P + A++ L ++ +Q + +E LP Sbjct: 2 HPADIAELLEELPPEERLALLRLLPPERAAEV------LEELDEDVQAEL----LEALPP 51 Query: 204 SNSNTSTG---PEKVANLINELEKPQVDKLLTSLQEVSKEAFDKV 245 P+ A+L+ EL + ++LL+ L +E ++ Sbjct: 52 EELAELLEELDPDDAADLLEELPEEVREELLSLLDPEEREEIREL 96 Score = 28.3 bits (64), Expect = 3.6 Identities = 12/54 (22%), Positives = 27/54 (50%), Gaps = 6/54 (11%) Query: 25 KDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFE 78 ++A +L +++ V +LL EL E++ E+ P++ D+++E Sbjct: 27 PERAAEVLEELDEDVQAELLEALPPEELAELLE------ELDPDDAADLLEELP 74 >gnl|CDD|33843 COG4086, COG4086, Predicted secreted protein [Function unknown]. Length = 299 Score = 29.2 bits (65), Expect = 1.9 Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 5/45 (11%) Query: 50 AELKEIVASAKLLPEISPEELEDIIDEFESQFIAGIGLTENSKNI 94 AE+KE VA K+ P ++ ++D+ + + + LT+ N Sbjct: 198 AEVKEEVAKQKVD---DPADIRKVVDDVANNY--NVNLTDTQVNQ 237 >gnl|CDD|119333 cd06563, GH20_chitobiase-like, The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. This GH20 domain family includes an N-acetylglucosamidase (GlcNAcase A) from Pseudoalteromonas piscicida and an N-acetylhexosaminidase (SpHex) from Streptomyces plicatus. SpHex lacks the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.. Length = 357 Score = 29.1 bits (66), Expect = 2.1 Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 5/25 (20%) Query: 46 HFTHAELKEIVASAK-----LLPEI 65 +T E++EIVA A ++PEI Sbjct: 82 FYTQEEIREIVAYAAERGITVIPEI 106 >gnl|CDD|133299 cd01899, Ygr210, Ygr210 subfamily. Ygr210 is a member of Obg-like family and present in archaea and fungi. They are characterized by a distinct glycine-rich motif immediately following the Walker B motif. The Ygr210 and YyaF/YchF subfamilies appear to form one major branch of the Obg-like family. Among eukaryotes, the Ygr210 subfamily is represented only in fungi. These fungal proteins form a tight cluster with their archaeal orthologs, which suggests the possibility of horizontal transfer from archaea to fungi. Length = 318 Score = 28.3 bits (64), Expect = 3.2 Identities = 22/85 (25%), Positives = 32/85 (37%), Gaps = 24/85 (28%) Query: 74 IDEFESQFIAGIGLTENSKNIESILEEGLE--------QNELEKL--------------L 111 I E S+ ++G G+ E K++ LEE +L +L Sbjct: 164 IVEALSEQLSGFGVNE--KDVIEALEELELPEDLSKWTDEDLLRLARALRKRSKPMVIAA 221 Query: 112 NKSDISQENNNSIWDHLKETDPGVI 136 NK+DI NN LK D V+ Sbjct: 222 NKADIPDAENNISKLRLKYPDEIVV 246 >gnl|CDD|144739 pfam01255, Prenyltransf, Putative undecaprenyl diphosphate synthase. Previously known as uncharacterized protein family UPF0015, a single member of this family has been identified as an undecaprenyl diphosphate synthase. Length = 222 Score = 27.9 bits (63), Expect = 4.2 Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 3/45 (6%) Query: 36 EKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQ 80 EK++S LL +AEL + L P+ + E+L I +++S+ Sbjct: 175 EKRLSNFLLWQSAYAEL---YFTDTLWPDFTKEDLLRAIRDYQSR 216 >gnl|CDD|73400 cd04738, DHOD_2_like, Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences, their cellular location and their natural electron acceptor used to reoxidize the flavin group. Members of class 1 are cytosolic enzymes and multimers, while class 2 enzymes are membrane associated, monomeric and use respiratory quinones as their physiological electron acceptors.. Length = 327 Score = 27.8 bits (62), Expect = 4.9 Identities = 13/29 (44%), Positives = 17/29 (58%) Query: 60 KLLPEISPEELEDIIDEFESQFIAGIGLT 88 K+ P++S EELEDI D + GI T Sbjct: 208 KIAPDLSDEELEDIADVALEHGVDGIIAT 236 >gnl|CDD|145673 pfam02637, GatB_Yqey, GatB domain. This domain is found in GatB. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB, which transamidates Glu-tRNA to Gln-tRNA. Length = 148 Score = 27.5 bits (62), Expect = 5.4 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 14/72 (19%) Query: 65 ISPEELEDIIDEFESQFIAG-------IGLTENSKNIESILEE-GLEQ----NELEKLLN 112 ++PE L ++I + I+G L EN K+ E I+EE GL Q ELEK+++ Sbjct: 40 LTPEHLAELIKLIDEGTISGKIAKEVLEELLENGKSPEEIVEEKGLVQISDEEELEKIVD 99 Query: 113 KSDISQENNNSI 124 ++ EN ++ Sbjct: 100 --EVIAENPKAV 109 >gnl|CDD|163687 cd08056, MPN_PRP8, Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8. Members of this family are found in pre-mRNA-processing factor 8 (Prp8) which is a critical splicing factor, interacting with several other spliceosomal proteins, snRNAs, and the pre-mRNA, thus organizing and stabilizing the spliceosome catalytic core. Prp8 is one of the largest and most highly conserved of nuclear proteins, occupying a central position in the catalytic core of the spliceosome. Its C-terminal domain exhibits a JAB1/MPN-like core similar to deubiquitinating enzymes, but does not show catalytic isopeptidase activity, possibly because the putative isopeptidase center is covered by insertions and terminal appendices that are grafted onto this core, thus impairing the metal binding site. It is proposed that this domain is a protein interaction domain instead of a Zn(2+)-dependent metalloenzyme as proposed for some MPN proteins. The DEAD-box protein Brr2 and the GTPase Snu114 bind to the Prp8 C-terminus, a region where mutations in human Prp8 (hPrp8) cause a severe form of the genetic disorder retinitis pigmentosa, RP13, which leads to progressive photoreceptor degeneration in the retina and eventual blindness. At the N-terminus of Prp8, there are several domains, including a highly variable nuclear localization signal (NLS) motif rich in prolines, a conserved RNA recognition motif (RRM), and U5 and U6 snRNA binding sites. Length = 252 Score = 27.6 bits (62), Expect = 5.4 Identities = 29/137 (21%), Positives = 52/137 (37%), Gaps = 41/137 (29%) Query: 76 EFESQFIAGIGLTENSKNI----ESILEEG----LEQNELEKLLNKSDI-SQENNNSIWD 126 ++ + IA L +KNI + I E G L +N L+K ++ SD+ +Q Sbjct: 6 DWRVRAIAATNLHLRTKNIYVSSDDIKETGYTYILPKNLLKKFISISDLRTQ-------- 57 Query: 127 HLKETDPGVIADFL----SKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHAD-------- 174 IA +L ++PQ ++ P +G + P ++ Sbjct: 58 ---------IAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQLPQHEYLEDLEP 108 Query: 175 ---IMKRTVNLPKISPY 188 I + LP++SP Sbjct: 109 LGWIHTQPNELPQLSPQ 125 >gnl|CDD|30898 COG0552, FtsY, Signal recognition particle GTPase [Intracellular trafficking and secretion]. Length = 340 Score = 27.5 bits (61), Expect = 5.4 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 2/63 (3%) Query: 68 EELEDIIDEFESQFIAGIGLTENSKNIESILEEGLEQNELEKLLNKSDISQENNNSIWDH 127 E L+ + + + F GI K E + E+ LE ELE+LL ++D+ E I + Sbjct: 35 ERLKQGLSKTKKNFGKGIKGLFLKKIKEKLDEDLLE--ELEELLIEADVGVETAEEIIEE 92 Query: 128 LKE 130 L++ Sbjct: 93 LRK 95 >gnl|CDD|30955 COG0610, COG0610, Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]. Length = 962 Score = 27.3 bits (60), Expect = 6.9 Identities = 16/129 (12%), Positives = 43/129 (33%), Gaps = 1/129 (0%) Query: 24 QKDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEIS-PEELEDIIDEFESQFI 82 ++ L + K K + + + + ++ + S +L+DI E E Sbjct: 751 TLEEEIQYLEDLLKARLEKDYQSKYLDLIDNLNDAREIKDKESKAIDLDDIDFELELIGK 810 Query: 83 AGIGLTENSKNIESILEEGLEQNELEKLLNKSDISQENNNSIWDHLKETDPGVIADFLSK 142 I + + +++ ++ L++L+ + + L E I + +K Sbjct: 811 QEINIDYILELLQTFNDKNGAYESLKELIERIIKEWIEDLRQKKKLIERLIEAINQYRAK 870 Query: 143 EHPQTTAYV 151 + Sbjct: 871 KLDTAEKLE 879 >gnl|CDD|36947 KOG1736, KOG1736, KOG1736, Glia maturation factor beta [Extracellular structures]. Length = 143 Score = 26.9 bits (59), Expect = 7.7 Identities = 14/30 (46%), Positives = 19/30 (63%) Query: 53 KEIVASAKLLPEISPEELEDIIDEFESQFI 82 EIV + L EISPEEL D + E + +F+ Sbjct: 42 YEIVLDEEELDEISPEELADELPERQPRFV 71 >gnl|CDD|153247 cd07985, LPLAT_GPAT, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT. Lysophospholipid acyltransferase (LPLAT) superfamily member: glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB). LPLATs are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. This subgroup includes glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB). Length = 235 Score = 27.0 bits (60), Expect = 7.7 Identities = 10/21 (47%), Positives = 12/21 (57%) Query: 126 DHLKETDPGVIADFLSKEHPQ 146 +H E DP VI+ L K HP Sbjct: 29 NHQTEADPAVISLLLEKTHPY 49 >gnl|CDD|111365 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein. This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548 Score = 26.5 bits (59), Expect = 9.5 Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 8/35 (22%) Query: 64 EISPEELEDIIDEFESQFIAGIGLTENSKNIESIL 98 E+ EE E QF++ I ENS ++E IL Sbjct: 471 ELDEEEQE--------QFLSDIAYRENSGDVEEIL 497 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 0.312 0.130 0.346 Gapped Lambda K H 0.267 0.0732 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,819,403 Number of extensions: 197204 Number of successful extensions: 646 Number of sequences better than 10.0: 1 Number of HSP's gapped: 640 Number of HSP's successfully gapped: 41 Length of query: 345 Length of database: 6,263,737 Length adjustment: 95 Effective length of query: 250 Effective length of database: 4,210,882 Effective search space: 1052720500 Effective search space used: 1052720500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 58 (26.1 bits)