RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781215|ref|YP_003065628.1| putative phage terminase, large subunit [Candidatus Liberibacter asiaticus str. psy62] (511 letters) >gnl|CDD|146059 pfam03237, Terminase_6, Terminase-like family. This family represents a group of terminase proteins. Length = 380 Score = 60.9 bits (148), Expect = 8e-10 Identities = 66/373 (17%), Positives = 95/373 (25%), Gaps = 65/373 (17%) Query: 82 ISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWL-SLLPNKHW 140 I R GKT A L + I L+ S+ Q + + + LL Sbjct: 2 ILGSRQSGKTFAFAREALRHALGNGPKNQIILSASKAQARLEFKKGIIEIAGDLLEITFE 61 Query: 141 FEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHH-NTYGMAIINDE 199 + + + P L+ E T G+ + DE Sbjct: 62 EKNGNPIILPNGA---KLYF---------------LGLESETTAQGYRGASIAGIYF-DE 102 Query: 200 ASGTPDVINLGILGFLTERNANRFWIMT----SNPRRLSGKFYEIFNKPLDDWKRFQIDT 255 A+ P L R S P Y+ + LDD + Sbjct: 103 ATWLPKFQES----ELVRRLRATKGKWRKTFFSTPPSPGHWVYDFWTGWLDDKGKRTFIP 158 Query: 256 RTVEG-------IDPSFHEGIIARYGLDSDVTRVEVCGQFPQQDIDSFIPLNIIEEALNR 308 VE + P + E + A Y + + G++ S E Sbjct: 159 ADVEVTIEDARALGPEYKEELRALYSDE--EFARLLMGEW---VDTSGSIFKRFELERCD 213 Query: 309 EPCPDPYA--PLIMGCDIAE-EGGDNT---VVVLRRGPVIEHL--FDWSKTDLRTTNNKI 360 P +I G D A GGD V+ G L I Sbjct: 214 VDEERPPEHREVIGGVDPAASRGGDYAALVVIAEVDGDKFYVLAREHERGLSPAEQAAII 273 Query: 361 SGLVEKYRPDAIIIDANNTGARTCDYLEM-LGYHVYRVLGQKRAVDLEFCRNRRTELHVK 419 L E+Y I ID G L L + V K Sbjct: 274 KKLAERYNVIYIYIDDTGGGESVAQLLRRELPGAAFTVRP---------------APKGK 318 Query: 420 MADWLEFASLINH 432 A L+ + LI Sbjct: 319 NARVLKVSDLIES 331 >gnl|CDD|35312 KOG0089, KOG0089, KOG0089, Methylenetetrahydrofolate dehydrogenase/methylenetetrahydrofolate cyclohydrolase [Coenzyme transport and metabolism]. Length = 309 Score = 32.3 bits (73), Expect = 0.31 Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 8/62 (12%) Query: 262 DPSFHEGIIARYGLDSDVTRVEVCGQF-PQQDIDSFIPLNIIEEALNREPCPDPYAPLIM 320 DPS H GI+ + + + + P++D+D F PLNI D PL + Sbjct: 94 DPSVH-GILVQLPVPQHIQEQYILNAVSPEKDVDGFHPLNI------GRLALDGREPLFL 146 Query: 321 GC 322 C Sbjct: 147 PC 148 >gnl|CDD|99779 cd06182, CYPOR_like, NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. CYPOR has a C-terminal ferredoxin reducatase (FNR)- like FAD and NAD binding module, an FMN-binding domain, and an additional conecting domain (inserted within the FAD binding region) that orients the FNR and FMN binding domains. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria and participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2, which then transfers two electrons and a proton to NADP+ to form NADPH.. Length = 267 Score = 30.8 bits (70), Expect = 1.0 Identities = 19/93 (20%), Positives = 32/93 (34%), Gaps = 17/93 (18%) Query: 230 PRRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPS--FHEGIIARYGLDSDVTRVEVCGQ 287 P L ++Y I + P D + R V P+ +G+ + + + G Sbjct: 43 PNPLQPRYYSIASSPDVDPGEVHLCVRVVSYEAPAGRIRKGVCSNF----------LAGL 92 Query: 288 FPQQDIDSFIPLNIIEEALNREPCPDPYAPLIM 320 + FI A + DP P+IM Sbjct: 93 QLGAKVTVFIR-----PAPSFRLPKDPTTPIIM 120 >gnl|CDD|39672 KOG4471, KOG4471, KOG4471, Phosphatidylinositol 3-phosphate 3-phosphatase myotubularin MTM1 [Lipid transport and metabolism, Intracellular trafficking, secretion, and vesicular transport]. Length = 717 Score = 30.4 bits (68), Expect = 1.2 Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 9/48 (18%) Query: 127 EVSKWLSLLPNKHWFEMQSLSLHPAPWYSD---------VLHCSLGID 165 + S WLS L + HW E S L A +D ++HCS G D Sbjct: 339 DESNWLSALESTHWLEHISSLLAGAVRIADKVESESRSVLVHCSDGWD 386 >gnl|CDD|29127 cd02052, PEDF, Pigment epithelium-derived factor (PEDF)_like. PEDF is non-inhibitory member of the Serpin superfamily. It exhibits neurotrophic, neuroprotective and antiangiogenic properties and is widely expressed in the developing and adult nervous systems. This subgroup corresponds to clade F1 of the serpin superfamily.. Length = 374 Score = 30.0 bits (67), Expect = 1.7 Identities = 24/88 (27%), Positives = 34/88 (38%), Gaps = 15/88 (17%) Query: 233 LSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIARYGLDSDVTRVEVC--GQFPQ 290 G++ F+K F +D + + RYGLDSD+ C Q P Sbjct: 173 FKGQWITKFDKRNTVLTDFHLDEQRTVVVPMMSDPNAPVRYGLDSDLN----CKIAQLPL 228 Query: 291 QDIDS---FIP------LNIIEEALNRE 309 S F+P L +IEE+L E Sbjct: 229 TGGVSIMFFLPDKVTQNLTLIEESLTSE 256 >gnl|CDD|163676 cd07938, DRE_TIM_HMGL, 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain. 3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes the cleavage of HMG-CoA to acetyl-CoA and acetoacetate, one of the terminal steps in ketone body generation and leucine degradation, and is a key enzyme in the pathway that supplies metabolic fuel to extrahepatic tissues. Mutations in HMGL cause a human autosomal recessive disorder called primary metabolic aciduria that affects ketogenesis and leucine catabolism and can be fatal due to an inability to tolerate hypoglycemia. HMGL has a TIM barrel domain with a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. The cleavage of HMG-CoA requires the presence of a divalent cation like Mg2+ or Mn2+, and the reaction is thought to involve general acid/base catalysis. 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 = 274 Score = 29.7 bits (68), Expect = 2.2 Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 2/28 (7%) Query: 172 MCRTYSEERPDT-FVGH-HNTYGMAIIN 197 + E PD H H+T G A+ N Sbjct: 183 LLEAVLERFPDEKLALHFHDTRGQALAN 210 >gnl|CDD|133424 cd01339, LDH-like_MDH, L-lactate dehydrogenase-like malate dehydrogenase proteins. Members of this subfamily have an LDH-like structure and an MDH enzymatic activity. Some members, like MJ0490 from Methanococcus jannaschii, exhibit both MDH and LDH activities. Tetrameric MDHs, including those from phototrophic bacteria, are more similar to LDHs than to other MDHs. LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. Length = 300 Score = 29.4 bits (67), Expect = 2.6 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 4/31 (12%) Query: 348 WSKTDLRTTNNKI----SGLVEKYRPDAIII 374 S+ DL TN KI + ++KY P+AI+I Sbjct: 82 MSRDDLLGTNAKIVKEVAENIKKYAPNAIVI 112 >gnl|CDD|37048 KOG1837, KOG1837, KOG1837, Uncharacterized conserved protein [Function unknown]. Length = 1621 Score = 29.2 bits (65), Expect = 2.7 Identities = 13/59 (22%), Positives = 20/59 (33%), Gaps = 3/59 (5%) Query: 11 TEQKLFDLMWSDEIKLSFSNFVLHFFP---WGEKGTPLEGFSAPRSWQLEFMEVVDAHC 66 E+ + + + +KLS S F F P W E G + + F D Sbjct: 1365 LERSVQNKAVAKVLKLSESTFRPLFSPLFDWAEPGLEAKAEQKCLERLISFYHFADYLQ 1423 >gnl|CDD|36305 KOG1089, KOG1089, KOG1089, Myotubularin-related phosphatidylinositol 3-phosphate 3-phosphatase MTM6 [General function prediction only]. Length = 573 Score = 28.8 bits (64), Expect = 4.0 Identities = 33/147 (22%), Positives = 48/147 (32%), Gaps = 33/147 (22%) Query: 44 PLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWL------ 97 PL GF A R + E + L ++ NP +G I R N Sbjct: 220 PLSGFIAKRCREDEKI-------LEAILKANPNSKRGYIVDTRPRTNAMANRAKGGGYEN 272 Query: 98 ------VLWLMSTRPGISVICLANSETQLK---TTLWAEVSKWLSLLPNKHWFEMQSLSL 148 +L I V+ +S +L + KWLSLL + W + L Sbjct: 273 EDNYSQWKFLFLGIENIHVV--RSSLQKLLEVCNNFLPTMDKWLSLLESSGWLKHIRAIL 330 Query: 149 HPAPWYSD---------VLHCSLGIDS 166 A + ++HCS G D Sbjct: 331 KAAAEIAKCLSSEGASVLVHCSDGWDR 357 >gnl|CDD|112181 pfam03354, Terminase_1, Phage Terminase. The majority of the members of this family are bacteriophage proteins, several of which are thought to be terminase large subunit proteins. There are also a number of bacterial proteins of unknown function. Length = 473 Score = 28.6 bits (64), Expect = 4.4 Identities = 31/179 (17%), Positives = 65/179 (36%), Gaps = 19/179 (10%) Query: 82 ISAGRGIGKTTLNAWLVLWLM--STRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKH 139 +S GR GK+ L A VL+ + + ++ A + Q + L+ V + L P Sbjct: 27 VSVGRKNGKSYLMAIRVLYELLLGGKSNQEILVAATTFKQAE-KLFKYVKNQVKLSPFLS 85 Query: 140 WFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDE 199 L S GI+ K + + + S D + G + + +AI ++ Sbjct: 86 IANENKLL------KSQ----KDGIEMKINNNVFKALSNN-GDQYDGGNPS--LAIFDEM 132 Query: 200 ASGTPDVINLGILGFLTERNANRFWIMTSNPRRLSGKFYE---IFNKPLDDWKRFQIDT 255 + I+ + +++ + +T+ G + E + L+ D+ Sbjct: 133 HEFKDRELVSTIVTGMRKQDNPQTIQITTAGPNRGGPYDEEREYIKRILEGDVERDDDS 191 >gnl|CDD|30377 COG0027, PurT, Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) [Nucleotide transport and metabolism]. Length = 394 Score = 28.3 bits (63), Expect = 5.4 Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 4/39 (10%) Query: 358 NKISGLVEKYRPDAII--IDANNTGARTCDYLEMLGYHV 394 + + +VE+ +PD I+ I+A T A LE GY V Sbjct: 65 DALRAVVEREKPDYIVPEIEAIATDA--LVELEEEGYTV 101 >gnl|CDD|110578 pfam01583, APS_kinase, Adenylylsulphate kinase. Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif. Length = 157 Score = 28.0 bits (63), Expect = 5.7 Identities = 22/67 (32%), Positives = 27/67 (40%), Gaps = 11/67 (16%) Query: 386 YLEMLGYHVYRVLGQ----KRAVDLEFCRNRRTELHVKMADWLEFASLINHSGLIQNLKS 441 L G VY + G DL F RTE ++A E A L +GLI Sbjct: 25 KLFAQGISVYVLDGDNVRHGLNKDLGFSEEDRTENIRRIA---EVAKLFADAGLI----V 77 Query: 442 LKSFIVP 448 + SFI P Sbjct: 78 ITSFISP 84 >gnl|CDD|144324 pfam00682, HMGL-like, HMGL-like. This family contains a diverse set of enzymes. These include various aldolases and a region of pyruvate carboxylase. Length = 237 Score = 27.7 bits (62), Expect = 7.3 Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 3/36 (8%) Query: 188 HNTYGMAIINDEA--SGTPDVINLGILGFLTERNAN 221 HN GMA+ N A D ++ + G L ER N Sbjct: 189 HNDLGMAVANSLAAVEAGADRVDGTVNG-LGERAGN 223 >gnl|CDD|147641 pfam05582, Peptidase_U57, YabG peptidase U57. YabG is a protease involved in the proteolysis and maturation of SpoIVA and YrbA proteins, conserved with the cortex and/or coat assembly by Bacillus subtilis. Length = 287 Score = 27.5 bits (62), Expect = 7.7 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 5/38 (13%) Query: 359 KISGLVEKYRPDAIII---DANNTGARTCDYLEMLGYH 393 KI L+EKYRPD ++I DA DY ++ Y Sbjct: 145 KIESLLEKYRPDILVITGHDAYLKNKG--DYGDLNNYR 180 >gnl|CDD|33745 COG3964, COG3964, Predicted amidohydrolase [General function prediction only]. Length = 386 Score = 27.6 bits (61), Expect = 8.3 Identities = 17/65 (26%), Positives = 28/65 (43%) Query: 317 PLIMGCDIAEEGGDNTVVVLRRGPVIEHLFDWSKTDLRTTNNKISGLVEKYRPDAIIIDA 376 PL++ D + LRRG +I H F+ + T + + V + R +I DA Sbjct: 187 PLMVHIGEPPVLMDEVLERLRRGDIITHCFNGKPNTILTDDGVVRAEVRRARERGVIFDA 246 Query: 377 NNTGA 381 + A Sbjct: 247 GHGRA 251 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 0.320 0.137 0.431 Gapped Lambda K H 0.267 0.0793 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 6,680,371 Number of extensions: 361916 Number of successful extensions: 816 Number of sequences better than 10.0: 1 Number of HSP's gapped: 814 Number of HSP's successfully gapped: 18 Length of query: 511 Length of database: 6,263,737 Length adjustment: 98 Effective length of query: 413 Effective length of database: 4,146,055 Effective search space: 1712320715 Effective search space used: 1712320715 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: 60 (26.8 bits)