RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780741|ref|YP_003065154.1| carboxynorspermidine decarboxylase [Candidatus Liberibacter asiaticus str. psy62] (367 letters) >gnl|CDD|143502 cd06829, PLPDE_III_CANSDC, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase. Carboxynorspermidine decarboxylase (CANSDC) catalyzes the decarboxylation of carboxynorspermidine, the last step in the biosynthesis of norspermidine. It is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC), which are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. Based on this similarity, CANSDC may require homodimer formation and the presence of the PLP cofactor for its catalytic activity. Length = 346 Score = 481 bits (1241), Expect = e-136 Identities = 153/347 (44%), Positives = 222/347 (63%), Gaps = 5/347 (1%) Query: 4 TPYYLIDKQKLLNNLDTALYIRKNAGVKLLLALKCFAAWGMFDTLNQYMDGTTSSSLYEV 63 TP Y++D+ KL NL+ +++ +G K+LLALK F+ W +F + +Y+DGTT+SSL+E Sbjct: 1 TPCYVLDEAKLRRNLEILKRVQERSGAKILLALKAFSMWSVFPLIREYLDGTTASSLFEA 60 Query: 64 MLGHEKFGGETHAYNVAYKDCEIDAVLSNCDTIIFNTVSQLNKFKDKAQKLHKKIGLRIN 123 LG E+FGGE H Y+ AY+D EID +L D IIFN++SQL +FKD+A+ +GLRIN Sbjct: 61 RLGREEFGGEVHTYSPAYRDDEIDEILRLADHIIFNSLSQLERFKDRAKAAGISVGLRIN 120 Query: 124 PSVSYSKFILADPNRPFSRLGEKCKDKIESEIKNVNGLMFHNNCENKSFLCFSAMLKNIE 183 P S + L DP P SRLG + E ++ + GL FH CE F L+ +E Sbjct: 121 PEYSEVETDLYDPCAPGSRLGVTLDELEEEDLDGIEGLHFHTLCEQ-DFDALERTLEAVE 179 Query: 184 KEFGHFITQIEWISLGGGIHFTDKDYPVKDFCQRLKEFSEKYSVQIYLEPGEAIVTNTTT 243 + FG ++ Q++W++LGGG H T DY V +K F EKY V++YLEPGEA+ NT Sbjct: 180 ERFGEYLPQLKWLNLGGGHHITRPDYDVDRLIALIKRFKEKYGVEVYLEPGEAVALNTGY 239 Query: 244 LNTTVLDISENIKNLVIVDSSVEAHVPDYLL--YQESATI--YPNTGPYTAMVCGRSCLA 299 L TVLDI EN + I+D+S AH+PD L Y+ P G +T + G SCLA Sbjct: 240 LVATVLDIVENGMPIAILDASATAHMPDVLEMPYRPPIRGAGEPGEGAHTYRLGGNSCLA 299 Query: 300 GDIFGEFHFEKPVKIGDRISFEDVAGYNINRKNWFNGINMPTIAVKN 346 GD+ G++ F++P+++GDR+ FED+A Y + + N FNG+ +P+IA+++ Sbjct: 300 GDVIGDYSFDEPLQVGDRLVFEDMAHYTMVKTNTFNGVRLPSIAIRD 346 >gnl|CDD|30369 COG0019, LysA, Diaminopimelate decarboxylase [Amino acid transport and metabolism]. Length = 394 Score = 256 bits (655), Expect = 8e-69 Identities = 93/370 (25%), Positives = 143/370 (38%), Gaps = 28/370 (7%) Query: 2 IKTPYYLIDKQKLLNNLDTALYIRKNAGVKLLLALKCFAAWGMFDTLNQYMDGTTSSSLY 61 TP Y+ D+ L N +G K+ A+K + + L + G +SL Sbjct: 25 FGTPVYVYDEATLRRNARELKSAFPGSGAKVFYAVKANSNPAILRLLAEEGSGFDVASLG 84 Query: 62 EVMLGHEKF--GGETHAYNVAYKDCEIDAVLSNCD-TIIFNTVSQLNKFKDKAQKLHKKI 118 E+ L A + EI L I ++ +L + A L ++ Sbjct: 85 ELELALAAGFPPERIVFSGPAKSEEEIAFALELGIKLINVDSEEELERLSAIAPGLVARV 144 Query: 119 GLRINPSVSYSKFILADPNRPFSRLG-------EKCKDKIESEIKNVNGLMFHNNCENKS 171 LRINP VS S+ G + + + + GL FH + Sbjct: 145 SLRINPGVSAGTHEYIATGGKSSKFGISPEEALDVLERAAKLLGLELVGLHFHIGSQITD 204 Query: 172 FLCFSAMLKNIEKEFGHFIT----QIEWISLGGGIHFT-DKDYPVKDFCQRLKEFSEKYS 226 F L +E+ FG Q+EW++LGGG+ T + +Y D K E + Sbjct: 205 LDPFEEALAKVEELFGRLAEELGIQLEWLNLGGGLGITYEDEYDPPDLAAYAKALKEAFG 264 Query: 227 -----VQIYLEPGEAIVTNTTTLNTTVLDISEN-IKNLVIVDSSVEAHVPDYLLYQESAT 280 V++ LEPG AIV N L T VLD+ EN +N VIVD + + LY Sbjct: 265 EYAEDVELILEPGRAIVANAGVLVTEVLDVKENGERNFVIVDGGMNDLMRP-ALYGAYHH 323 Query: 281 IYPN-----TGPYTAMVCGRSCLAGDIFG-EFHFEKPVKIGDRISFEDVAGYNINRKNWF 334 I N V G +C +GD+ + +P+K+GD + D Y + + + Sbjct: 324 IRLNRTDEDAEREEYDVVGPTCESGDVLARDRALPEPLKVGDLLVILDAGAYGASMSSNY 383 Query: 335 NGINMPTIAV 344 NG P + Sbjct: 384 NGRPRPAEVL 393 >gnl|CDD|143485 cd06810, PLPDE_III_ODC_DapDC_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Ornithine and Diaminopimelate Decarboxylases, and Related Enzymes. This family includes eukaryotic ornithine decarboxylase (ODC, EC 4.1.1.17), diaminopimelate decarboxylase (DapDC, EC 4.1.1.20), plant and prokaryotic biosynthetic arginine decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine decarboxylase (CANSDC), and ODC-like enzymes from diverse bacterial species. These proteins are fold type III PLP-dependent enzymes that catalyze essential steps in the biosynthesis of polyamine and lysine. ODC and ADC participate in alternative pathways of the biosynthesis of putrescine, which is the precursor of aliphatic polyamines in many organisms. ODC catalyzes the direct synthesis of putrescine from L-ornithine, while ADC converts L-arginine to agmatine, which is hydrolysed to putrescine by agmatinase in a pathway that exists only in plants and bacteria. DapDC converts meso-2,6-diaminoheptanedioate to L-lysine, which is the final step of lysine biosynthesis. CANSDC catalyzes the decarboxylation of carboxynorspermidine, which is the last step in the synthesis of norspermidine. The PLP-dependent decarboxylases in this family contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Prokaryotic ornithine, lysine and biodegradative arginine decarboxylases are fold type I PLP-dependent enzymes and are not included in this family. Length = 368 Score = 147 bits (373), Expect = 5e-36 Identities = 83/369 (22%), Positives = 143/369 (38%), Gaps = 30/369 (8%) Query: 4 TPYYLIDKQKLLNNLDTALYIRKNAGVKLLLALKCFAAWGMFDTLNQYMDGTTSSSLYEV 63 TP+Y+ D + + AL +GVKL A+K + TL + G +S E+ Sbjct: 1 TPFYVYDLDIIRAHYA-ALKEALPSGVKLFYAVKANPNPHVLRTLAEAGTGFDVASKGEL 59 Query: 64 MLG-HEKFGGETHAYNVAYKDCE--IDAVLSNCDTIIFNTVSQLNKFKDKAQKLHK--KI 118 L E + K A+ S D I+ +++ +L + + A+KL +I Sbjct: 60 ALALAAGVPPERIIFTGPAKSVSEIEAALASGVDHIVVDSLDELERLNELAKKLGPKARI 119 Query: 119 GLRINPSVSYSKFILADPNRPFSRLG------EKCKDKIESEIKNVNGLMFHNNCENKSF 172 LR+NP VS + S+ G ++ + + GL FH + Sbjct: 120 LLRVNPDVS-AGTHKISTGGLKSKFGLSLSEARAALERAKELDLRLVGLHFHVGSQILDL 178 Query: 173 LCFSAMLKN---IEKEFGHFITQIEWISLGGG--IHFTDKDYPVKDFCQRLKEFSEKYS- 226 L + + +E +E + LGGG I + ++ +++ + +KY Sbjct: 179 ETIVQALSDARELIEELVEMGFPLEMLDLGGGLGIPYDEQPLDFEEYAALINPLLKKYFP 238 Query: 227 ----VQIYLEPGEAIVTNTTTLNTTVLDISEN-IKNLVIVDSSVEAHVPDYLLYQESATI 281 V + LEPG IV L T V+ + N + +VD + L Y I Sbjct: 239 NDPGVTLILEPGRYIVAQAGVLVTRVVAVKVNGGRFFAVVDGGMNHSFRPALAYDAYHPI 298 Query: 282 YP------NTGPYTAMVCGRSCLAGDIFGEFHFEKPVKIGDRISFEDVAGYNINRKNWFN 335 P + A + G C +GD+ G +++GD + FED+ Y + + FN Sbjct: 299 TPLKAPGPDEPLVPATLAGPLCDSGDVIGRDRLLPELEVGDLLVFEDMGAYGFSESSNFN 358 Query: 336 GINMPTIAV 344 P + Sbjct: 359 SHPRPAEYL 367 >gnl|CDD|143501 cd06828, PLPDE_III_DapDC, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase. Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20) participates in the last step of lysine biosynthesis. It converts meso-2,6-diaminoheptanedioate to L-lysine. It is a fold type III PLP-dependent enzyme that contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. DapDC exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity. Length = 373 Score = 75.6 bits (187), Expect = 2e-14 Identities = 80/370 (21%), Positives = 141/370 (38%), Gaps = 63/370 (17%) Query: 4 TPYYLIDKQKLLNN---LDTALYIRKNAGVKLLLALKCFAAWGMFDTLNQYMDGTTSSSL 60 TP Y+ D+ + N L A G K+ A+K + + L + G S Sbjct: 3 TPLYVYDEATIRENYRRLKEAF---SGPGFKICYAVKANSNLAILKLLAEEGLGADVVSG 59 Query: 61 YEVMLGHE-KFGGET---HAYNVAYKDCEIDAVLSNCDTIIFN--TVSQLNKFKDKAQKL 114 E+ + F E + + E++ L + N ++S+L + + A +L Sbjct: 60 GELYRALKAGFPPERIVFTGNGKSDE--ELELALEL-GILRINVDSLSELERLGEIAPEL 116 Query: 115 HKK--IGLRINPSV------------SYSKF-ILADPNRPFSRLGEKCKDKIESEIKNVN 159 K + LR+NP V SKF I P + E + E + Sbjct: 117 GKGAPVALRVNPGVDAGTHPYISTGGKDSKFGI------PLEQALEAYRRAKELPGLKLV 170 Query: 160 GLMFH---NNCENKSFLCFSAMLKNIEKEFGHFITQIEWISLGGG--IHFTDKDYP--VK 212 GL H + + F+ + L ++ E +E++ LGGG I + D+D P ++ Sbjct: 171 GLHCHIGSQILDLEPFVEAAEKLLDLAAELRELGIDLEFLDLGGGLGIPYRDEDEPLDIE 230 Query: 213 DFCQRLKEFSEKYS-----VQIYLEPGEAIVTNTTTLNTTVLDISEN-IKNLVIVDSSV- 265 ++ + + E ++ +++ +EPG IV N L T V + E K V VD+ + Sbjct: 231 EYAEAIAEALKELCEGGPDLKLIIEPGRYIVANAGVLLTRVGYVKETGGKTFVGVDAGMN 290 Query: 266 --------EAHVPDYLLYQESATIYPNTGPYTAMVCGRSCLAGDIFGEFHFEKPVKIGDR 317 A+ + + T V G C +GD+F + V+ GD Sbjct: 291 DLIRPALYGAYHEIVPVNKPGE---GETEKVD--VVGPICESGDVFAKDRELPEVEEGDL 345 Query: 318 ISFEDVAGYN 327 ++ D Y Sbjct: 346 LAIHDAGAYG 355 >gnl|CDD|144023 pfam00278, Orn_DAP_Arg_deC, Pyridoxal-dependent decarboxylase, C-terminal sheet domain. These pyridoxal-dependent decarboxylases act on ornithine, lysine, arginine and related substrates. Length = 110 Score = 71.5 bits (176), Expect = 3e-13 Identities = 29/110 (26%), Positives = 46/110 (41%), Gaps = 9/110 (8%) Query: 243 TLNTTVLDISEN--IKNLVIVDSSVEAHVPDYLLYQESATIYP-----NTGPYTAMVCGR 295 TL T V+D+ E + V +D V PD LY I P + + G Sbjct: 1 TLVTEVIDVKERGDDRKFVYLDDGVYGS-PDPALYDALHPILPVSRLDDEPLRPYTLAGP 59 Query: 296 SCLAGDIFG-EFHFEKPVKIGDRISFEDVAGYNINRKNWFNGINMPTIAV 344 +C +GD+ + +++GD + F D Y I+ + FNG P + Sbjct: 60 TCDSGDVLARDVSLPLELEVGDWLVFFDAGAYTISLSSNFNGFPRPAEVL 109 >gnl|CDD|35841 KOG0622, KOG0622, KOG0622, Ornithine decarboxylase [Amino acid transport and metabolism]. Length = 448 Score = 57.3 bits (138), Expect = 7e-09 Identities = 74/394 (18%), Positives = 134/394 (34%), Gaps = 44/394 (11%) Query: 3 KTPYYLIDKQKLLNNLDTALYIRKNAGVKLLLALKCFAAWGMFDTLNQYMDGTTSSSLYE 62 K +++ D + L+ + + V+ A+KC + + L G +S E Sbjct: 55 KQAFFVADLGAIERKLE--AWKKALPRVRPFYAVKCNSDPKVLRLLASLGCGFDCASKNE 112 Query: 63 VMLG-HEKFGGETHAYNVAYKDCE--IDAVLSNCDTIIFNTVSQLNKFKDKAQKLHK--K 117 + L E Y K A + F+ +L K K H Sbjct: 113 LDLVLSLGVSPERIIYANPCKQVSQIKYAAKHGVSVMTFDNEEELEKVA----KSHPNAN 168 Query: 118 IGLRINPSVSYSKFILADPNRPFSRLGEKCK---DKIESEIKNVNGLMFH--NNC-ENKS 171 + LRI S + N F + C+ D + NV G+ FH + C + ++ Sbjct: 169 LLLRIATDDSTA---TCRLNLKFGCSLDNCRHLLDMAKELELNVVGVSFHVGSGCTDLQA 225 Query: 172 FLCFSAMLKNIEKEFGHFITQIEWISLGGGIHFTD-KDYPVKDFCQRLKEFSEKY----S 226 + + +N+ +++ + +GGG + ++ + + Y Sbjct: 226 YRDAISDARNVFDMGAELGFEMDILDIGGGFPGDEGHAVVFEEIADVINTALDLYFPSGG 285 Query: 227 VQIYLEPGEAIVTNTTTLNTTVLDISENIKNLVIVDSSVEAHVPDY------------LL 274 V I EPG V + TL V+ E + D + Y +L Sbjct: 286 VDIIAEPGRFFVASAFTLAVNVIAKKEVDAKKITSDDEDDEVTFMYYVNDGVYGSFNCIL 345 Query: 275 YQESATI-------YPNTGPYTAMVCGRSCLAGDIFGEFHFEKPVKIGDRISFEDVAGYN 327 + I Y + + G +C D+ E + +GD + FE++ Y Sbjct: 346 FDHQHPIPLVVKDPSEEEPLYKSSIWGPTCDGLDVIAEDCLLPQLNVGDWLVFENMGAYT 405 Query: 328 INRKNWFNGINMPTIAVKNVDGTIKAIREFSYND 361 ++ + FNG P I DG + IR+ D Sbjct: 406 MSAASTFNGFQRPKIYYVMSDGDWEKIRDAETFD 439 >gnl|CDD|143508 cd06841, PLPDE_III_MccE_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme MccE. This subfamily is composed of uncharacterized proteins with similarity to Escherichia coli MccE, a hypothetical protein that is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Most members of this subfamily share the same domain architecture as ODC and DapDC. A few members, including Escherichia coli MccE, contain an additional acetyltransferase domain at the C-terminus. Length = 379 Score = 53.8 bits (130), Expect = 8e-08 Identities = 59/282 (20%), Positives = 109/282 (38%), Gaps = 53/282 (18%) Query: 89 VLSNCDTIIFNTVSQLNKFKDKAQKLHK--KIGLRINPSVS---YSKFILADPNRPFSRL 143 L N D+ +L + + A++L + K+G+R+N + +S+F Sbjct: 101 ALINIDSF-----DELERILEIAKELGRVAKVGIRLNMNYGNNVWSRFGF--DIEENGEA 153 Query: 144 GEKCKDKIESEIKNVNGLMFH-----NNCENKSFLCFSAMLKN----IEKEFGHFITQIE 194 K ES+ ++ GL H N E +SA K +++ FG ++E Sbjct: 154 LAALKKIQESKNLSLVGLHCHVGSNILNPEA-----YSAAAKKLIELLDRLFGL---ELE 205 Query: 195 WISLGGGIHFTDK--------DYPVKDF-------CQRLKEFSEKYSVQ--IYLEPGEAI 237 ++ LGGG + V D LKE+ + + LEPG A+ Sbjct: 206 YLDLGGGF-PAKTPLSLAYPQEDTVPDPEDYAEAIASTLKEYYANKENKPKLILEPGRAL 264 Query: 238 VTNTTTLNTTVLDISE-NIKNLVIVDSSVEAHVPDYLLYQESATI---YPNTGPYTA-MV 292 V + L V+ + +N+ + D+ + ++P Y + V Sbjct: 265 VDDAGYLLGRVVAVKNRYGRNIAVTDAGIN-NIPTIFWYHHPILVLRPGKEDPTSKNYDV 323 Query: 293 CGRSCLAGDIFGEFHFEKPVKIGDRISFEDVAGYNINRKNWF 334 G +C+ D+ P+ +GD ++ +V YN+ + N F Sbjct: 324 YGFNCMESDVLFPNVPLPPLNVGDILAIRNVGAYNMTQSNQF 365 >gnl|CDD|143484 cd06808, PLPDE_III, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes. The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity. Length = 211 Score = 40.8 bits (96), Expect = 6e-04 Identities = 42/192 (21%), Positives = 69/192 (35%), Gaps = 31/192 (16%) Query: 27 NAGVKLLLALKCFAAWGMFDTLNQYMDGTTSSSLYEVM-LGHEKFGGETHAYNVAYK--- 82 AG+ L +K A + TL G +SL E + L E + K Sbjct: 13 PAGITLFAVVKANANPEVARTLAALGTGFDVASLGEALLLRAAGIPPEPILFLGPCKQVS 72 Query: 83 DCEIDAVLSNCDTIIFNTVSQLNKFKDKAQKLHKK--IGLRINPSVSYSKFILADPNRPF 140 + E DA + +++ +L K ++ A K + LRI+ KF + Sbjct: 73 ELE-DAAEQGVIVVTVDSLEELEKLEEAALKAGPPARVLLRIDTGDENGKFGV------- 124 Query: 141 SRLGEKCKDKIESEIK----NVNGLMFH--NNCENKS-----FLCFSAMLKNIEKEFGHF 189 R E K +E + + GL H + E+ S F A L + + Sbjct: 125 -RPEE-LKALLERAKELPHLRLVGLHTHFGSADEDYSPFVEALSRFVAALDQLGELGID- 181 Query: 190 ITQIEWISLGGG 201 +E +S+GG Sbjct: 182 ---LEQLSIGGS 190 >gnl|CDD|143482 cd00622, PLPDE_III_ODC, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase. This subfamily is composed mainly of eukaryotic ornithine decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes from prokaryotes represented by Vibrio vulnificus LysineOrnithine decarboxylase. These are fold type III PLP-dependent enzymes that differ from most bacterial ODCs which are fold type I PLP-dependent enzymes. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. Members of this subfamily contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity. Also members of this subfamily are proteins with homology to ODC but do not possess any catalytic activity, the Antizyme inhibitor (AZI) and ODC-paralogue (ODC-p). AZI binds to the regulatory protein Antizyme with a higher affinity than ODC and prevents ODC degradation. ODC-p is a novel ODC-like protein, present only in mammals, that is specifically exressed in the brain and testes. ODC-p may function as a tissue-specific antizyme inhibitory protein. Length = 362 Score = 40.2 bits (95), Expect = 0.001 Identities = 33/182 (18%), Positives = 67/182 (36%), Gaps = 28/182 (15%) Query: 184 KEFGHFITQIEWISLGGG--IHFTDKDYPVKDFCQRLKEFSEKY----SVQIYLEPGEAI 237 E G +++ + +GGG + ++ + ++Y V+I EPG + Sbjct: 187 AELGF---KLKLLDIGGGFPGSYDGVVPSFEEIAAVINRALDEYFPDEGVRIIAEPGRYL 243 Query: 238 VTNTTTLNTTVL----DISENIKNLVIVDSSV----------EAHVPDYLLYQESATIYP 283 V + TL V+ ++ + ++ V P +L Sbjct: 244 VASAFTLAVNVIAKRKRGDDDRERWYYLNDGVYGSFNEILFDHIRYPPRVLKDGGRD--G 301 Query: 284 NTGPYTAMVCGRSCLAGD-IFGEFHFEKPVKIGDRISFEDVAGYNINRKNWFNGINMPTI 342 P + + G +C + D I+ + + + +GD + FE++ Y + FNG P I Sbjct: 302 ELYPSS--LWGPTCDSLDVIYEDVLLPEDLAVGDWLLFENMGAYTTAYASTFNGFPPPKI 359 Query: 343 AV 344 Sbjct: 360 VY 361 >gnl|CDD|33075 COG3264, COG3264, Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]. Length = 835 Score = 33.0 bits (75), Expect = 0.13 Identities = 9/19 (47%), Positives = 14/19 (73%) Query: 308 FEKPVKIGDRISFEDVAGY 326 FE+PVK+GD ++ V+G Sbjct: 657 FERPVKVGDTVTIGTVSGT 675 >gnl|CDD|144501 pfam00924, MS_channel, Mechanosensitive ion channel. Two members of this protein family from M. jannaschii have been functionally characterized. Both proteins form mechanosensitive (MS) ion channels upon reconstitution into liposomes and functional examination by the patch-clamp technique. Therefore this family are likely to also be MS channel proteins. Length = 203 Score = 31.4 bits (72), Expect = 0.41 Identities = 12/19 (63%), Positives = 12/19 (63%) Query: 308 FEKPVKIGDRISFEDVAGY 326 FEKP KIGD I DV G Sbjct: 55 FEKPFKIGDWIEIGDVEGT 73 >gnl|CDD|35573 KOG0352, KOG0352, KOG0352, ATP-dependent DNA helicase [Replication, recombination and repair]. Length = 641 Score = 30.5 bits (68), Expect = 0.68 Identities = 27/116 (23%), Positives = 45/116 (38%), Gaps = 20/116 (17%) Query: 229 IYLEPGEAIVTNTT--TLNTTVLDISENIKNLVIVDSSVEAHV---------PDYLLYQE 277 +Y+ P E T+ LN + ++ ++VD EAH PDYL Sbjct: 117 LYITP-EGAATDGFQKLLNGLA---NRDVLRYIVVD---EAHCVSQWGHDFRPDYLTLGS 169 Query: 278 SATIYPNTGPYTAMVCGRSCLAG-DIFGEFHFEKPVKIGDRISFEDVAGYNINRKN 332 ++ P P+ A+ + DI + PV I +F D Y+ + K+ Sbjct: 170 LRSVCPGV-PWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTFRDNLFYDNHMKS 224 >gnl|CDD|146017 pfam03180, Lipoprotein_9, NLPA lipoprotein. This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to pfam00497 which are solute binding proteins. Length = 236 Score = 28.0 bits (63), Expect = 4.5 Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 2/28 (7%) Query: 240 NTTTLNTTVLDISENIKNLVIVDSSVEA 267 + L TV DI+EN KNL I + +EA Sbjct: 126 DGAGLLATVKDITENPKNLKIKE--LEA 151 >gnl|CDD|36534 KOG1320, KOG1320, KOG1320, Serine protease [Posttranslational modification, protein turnover, chaperones]. Length = 473 Score = 27.6 bits (61), Expect = 5.4 Identities = 16/84 (19%), Positives = 22/84 (26%), Gaps = 9/84 (10%) Query: 187 GHFITQIEWISLGGGIHFTDKDYPVKDFCQRLKEFSEKYSVQIYLEPGEAIVTNTT---- 242 G ++ I GI F V RL EF L P + + Sbjct: 319 GVNTRKVTRIGFSHGISFKIPIDTVLVIVLRLGEFQISLRPVKPLVPVHQYIGLPSYYIF 378 Query: 243 -----TLNTTVLDISENIKNLVIV 261 T + LV+V Sbjct: 379 AGLVFVPLTKSYIFPSGVVQLVLV 402 >gnl|CDD|100009 cd06152, YjgF_YER057c_UK114_like_4, YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.. Length = 114 Score = 27.3 bits (61), Expect = 7.1 Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 13/55 (23%) Query: 306 FHFEKPVKIGDRISFEDVAGYNINRKNWFNGINMPTI-------AVKNVDGTIKA 353 H+ + V+IGDRI G++ + +P A NV+ +KA Sbjct: 1 LHYSQAVRIGDRIEISGQGGWDP------DTGKIPEDLEEEIDQAFDNVELALKA 49 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 0.409 Gapped Lambda K H 0.267 0.0751 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,458,575 Number of extensions: 236775 Number of successful extensions: 643 Number of sequences better than 10.0: 1 Number of HSP's gapped: 622 Number of HSP's successfully gapped: 23 Length of query: 367 Length of database: 6,263,737 Length adjustment: 95 Effective length of query: 272 Effective length of database: 4,210,882 Effective search space: 1145359904 Effective search space used: 1145359904 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: 58 (26.1 bits)