RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780673|ref|YP_003065086.1| pyruvate dehydrogenase subunit beta [Candidatus Liberibacter asiaticus str. psy62] (467 letters) >gnl|CDD|183363 PRK11892, PRK11892, pyruvate dehydrogenase subunit beta; Provisional. Length = 464 Score = 874 bits (2261), Expect = 0.0 Identities = 323/469 (68%), Positives = 375/469 (79%), Gaps = 12/469 (2%) Query: 1 MPILVTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKIL 60 M I + MP+LSPTM EG +AKW K EGD +K GD+I E+ETDKA MEVE++DEG LGKIL Sbjct: 1 MAIEILMPALSPTMEEGTLAKWLKKEGDKVKSGDVIAEIETDKATMEVEAVDEGTLGKIL 60 Query: 61 CPNGTKNVKVNTPIAAILQEGETALDIDKMLLEKPDVAISPSSKNTTLVFSNEDNDKVDH 120 P GT+ VKVNTPIA +L+EGE+A D + A + + + K Sbjct: 61 VPEGTEGVKVNTPIAVLLEEGESASDAGAAPAAAAEAAAAAPA-----AAAAAAAKKAAP 115 Query: 121 QKSKNDIQDSSFAHAP-------TSSITVREALRDAIAEEMRRDKDVFIMGEEVAEYQGA 173 + + A P ++TVREALRDA+AEEMRRD+DVF+MGEEVAEYQGA Sbjct: 116 APAAPAAPAAEVAADPDIPAGTEMVTMTVREALRDAMAEEMRRDEDVFVMGEEVAEYQGA 175 Query: 174 YKVTQGLLQEFGCERVIDTPITEHGFAGIGIGASFAGLKPIVEFMTFNFAMQAIDQIINS 233 YKVTQGLLQEFG RVIDTPITEHGFAGIG+GA+FAGLKPIVEFMTFNFAMQAIDQIINS Sbjct: 176 YKVTQGLLQEFGARRVIDTPITEHGFAGIGVGAAFAGLKPIVEFMTFNFAMQAIDQIINS 235 Query: 234 AAKTRYMSGGQITTSIVFRGPNGAAARVAAQHSQCYAAWYSHVPGLKVVIPYTASDAKGL 293 AAKT YMSGGQ+ IVFRGPNGAAARVAAQHSQ YAAWYSH+PGLKVV PY+A+DAKGL Sbjct: 236 AAKTLYMSGGQMGCPIVFRGPNGAAARVAAQHSQDYAAWYSHIPGLKVVAPYSAADAKGL 295 Query: 294 LKAAIRDPNPVIFLENEILYGSSFEVPMVDDLVIPIGRARIHRQGSDVTIISFGIGMTYA 353 LKAAIRDPNPVIFLENEILYG SF+VP +DD V+PIG+ARIHR+G DVTI+SF IGMTYA Sbjct: 296 LKAAIRDPNPVIFLENEILYGQSFDVPKLDDFVLPIGKARIHREGKDVTIVSFSIGMTYA 355 Query: 354 TKAAIELEKNGIDAELIDLRTIRPMDWQTIFESVKKTGRLVTVEEGYPQSSVGSTIANQV 413 KAA EL K GIDAE+IDLRTIRPMD +TI ESVKKT RLVTVEEG+PQS VG+ IA +V Sbjct: 356 LKAAEELAKEGIDAEVIDLRTIRPMDTETIVESVKKTNRLVTVEEGWPQSGVGAEIAARV 415 Query: 414 QRKVFDYLDAPILTITGRDVPMPYAANLEKLALPNVDEIIESVESICYK 462 + FDYLDAP+L +TG+DVPMPYAANLEKLALP+V E++E+V+++CY+ Sbjct: 416 MEQAFDYLDAPVLRVTGKDVPMPYAANLEKLALPSVAEVVEAVKAVCYR 464 >gnl|CDD|169719 PRK09212, PRK09212, pyruvate dehydrogenase subunit beta; Validated. Length = 327 Score = 564 bits (1456), Expect = e-161 Identities = 231/326 (70%), Positives = 275/326 (84%), Gaps = 1/326 (0%) Query: 139 SITVREALRDAIAEEMRRDKDVFIMGEEVAEYQGAYKVTQGLLQEFGCERVIDTPITEHG 198 +TVREALRDA+ EEM RD VF+MGEEV EYQGAYKVTQGLL++FG +RVIDTPITEHG Sbjct: 3 QLTVREALRDAMQEEMERDPKVFLMGEEVGEYQGAYKVTQGLLEQFGPKRVIDTPITEHG 62 Query: 199 FAGIGIGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTRYMSGGQITTSIVFRGPNGAA 258 FAG+ +GA+FAGL+PIVEFMTFNF+MQAIDQI+NSAAKT YMSGGQ+ IVFRGPNGAA Sbjct: 63 FAGLAVGAAFAGLRPIVEFMTFNFSMQAIDQIVNSAAKTNYMSGGQLKCPIVFRGPNGAA 122 Query: 259 ARVAAQHSQCYAAWYSHVPGLKVVIPYTASDAKGLLKAAIRDPNPVIFLENEILYGSSFE 318 ARVAAQHSQCYAAWYSH+PGLKVV PY A+D KGLLK AIRDPNPVIFLENEILYG S E Sbjct: 123 ARVAAQHSQCYAAWYSHIPGLKVVAPYFAADCKGLLKTAIRDPNPVIFLENEILYGHSHE 182 Query: 319 VPMVDDLVIPIGRARIHRQGSDVTIISFGIGMTYATKAAIELEKNGIDAELIDLRTIRPM 378 VP ++ IPIG+A I R+GSDVTI++F I + A +AA LEK GI E+IDLRT+RP+ Sbjct: 183 VPE-EEESIPIGKAAILREGSDVTIVTFSIQVKLALEAAELLEKEGISVEVIDLRTLRPL 241 Query: 379 DWQTIFESVKKTGRLVTVEEGYPQSSVGSTIANQVQRKVFDYLDAPILTITGRDVPMPYA 438 D +TI ESVKKT RLV VEEG+P + VG+ IA + ++ FDYLDAP+ +TG+DVP+PYA Sbjct: 242 DTETIIESVKKTNRLVVVEEGWPFAGVGAEIAALIMKEAFDYLDAPVERVTGKDVPLPYA 301 Query: 439 ANLEKLALPNVDEIIESVESICYKRK 464 ANLEKLALP+ ++IIE+V+ +CY+ Sbjct: 302 ANLEKLALPSEEDIIEAVKKVCYRSI 327 >gnl|CDD|178287 PLN02683, PLN02683, pyruvate dehydrogenase E1 component subunit beta. Length = 356 Score = 523 bits (1349), Expect = e-149 Identities = 213/335 (63%), Positives = 261/335 (77%), Gaps = 3/335 (0%) Query: 135 APTSSITVREALRDAIAEEMRRDKDVFIMGEEVAEYQGAYKVTQGLLQEFGCERVIDTPI 194 + +TVR+AL A+ EEM D VFIMGEEV EYQGAYK+T+GLLQ++G +RV+DTPI Sbjct: 22 SAAKEMTVRDALNSALDEEMSADPKVFIMGEEVGEYQGAYKITKGLLQKYGPDRVLDTPI 81 Query: 195 TEHGFAGIGIGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTRYMSGGQITTSIVFRGP 254 TE GF GIG+GA++AGLKP+VEFMTFNF+MQAID IINSAAKT YMS GQI+ IVFRGP Sbjct: 82 TEAGFTGIGVGAAYAGLKPVVEFMTFNFSMQAIDHIINSAAKTNYMSAGQISVPIVFRGP 141 Query: 255 NGAAARVAAQHSQCYAAWYSHVPGLKVVIPYTASDAKGLLKAAIRDPNPVIFLENEILYG 314 NGAAA V AQHSQC+AAWYS VPGLKV+ PY++ DA+GLLKAAIRDP+PV+FLENE+LYG Sbjct: 142 NGAAAGVGAQHSQCFAAWYSSVPGLKVLAPYSSEDARGLLKAAIRDPDPVVFLENELLYG 201 Query: 315 SSFEVP---MVDDLVIPIGRARIHRQGSDVTIISFGIGMTYATKAAIELEKNGIDAELID 371 SF V + V+PIG+A+I R+G DVTI++F + YA KAA L K GI AE+I+ Sbjct: 202 ESFPVSAEVLDSSFVLPIGKAKIEREGKDVTIVAFSKMVGYALKAAEILAKEGISAEVIN 261 Query: 372 LRTIRPMDWQTIFESVKKTGRLVTVEEGYPQSSVGSTIANQVQRKVFDYLDAPILTITGR 431 LR+IRP+D TI SV+KT RLVTVEEG+PQ VG+ I V + FDYLDAP+ I G Sbjct: 262 LRSIRPLDRDTINASVRKTNRLVTVEEGWPQHGVGAEICASVVEESFDYLDAPVERIAGA 321 Query: 432 DVPMPYAANLEKLALPNVDEIIESVESICYKRKAK 466 DVPMPYAANLE+LALP V++I+ + + CY+ Sbjct: 322 DVPMPYAANLERLALPQVEDIVRAAKRACYRSVPM 356 >gnl|CDD|185502 PTZ00182, PTZ00182, 3-methyl-2-oxobutanate dehydrogenase; Provisional. Length = 355 Score = 508 bits (1311), Expect = e-145 Identities = 171/325 (52%), Positives = 221/325 (68%) Query: 136 PTSSITVREALRDAIAEEMRRDKDVFIMGEEVAEYQGAYKVTQGLLQEFGCERVIDTPIT 195 T + VREA+ A+ EE+ RD VF++GE+VA+Y G YK T+GLL ++G +RV DTPIT Sbjct: 31 ATVKMNVREAINSALDEELARDPKVFVLGEDVAQYGGVYKCTKGLLDKYGPDRVFDTPIT 90 Query: 196 EHGFAGIGIGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTRYMSGGQITTSIVFRGPN 255 E GFAG IGA+ GL+PI EFM +F A DQI+N AAK RYMSGGQ IV RGPN Sbjct: 91 EQGFAGFAIGAAMNGLRPIAEFMFADFIFPAFDQIVNEAAKYRYMSGGQFDCPIVIRGPN 150 Query: 256 GAAARVAAQHSQCYAAWYSHVPGLKVVIPYTASDAKGLLKAAIRDPNPVIFLENEILYGS 315 GA A HSQ + A+++HVPGLKVV P DAKGLLKAAIRDPNPV+F E ++LY Sbjct: 151 GAVGHGGAYHSQSFEAYFAHVPGLKVVAPSDPEDAKGLLKAAIRDPNPVVFFEPKLLYRE 210 Query: 316 SFEVPMVDDLVIPIGRARIHRQGSDVTIISFGIGMTYATKAAIELEKNGIDAELIDLRTI 375 S EV D +P+G+A++ R+G DVTI+ +G + A KAA EL K GI E+IDLR++ Sbjct: 211 SVEVVPEADYTLPLGKAKVVREGKDVTIVGYGSQVHVALKAAEELAKEGISCEVIDLRSL 270 Query: 376 RPMDWQTIFESVKKTGRLVTVEEGYPQSSVGSTIANQVQRKVFDYLDAPILTITGRDVPM 435 RP D +TI +SVKKTGR V V E P +G+ IA Q+ F YL+API + G D P Sbjct: 271 RPWDRETIVKSVKKTGRCVIVHEAPPTCGIGAEIAAQIMEDCFLYLEAPIKRVCGADTPF 330 Query: 436 PYAANLEKLALPNVDEIIESVESIC 460 PYA NLE LP+ ++++E+ + + Sbjct: 331 PYAKNLEPAYLPDKEKVVEAAKRVL 355 >gnl|CDD|129094 smart00861, Transket_pyr, Transketolase, pyrimidine binding domain. Transketolase (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Hansenula polymorpha, there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. Length = 168 Score = 142 bits (360), Expect = 2e-34 Identities = 65/180 (36%), Positives = 87/180 (48%), Gaps = 23/180 (12%) Query: 141 TVREALRDAIAEEMRRD-KDVFIMGEEVA-----EYQGAYKVTQGLLQEFGCERVIDTPI 194 R+A +A+AE RD + V + G +V + G + T+GL G RVIDT I Sbjct: 1 ATRKAFGEALAELAERDPERVVVSGADVGGSTGLDRGGVFPDTKGL----GPGRVIDTGI 56 Query: 195 TEHGFAGIGIGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTRYMSGGQITTSIVFRGP 254 E G G + AGL+P+V F F +A DQI + A R +V R Sbjct: 57 AEQAMVGFAAGLALAGLRPVVAIF-FTFFDRAKDQIRSDGAMGR--------VPVVVRHD 107 Query: 255 NGAAARV--AAQHSQCYAAWYSHVPGLKVVIPYTASDAKGLLKAAIRDPN--PVIFLENE 310 +G HSQ A +PGLKVV P ++AKGLL+AAIR + PVI LE + Sbjct: 108 SGGGVGEDGPTHHSQEDEALLRAIPGLKVVAPSDPAEAKGLLRAAIRRDDGPPVIRLERK 167 >gnl|CDD|162311 TIGR01349, PDHac_trf_mito, pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form. This model represents one of several closely related clades of the dihydrolipoamide acetyltransferase subunit of the pyruvate dehydrogenase complex. It includes sequences from mitochondria and from alpha and beta branches of the proteobacteria, as well as from some other bacteria. Sequences from Gram-positive bacteria are not included. The non-enzymatic homolog protein X, which serves as an E3 component binding protein, falls within the clade phylogenetically but is rejected by its low score. Length = 435 Score = 127 bits (321), Expect = 5e-30 Identities = 55/102 (53%), Positives = 68/102 (66%), Gaps = 1/102 (0%) Query: 4 LVTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPN 63 +TMP+LSPTMT GN+AKW K EGD + GD+I E+ETDKA ME E+++EG L KIL P Sbjct: 1 KITMPALSPTMTTGNLAKWLKKEGDKVNPGDVIAEIETDKATMEFEAVEEGYLAKILVPE 60 Query: 64 GTKNVKVNTPIAAILQEGETALDIDKML-LEKPDVAISPSSK 104 GTK+V VN PIA +++E E D K LE A PS Sbjct: 61 GTKDVPVNKPIAVLVEEKEDVADAFKNYKLESSASAPKPSEI 102 >gnl|CDD|183339 PRK11856, PRK11856, branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed. Length = 411 Score = 117 bits (296), Expect = 6e-27 Identities = 35/84 (41%), Positives = 45/84 (53%), Gaps = 1/84 (1%) Query: 1 MPILVTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKIL 60 M MP L MTEG I +W GD +K+G + EVETDKA +E+ S G + K+L Sbjct: 1 MMFEFKMPDLGEGMTEGEIVEWLVKVGDTVKEGQPLAEVETDKATVEIPSPVAGTVAKLL 60 Query: 61 CPNGTKNVKVNTPIAAILQEGETA 84 G V V + IA I +EGE Sbjct: 61 VEEGDV-VPVGSVIAVIEEEGEAE 83 >gnl|CDD|178345 PLN02744, PLN02744, dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex. Length = 539 Score = 104 bits (262), Expect = 3e-23 Identities = 48/95 (50%), Positives = 64/95 (67%), Gaps = 3/95 (3%) Query: 7 MPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNGTK 66 MPSLSPTMTEGNIA+W K EGD + G+++ EVETDKA +E+E ++EG L KI+ +G K Sbjct: 117 MPSLSPTMTEGNIARWLKKEGDKVSPGEVLCEVETDKATVEMECMEEGYLAKIVKGDGAK 176 Query: 67 NVKVNTPIAAILQEGETALDIDKMLLEKPDVAISP 101 +KV IA ++E E DI K KP + +P Sbjct: 177 EIKVGEVIAITVEEEE---DIGKFKDYKPSSSAAP 208 >gnl|CDD|180086 PRK05444, PRK05444, 1-deoxy-D-xylulose-5-phosphate synthase; Provisional. Length = 580 Score = 81.7 bits (203), Expect = 4e-16 Identities = 71/263 (26%), Positives = 116/263 (44%), Gaps = 49/263 (18%) Query: 182 QEFGCERVIDTPITE-HG--FAGIGIGASFAGLKPIVE-FMTFNFAMQ-AIDQIINSAAK 236 + F +R D I E H FA G + GLKP+V + TF +Q A DQ+I+ A Sbjct: 317 KRFP-DRYFDVGIAEQHAVTFAA---GLATEGLKPVVAIYSTF---LQRAYDQVIHDVAL 369 Query: 237 TRYMSGGQITTSIVF---R----GPNGAAARVAAQHSQCY-AAWYSHVPGLKVVIPYTAS 288 + F R G +G H + ++ +P + ++ P + Sbjct: 370 QN--------LPVTFAIDRAGLVGADGPT------HQGAFDLSYLRCIPNMVIMAPSDEN 415 Query: 289 DAKGLLKAAIR-DPNPVIFLENEILY--GSSFEVPMVDDLVIPIGRARIHRQGSDVTIIS 345 + + +L A+ D P+ I Y G+ V + + +PIG+ + R+G DV I++ Sbjct: 416 ELRQMLYTALAYDDGPIA-----IRYPRGNGVGVELPELEPLPIGKGEVLREGEDVAILA 470 Query: 346 FGIGMTYATKAAIELEKNGIDAELIDLRTIRPMDWQTIFESVKKTGRLVTVEEGYPQSSV 405 FG + A KAA L A ++D R ++P+D + + E K +VTVEEG Sbjct: 471 FGTMLAEALKAAERLA----SATVVDARFVKPLDEELLLELAAKHDLVVTVEEGAIMGGF 526 Query: 406 GSTIANQVQRKVFDYLDAPILTI 428 GS + + LD P+L + Sbjct: 527 GSAVLEFLADH---GLDVPVLNL 546 >gnl|CDD|129308 TIGR00204, dxs, 1-deoxy-D-xylulose-5-phosphate synthase. DXP synthase is a thiamine diphosphate-dependent enzyme related to transketolase and the pyruvate dehydrogenase E1-beta subunit. By an acyloin condensation of pyruvate with glyceraldehyde 3-phosphate, it produces 1-deoxy-D-xylulose 5-phosphate, a precursor of thiamine diphosphate (TPP), pyridoxal phosphate, and the isoprenoid building block isopentenyl diphosphate (IPP). Length = 617 Score = 79.4 bits (196), Expect = 2e-15 Identities = 54/237 (22%), Positives = 99/237 (41%), Gaps = 19/237 (8%) Query: 179 GLLQEFGCERVIDTPITEHGFAGIGIGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTR 238 ++F +R D I E G + G KP V + F +A DQ+++ Sbjct: 345 KFSRKFP-DRYFDVAIAEQHAVTFAAGMAIEGYKPFVAIYS-TFLQRAYDQVVHDVC--- 399 Query: 239 YMSGGQITTSIVFRGPNGAAARVA--AQHSQCY-AAWYSHVPGLKVVIPYTASDAKGLLK 295 I V + A A H + ++ +P + ++ P ++ + +L Sbjct: 400 ------IQKLPVLFAIDRAGIVGADGETHQGAFDISYLRCIPNMVIMAPSDENELRQMLY 453 Query: 296 AAIR-DPNPVIFLENEILYGSSFEVPMVDDL-VIPIGRARIHRQGSDVTIISFGIGMTYA 353 D P+ G++ V + + +PIG++ + R+G + I+ FG + A Sbjct: 454 TGYHYDDGPIAV---RYPRGNAVGVELTPEPEKLPIGKSEVLRKGEKILILGFGTLVPEA 510 Query: 354 TKAAIELEKNGIDAELIDLRTIRPMDWQTIFESVKKTGRLVTVEEGYPQSSVGSTIA 410 + A L + GI+A ++D R ++P+D + I E +LVTVEE GS + Sbjct: 511 LEVAESLNEKGIEATVVDARFVKPLDEELILEIAASHEKLVTVEENAIMGGAGSAVL 567 >gnl|CDD|184875 PRK14875, PRK14875, acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional. Length = 371 Score = 75.4 bits (186), Expect = 3e-14 Identities = 29/84 (34%), Positives = 45/84 (53%), Gaps = 1/84 (1%) Query: 5 VTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNG 64 +TMP +MTEG +A W EGD +++GD + +VETDK EVE+ G L + + G Sbjct: 5 ITMPKWGLSMTEGKVAGWLVQEGDEVEKGDELLDVETDKITNEVEAPAAGTLRRQVAQEG 64 Query: 65 TKNVKVNTPIAAILQEGETALDID 88 + V +A + + +ID Sbjct: 65 E-TLPVGALLAVVADAEVSDAEID 87 >gnl|CDD|162309 TIGR01347, sucB, 2-oxoglutarate dehydrogenase complex dihydrolipoamide succinyltransferase (E2 component). dihydrolipoamide acetyltransferase. The seed for this model includes mitochondrial and Gram-negative bacterial forms. Mycobacterial candidates are highly derived, differ in having and extra copy of the lipoyl-binding domain at the N-terminus. They score below the trusted cutoff, but above the noise cutoff and above all examples of dihydrolipoamide acetyltransferase. Length = 403 Score = 67.1 bits (164), Expect = 8e-12 Identities = 34/82 (41%), Positives = 52/82 (63%), Gaps = 2/82 (2%) Query: 3 ILVTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCP 62 I + +P L+ ++TEG +A+W K GD +K+ + I E+ETDK V+EV S +G+L +IL Sbjct: 1 IEIKVPELAESITEGTVAEWHKKVGDTVKRDENIVEIETDKVVLEVPSPADGVLQEILFK 60 Query: 63 NGTKNVKVNTPIAAILQEGETA 84 G V+ + AIL+EG A Sbjct: 61 EGDT-VESGQVL-AILEEGNDA 80 >gnl|CDD|180214 PRK05704, PRK05704, dihydrolipoamide succinyltransferase; Validated. Length = 407 Score = 67.2 bits (165), Expect = 1e-11 Identities = 31/84 (36%), Positives = 48/84 (57%), Gaps = 2/84 (2%) Query: 1 MPILVTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKIL 60 M + + +P+L ++TE IA W K GD +K+ +++ E+ETDK V+EV + G+L +IL Sbjct: 1 MMVEIKVPTLPESVTEATIATWHKKPGDAVKRDEVLVEIETDKVVLEVPAPAAGVLSEIL 60 Query: 61 CPNGTKNVKVNTPIAAILQEGETA 84 G V V + I EG A Sbjct: 61 AEEGD-TVTVGQVLGRI-DEGAAA 82 >gnl|CDD|183601 PRK12571, PRK12571, 1-deoxy-D-xylulose-5-phosphate synthase; Provisional. Length = 641 Score = 61.7 bits (150), Expect = 4e-10 Identities = 79/344 (22%), Positives = 138/344 (40%), Gaps = 37/344 (10%) Query: 113 EDNDKVDHQKSKNDIQDSSFAHAPTSSITVREALRDAIAEEMRRDKDVFIMGEEVAEYQG 172 D DK H K D+ + S+ + + + +E D D I+ A G Sbjct: 293 ADEDKY-HAVGKFDVVTGLQKKSAPSAPSYTSVFGEELTKEAAEDSD--IVAITAAMPLG 349 Query: 173 AYKVTQGLLQEFGCERVIDTPITEHGFAGIGIGASFAGLKPIVEFMTFNFAMQAIDQIIN 232 LQ+ RV D I E G + AGLKP + F + DQ+++ Sbjct: 350 ---TGLDKLQKRFPNRVFDVGIAEQHAVTFAAGLAAAGLKPFCAVYS-TFLQRGYDQLLH 405 Query: 233 SAA----KTRYM---SGGQITTSIVFRGPNGAAARVAAQHSQCY-AAWYSHVPGLKVVIP 284 A R++ +G G +GA H+ + A+ +++P + V+ P Sbjct: 406 DVALQNLPVRFVLDRAG--------LVGADGAT------HAGAFDLAFLTNLPNMTVMAP 451 Query: 285 YTASDAKGLLKAAI---RDPNPVIFLENEILYGSSFEVPMVDDLVIPIGRARIHRQGSDV 341 ++ + +L+ A P V F E G E+P ++ IG+ R+ R+G DV Sbjct: 452 RDEAELRHMLRTAAAHDDGPIAVRFPRGE---GVGVEIPAEGT-ILGIGKGRVPREGPDV 507 Query: 342 TIISFGIGMTYATKAAIELEKNGIDAELIDLRTIRPMDWQTIFESVKKTGRLVTVEEGYP 401 I+S G + AA LE GI + D R ++P+D + + + + + +V VEE Sbjct: 508 AILSVGAHLHECLDAADLLEAEGISVTVADPRFVKPLD-EALTDLLVRHHIVVIVEEQGA 566 Query: 402 QSSVGSTIANQVQRKVFDYLDAPILTITGRDVPMPYAANLEKLA 445 G+ + + + + T+ D + +A+ E A Sbjct: 567 MGGFGAHVLHHLADTGLLDGGLKLRTLGLPDRFIDHASREEMYA 610 >gnl|CDD|183338 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed. Length = 547 Score = 57.5 bits (140), Expect = 7e-09 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 1/63 (1%) Query: 15 TEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNGTKNVKVNTPI 74 TE + +W GD +++ + VETDKA ME+ S G++ +I G K V V + + Sbjct: 131 TEVEVIEWLVKVGDTVEEDQSLITVETDKATMEIPSPVAGVVKEIKVKVGDK-VSVGSLL 189 Query: 75 AAI 77 I Sbjct: 190 VVI 192 Score = 55.2 bits (134), Expect = 4e-08 Identities = 23/70 (32%), Positives = 34/70 (48%), Gaps = 1/70 (1%) Query: 15 TEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNGTKNVKVNTPI 74 E + +W EGD +++ + VETDKA ME+ S G++ +I G V V + Sbjct: 14 VEVEVIEWLVKEGDTVEEDQPLVTVETDKATMEIPSPAAGVVKEIKVKVGDT-VSVGGLL 72 Query: 75 AAILQEGETA 84 A I G A Sbjct: 73 AVIEAAGAAA 82 >gnl|CDD|177870 PLN02225, PLN02225, 1-deoxy-D-xylulose-5-phosphate synthase. Length = 701 Score = 57.0 bits (137), Expect = 9e-09 Identities = 64/264 (24%), Positives = 112/264 (42%), Gaps = 22/264 (8%) Query: 141 TVREALRDAIAEEMRRDKDVFIMGEEVAEYQGAYKVTQGLLQEFGCERVIDTPITEHGFA 200 T + +A+ E +D+D+ ++ A +T QE +R + + E Sbjct: 382 TYSDCFVEALVMEAEKDRDIVVV--HAGMEMDASLIT---FQERFPDRFFNVGMAEQHAV 436 Query: 201 GIGIGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTRYMSGGQITTSIVFRGPNGAAAR 260 G S GLKP + F +A DQ+++ + R IT++ + G +G Sbjct: 437 TFSAGLSSGGLKPFC-IIPSAFLQRAYDQVVHDVDRQRKAVRFVITSAGLV-GSDGPV-- 492 Query: 261 VAAQHSQCYA---AWYSHVPGLKVVIPYTASDAKGLL-KAAIRDPNPVIF-LENEILYGS 315 QC A A+ S +P + + P + ++ AA PV F + Sbjct: 493 ------QCGAFDIAFMSSLPNMIAMAPADEDELVNMVATAAYVTDRPVCFRFPRGSIVNM 546 Query: 316 SFEVPMVDDLVIPIGRARIHRQGSDVTIISFGIGMTYATKAAIELEKNGIDAELIDLRTI 375 ++ VP L I IGR R+ +G DV ++ +G + A L K G++ + D R Sbjct: 547 NYLVPT--GLPIEIGRGRVLVEGQDVALLGYGAMVQNCLHAHSLLSKLGLNVTVADARFC 604 Query: 376 RPMDWQTIFESVKKTGRLVTVEEG 399 +P+D + + + + L+TVEEG Sbjct: 605 KPLDIKLVRDLCQNHKFLITVEEG 628 >gnl|CDD|185477 PTZ00144, PTZ00144, dihydrolipoamide succinyltransferase; Provisional. Length = 418 Score = 52.8 bits (127), Expect = 2e-07 Identities = 27/135 (20%), Positives = 55/135 (40%), Gaps = 5/135 (3%) Query: 5 VTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNG 64 + +P++ +++EG + +WKK GD +K+ ++I +ETDK +++ + G++ KI G Sbjct: 47 IKVPTMGDSISEGTVVEWKKKVGDYVKEDEVICIIETDKVSVDIRAPASGVITKIFAEEG 106 Query: 65 TKNVKVNTPIAAILQEGETALDIDKMLLEKPDVAISPSSKNTTLVFSNEDNDKVDHQKSK 124 V+V P++ I G A + + + + K Sbjct: 107 D-TVEVGAPLSEIDTGGAPPAAA----PAAAAAAKAEKTTPEKPKAAAPTPEPPAASKPT 161 Query: 125 NDIQDSSFAHAPTSS 139 AP + Sbjct: 162 PPAAAKPPEPAPAAK 176 >gnl|CDD|131973 TIGR02927, SucB_Actino, 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase. This model represents an Actinobacterial clade of E2 enzyme, a component of the 2-oxoglutarate dehydrogenase complex involved in the TCA cycle. These proteins have multiple domains including the catalytic domain (pfam00198), one or two biotin domains (pfam00364) and an E3-component binding domain (pfam02817). Length = 590 Score = 51.3 bits (122), Expect = 5e-07 Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 1/82 (1%) Query: 1 MPILVTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKIL 60 M V MP+L ++TEG I +W K EGD ++ + + EV TDK E+ S G++ +I Sbjct: 1 MAFSVEMPALGESVTEGTITQWLKAEGDTVELDEPLLEVSTDKVDTEIPSPAAGVILEIK 60 Query: 61 CPNGTKNVKVNTPIAAILQEGE 82 V + IA I + GE Sbjct: 61 AEE-DDTVDIGGEIAIIGEAGE 81 Score = 44.4 bits (104), Expect = 6e-05 Identities = 36/137 (26%), Positives = 56/137 (40%), Gaps = 1/137 (0%) Query: 5 VTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNG 64 + MP L ++TEG I +W K GD I+ + I EV TDK E+ S G + +IL Sbjct: 138 IEMPELGESVTEGTITQWLKAVGDKIEVDEPILEVSTDKVDTEIPSPVAGTILEILA-EE 196 Query: 65 TKNVKVNTPIAAILQEGETALDIDKMLLEKPDVAISPSSKNTTLVFSNEDNDKVDHQKSK 124 V V IA I G A + K E A + + + D +++ Sbjct: 197 DDTVDVGAEIAKIGDAGAAAAEDAKAEEEAEAKAEAKPEEKPDPKKDEAAEPEPDEPEAE 256 Query: 125 NDIQDSSFAHAPTSSIT 141 + A A ++ + Sbjct: 257 KAEKKEEKAAAAPAANS 273 >gnl|CDD|183431 PRK12315, PRK12315, 1-deoxy-D-xylulose-5-phosphate synthase; Provisional. Length = 581 Score = 50.4 bits (121), Expect = 1e-06 Identities = 56/235 (23%), Positives = 97/235 (41%), Gaps = 32/235 (13%) Query: 187 ERVIDTPITEHGFAGIGIGASFAGLKPIVEFMTFNFAMQAIDQI-----INSAAKTRYMS 241 ++ +D I E G + G +P++ F+ F +A DQ+ IN+ + Sbjct: 320 DQYVDVGIAEQESVAFASGIAANGARPVI-FVNSTFLQRAYDQLSHDLAINNNPAVMIVF 378 Query: 242 GGQITTSIVFRGPNGAAARVAAQHSQCYA-AWYSHVPGLKVVIPYTASDAKGLLKAAIRD 300 GG I+ + V H + S++P L + P T + +L+ A+ Sbjct: 379 GGSISGNDV-------------THLGIFDIPMISNIPNLVYLAPTTKEELIAMLEWALTQ 425 Query: 301 PN-PVIFL--ENEILYGSSFEVPMVDDLVIPIGRARIHRQGSDVTIISFGIGMTYATKAA 357 PV E+ + G + D + + + G V I++ G K A Sbjct: 426 HEHPVAIRVPEHGVESGP----TVDTDYSTL--KYEVTKAGEKVAILALGDFYELGEKVA 479 Query: 358 IEL-EKNGIDAELIDLRTIRPMDWQTIFESVKKTGRLV-TVEEGYPQSSVGSTIA 410 +L E+ GIDA LI+ + I +D + + E +K+ LV T+E+G G IA Sbjct: 480 KKLKEELGIDATLINPKFITGLDEELL-EKLKEDHELVVTLEDGILDGGFGEKIA 533 >gnl|CDD|177878 PLN02234, PLN02234, 1-deoxy-D-xylulose-5-phosphate synthase. Length = 641 Score = 49.3 bits (117), Expect = 2e-06 Identities = 60/239 (25%), Positives = 98/239 (41%), Gaps = 20/239 (8%) Query: 188 RVIDTPITEHGFAGIGIGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTRYMSGGQITT 247 R D I E G + GLKP + +F +A DQ+++ + + Sbjct: 400 RCFDVGIAEQHAVTFAAGLACEGLKPFCTIYS-SFMQRAYDQVVHDVDLQKL----PVRF 454 Query: 248 SIVFRGPNGAAARVAAQHSQCY-AAWYSHVPGLKVVIPYTASDAKGLL-KAAIRDPNPVI 305 +I G GA H + + + +P + V+ P ++ ++ AA D P Sbjct: 455 AIDRAGLMGADG---PTHCGAFDVTFMACLPNMIVMAPSDEAELFNMVATAAAIDDRPSC 511 Query: 306 FLENEILYGSSFEV---PMVDDLVIPIGRARIHRQGSDVTIISFGIGMTYATKAAIELEK 362 F + G+ V P + + IGR RI R G V ++ +G + +AA L + Sbjct: 512 FRYHR---GNGIGVSLPPGNKGVPLQIGRGRILRDGERVALLGYGSAVQRCLEAASMLSE 568 Query: 363 NGIDAELIDLRTIRPMDWQTIFESVKKTGRLVTVEEGYPQSSVGSTIANQVQRKVFDYL 421 G+ + D R +P+D I K L+TVEEG S+G ++ VQ D L Sbjct: 569 RGLKITVADARFCKPLDVALIRSLAKSHEVLITVEEG----SIGGFGSHVVQFLALDGL 623 >gnl|CDD|183337 PRK11854, aceF, pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated. Length = 633 Score = 48.8 bits (117), Expect = 3e-06 Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 3/84 (3%) Query: 1 MPILVTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKIL 60 M I + +P + E + + GD ++ + VE DKA MEV S G++ +I Sbjct: 1 MAIEIKVPDIG--ADEVEVTEILVKVGDKVEAEQSLITVEGDKASMEVPSPQAGVVKEIK 58 Query: 61 CPNGTKNVKVNTPIAAILQEGETA 84 G K V+ I A Sbjct: 59 VKVGDK-VETGALIMIFESADGAA 81 Score = 40.0 bits (94), Expect = 0.001 Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 3/80 (3%) Query: 5 VTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNG 64 V +P + E + + GD ++ + VE DKA MEV + G + +I G Sbjct: 108 VHVPDIG--SDEVEVTEILVKVGDTVEAEQSLITVEGDKASMEVPAPFAGTVKEIKVNVG 165 Query: 65 TKNVKVNTPIAAILQEGETA 84 K V + I GE Sbjct: 166 DK-VSTGSLIMVFEVAGEAP 184 Score = 39.6 bits (93), Expect = 0.002 Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 3/77 (3%) Query: 5 VTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNG 64 V +P + E + + GD ++ + VE DKA MEV + G + +I G Sbjct: 209 VNVPDIG--GDEVEVTEVMVKVGDKVEAEQSLITVEGDKASMEVPAPFAGTVKEIKVNVG 266 Query: 65 TKNVKVNTPIAAILQEG 81 K VK + I EG Sbjct: 267 DK-VKTGSLIMRFEVEG 282 >gnl|CDD|178194 PLN02582, PLN02582, 1-deoxy-D-xylulose-5-phosphate synthase. Length = 677 Score = 47.2 bits (112), Expect = 8e-06 Identities = 25/73 (34%), Positives = 39/73 (53%) Query: 327 IPIGRARIHRQGSDVTIISFGIGMTYATKAAIELEKNGIDAELIDLRTIRPMDWQTIFES 386 I +G+ RI +G V ++ +G + AA LE++G+ A + D R +P+D I Sbjct: 532 IEVGKGRILLEGERVALLGYGTAVQSCLAAASLLERHGLSATVADARFCKPLDRALIRSL 591 Query: 387 VKKTGRLVTVEEG 399 K L+TVEEG Sbjct: 592 AKSHEVLITVEEG 604 >gnl|CDD|177871 PLN02226, PLN02226, 2-oxoglutarate dehydrogenase E2 component. Length = 463 Score = 42.0 bits (98), Expect = 3e-04 Identities = 24/101 (23%), Positives = 53/101 (52%), Gaps = 3/101 (2%) Query: 7 MPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNGTK 66 +P + ++T+G +A + K G+ ++ + I ++ETDK +++ S G++ + L G Sbjct: 96 VPHMGESITDGTLATFLKKPGERVQADEAIAQIETDKVTIDIASPASGVIQEFLVKEG-D 154 Query: 67 NVKVNTPIAAILQEGETALDI--DKMLLEKPDVAISPSSKN 105 V+ T +A I + + A + + + E D SP +++ Sbjct: 155 TVEPGTKVAIISKSEDAASQVTPSQKIPETTDPKPSPPAED 195 >gnl|CDD|181999 PRK09622, porA, pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed. Length = 407 Score = 39.7 bits (93), Expect = 0.002 Identities = 35/156 (22%), Positives = 67/156 (42%), Gaps = 28/156 (17%) Query: 291 KGLLKAAIRDPNPVI---FLENEILYGSSF---EVPMVDDLVIPIGRARIHRQGSDVTII 344 K L A+ + VI F + L G + E ++D ++V I+ Sbjct: 228 KAQLHHALMSSSSVIEEVFNDFAKLTGRKYNLVETYQLED--------------AEVAIV 273 Query: 345 SFGIGMTYATKAAIELEKNGIDAELIDLRTIRPMDWQTIFESVKKTGRLVTVEEGYPQSS 404 + G A AA E+ K GI A + +R +RP ++ + +++K L ++ P + Sbjct: 274 ALGTTYESAIVAAKEMRKEGIKAGVATIRVLRPFPYERLGQALKNLKALAILDRSSPAGA 333 Query: 405 VGSTIANQVQRKVFDY--LDAPILT-----ITGRDV 433 +G + N+V V+ P+++ + GRD+ Sbjct: 334 MG-ALFNEVTSAVYQTQGTKHPVVSNYIYGLGGRDM 368 >gnl|CDD|178143 PLN02528, PLN02528, 2-oxoisovalerate dehydrogenase E2 component. Length = 416 Score = 34.7 bits (80), Expect = 0.058 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 1/73 (1%) Query: 21 KWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNGTKNVKVNTPIAAILQE 80 +W EGD +++ + EV++DKA +E+ S +G + +I G VKV + I+ E Sbjct: 17 RWFVKEGDQVEEFQPLCEVQSDKATIEITSRYKGKVAQINFSPGDI-VKVGETLLKIMVE 75 Query: 81 GETALDIDKMLLE 93 L D +LL Sbjct: 76 DSQHLRSDSLLLP 88 >gnl|CDD|162983 TIGR02712, urea_carbox, urea carboxylase. Members of this family are ATP-dependent urea carboxylase, including characterized members from Oleomonas sagaranensis (alpha class Proteobacterium) and yeasts such as Saccharomyces cerevisiae. The allophanate hydrolase domain of the yeast enzyme is not included in this model and is represented by an adjacent gene in Oleomonas sagaranensis. The fusion of urea carboxylase and allophanate hydrolase is designated urea amidolyase. The enzyme from Oleomonas sagaranensis was shown to be highly active on acetamide and formamide as well as urea. Length = 1201 Score = 34.2 bits (79), Expect = 0.063 Identities = 16/48 (33%), Positives = 22/48 (45%) Query: 17 GNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNG 64 GN K GD ++ G + +E K M V + G + KILC G Sbjct: 1141 GNFWKVLVEVGDRVEAGQPLVILEAMKMEMPVSAPVAGKVTKILCQPG 1188 >gnl|CDD|162205 TIGR01108, oadA, oxaloacetate decarboxylase alpha subunit. This model describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea. The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane. Length = 582 Score = 33.6 bits (77), Expect = 0.10 Identities = 14/50 (28%), Positives = 27/50 (54%) Query: 17 GNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNGTK 66 G+I K K +EG + +G+++ +E K E+++ G + +IL G Sbjct: 526 GSIVKVKVSEGQTVAEGEVLLILEAMKMETEIKAAAAGTVREILVKVGDA 575 >gnl|CDD|163218 TIGR03336, IOR_alpha, indolepyruvate ferredoxin oxidoreductase, alpha subunit. Indolepyruvate ferredoxin oxidoreductase (IOR) is an alpha 2/beta 2 tetramer related to ketoacid oxidoreductases for pyruvate (1.2.7.1, POR), 2-ketoglutarate (1.2.7.3, KOR), and 2-oxoisovalerate (1.2.7.7, VOR). These multi-subunit enzymes typically are found in anaerobes and are inactiviated by oxygen. IOR in Pyrococcus acts in fermentation of all three aromatic amino acids, following removal of the amino group by transamination. In Methanococcus maripaludis, by contrast, IOR acts in the opposite direction, in pathways of amino acid biosynthesis from phenylacetate, indoleacetate, and p-hydroxyphenylacetate. In M. maripaludis and many other species, iorA and iorB are found next to an apparent phenylacetate-CoA ligase. Length = 595 Score = 33.5 bits (77), Expect = 0.11 Identities = 22/114 (19%), Positives = 45/114 (39%), Gaps = 10/114 (8%) Query: 333 RIHRQGSDVTIISFGIGMTYATKAAIELEKNGIDAELIDLRTIRPMDWQTIFESVKKTGR 392 R+ G+ + +I+ GI Y +A LE+ G+D ++ + P+ + E + Sbjct: 225 RLEINGAKIGVIASGIAYNYVKEA---LERLGVDVSVLKIGFTYPVPEGLVEEFLSGVEE 281 Query: 393 LVTVEEGYPQSSVGSTIANQVQRKVFDY-LDAPILTITGRDVPMPYAANLEKLA 445 ++ VEE P + QV+ L+ + +P N + + Sbjct: 282 VLVVEELEP------VVEEQVKALAGTAGLNIKVHGKEDGFLPREGELNPDIVV 329 >gnl|CDD|181526 PRK08659, PRK08659, 2-oxoglutarate ferredoxin oxidoreductase subunit alpha; Validated. Length = 376 Score = 33.3 bits (77), Expect = 0.15 Identities = 17/59 (28%), Positives = 28/59 (47%) Query: 339 SDVTIISFGIGMTYATKAAIELEKNGIDAELIDLRTIRPMDWQTIFESVKKTGRLVTVE 397 ++V ++++G A +A E + GI L L T+ P + I E KK +V E Sbjct: 274 AEVVVVAYGSVARSARRAVKEAREEGIKVGLFRLITVWPFPEEAIRELAKKVKAIVVPE 332 >gnl|CDD|162310 TIGR01348, PDHac_trf_long, pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form. This model describes a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and per cent identity (UPGMA) trees. Members of this set include two or three copies of the lipoyl-binding domain. E. coli AceF is a member of this model, while mitochondrial and some other bacterial forms belong to a separate model. Length = 546 Score = 32.9 bits (75), Expect = 0.17 Identities = 24/90 (26%), Positives = 40/90 (44%), Gaps = 9/90 (10%) Query: 16 EGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNGTKNVKV--NTP 73 EG + + GD ++ G + +E+DKA MEV S GI+ +I VKV P Sbjct: 13 EGEVIEVLVKPGDKVEAGQSLITLESDKASMEVPSSAAGIIKEI-------KVKVGDTLP 65 Query: 74 IAAILQEGETALDIDKMLLEKPDVAISPSS 103 + ++ E K + A +P++ Sbjct: 66 VGGVIATLEVGAGAQAQAEAKKEAAPAPTA 95 Score = 28.7 bits (64), Expect = 3.1 Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 10/67 (14%) Query: 5 VTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNG 64 VT+P + + + + + GD + + +E+DKA MEV + G++ Sbjct: 119 VTVPDIG-DIEKVTVIEVLVKVGDTVSADQSLITLESDKASMEVPAPASGVV-------- 169 Query: 65 TKNVKVN 71 K+VKV Sbjct: 170 -KSVKVK 175 >gnl|CDD|162672 TIGR02040, PpsR-CrtJ, transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954). Length = 442 Score = 32.9 bits (75), Expect = 0.21 Identities = 15/65 (23%), Positives = 27/65 (41%) Query: 281 VVIPYTASDAKGLLKAAIRDPNPVIFLENEILYGSSFEVPMVDDLVIPIGRARIHRQGSD 340 +V + + L A+R + +E + SSFE+PM LV + G D Sbjct: 44 IVTAESVEKFELRLSEALRTGRGAVRVELNHIDPSSFELPMRFILVRLGADRGVLALGRD 103 Query: 341 VTIIS 345 + ++ Sbjct: 104 LRAVA 108 >gnl|CDD|180309 PRK05899, PRK05899, transketolase; Reviewed. Length = 624 Score = 32.8 bits (76), Expect = 0.22 Identities = 22/71 (30%), Positives = 30/71 (42%), Gaps = 4/71 (5%) Query: 336 RQGSDVTIISFGIGMTYATKAAIELEKNGIDAELIDLRTIRPMDWQ--TIFESV--KKTG 391 R DV +I+ G + A +AA ELE GI ++ + + D Q ESV Sbjct: 508 RDDPDVILIATGSEVHLALEAADELEAEGIKVRVVSMPSTELFDEQDAAYKESVLPAAVT 567 Query: 392 RLVTVEEGYPQ 402 V VE G Sbjct: 568 ARVAVEAGVAD 578 >gnl|CDD|181304 PRK08225, PRK08225, acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated. Length = 70 Score = 30.1 bits (68), Expect = 1.1 Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 2/40 (5%) Query: 3 ILVTMPSLSPTMTE--GNIAKWKKNEGDLIKQGDIIYEVE 40 IL +M P + E G + K EGD + +GD++ E+E Sbjct: 31 ILESMKMEIPIVAEEAGTVKKINVQEGDFVNEGDVLLEIE 70 >gnl|CDD|181754 PRK09282, PRK09282, pyruvate carboxylase subunit B; Validated. Length = 592 Score = 29.0 bits (66), Expect = 2.4 Identities = 16/48 (33%), Positives = 26/48 (54%) Query: 17 GNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNG 64 G + K K EGD +K GD + +E K E+++ +G + +IL G Sbjct: 531 GTVVKVKVKEGDKVKAGDTVLVLEAMKMENEIQAPVDGTVKEILVKEG 578 >gnl|CDD|184752 PRK14573, PRK14573, bifunctional D-alanyl-alanine synthetase A/UDP-N-acetylmuramate--L-alanine ligase; Provisional. Length = 809 Score = 28.6 bits (64), Expect = 3.4 Identities = 14/30 (46%), Positives = 16/30 (53%), Gaps = 5/30 (16%) Query: 138 SSITV-----REALRDAIAEEMRRDKDVFI 162 SSI V E LRD I+E D DVF+ Sbjct: 622 SSIGVFEVHNVEELRDKISEAFLYDTDVFV 651 >gnl|CDD|163422 TIGR03710, OAFO_sf, 2-oxoacid:acceptor oxidoreductase, alpha subunit. The genes for this enzyme in Prevotella intermedia 17, Persephonella marina EX-H1 and Picrophilus torridus DSM 9790 are in close proximity to a variety of TCA cycle genes. Persephonella marina and P. torridus are believed to encode complete TCA cycles, and none of these contains the lipoate-based 2-oxoglutarate dehydrogenase (E1/E2/E3) system. That system is presumed to be replaced by this one. In fact, the lipoate system is absent in most organisms possessing a member of this family, providing additional circumstantial evidence that many of these enzymes are capable of acting as 2-oxoglutarate dehydrogenases and supporting flux through TCA cycles in either the forward or reverse directions. Length = 562 Score = 28.6 bits (65), Expect = 3.6 Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 2/62 (3%) Query: 340 DVTIISFGIGMTYATKAAIE-LEKNGIDAELIDLRTIRPMDWQTIFESVKKTGRLVTVEE 398 DV +I +G A + A+E L GI L+ LR + P + E ++ +++ VE+ Sbjct: 465 DVLVIGWG-STYGAIREAVERLRAEGIKVALLHLRLLYPFPKDELAELLEGAKKVIVVEQ 523 Query: 399 GY 400 Sbjct: 524 NA 525 >gnl|CDD|161960 TIGR00615, recR, recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 195 Score = 28.5 bits (64), Expect = 3.9 Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 11/43 (25%) Query: 149 AIAEEMRRD----------KDVFIMGEEVAEYQGAYKVTQGLL 181 I + RRD KDVF + E+ E++G Y V G + Sbjct: 69 NICSDERRDNSVICVVEDPKDVFAL-EKTKEFRGRYHVLGGHI 110 >gnl|CDD|184504 PRK14097, pgi, glucose-6-phosphate isomerase; Provisional. Length = 448 Score = 28.3 bits (64), Expect = 4.2 Identities = 9/23 (39%), Positives = 14/23 (60%) Query: 202 IGIGASFAGLKPIVEFMTFNFAM 224 IGIG S+ G + +EF+ +F Sbjct: 79 IGIGGSYLGARAAIEFLNHSFYN 101 >gnl|CDD|180286 PRK05848, PRK05848, nicotinate-nucleotide pyrophosphorylase; Provisional. Length = 273 Score = 28.5 bits (64), Expect = 4.4 Identities = 9/32 (28%), Positives = 18/32 (56%) Query: 15 TEGNIAKWKKNEGDLIKQGDIIYEVETDKAVM 46 G + +G+ K+GDI+ E+E D +++ Sbjct: 55 MTGIECVFTIKDGERFKKGDILMEIEGDFSML 86 >gnl|CDD|180516 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated. Length = 460 Score = 27.8 bits (63), Expect = 5.7 Identities = 11/25 (44%), Positives = 13/25 (52%), Gaps = 1/25 (4%) Query: 125 NDIQDSSFAHAPTSSITVREALRDA 149 D+ F H PT S +R ALRD Sbjct: 430 EDLLRMPFYH-PTLSEGLRTALRDL 453 >gnl|CDD|180860 PRK07152, nadD, putative nicotinate-nucleotide adenylyltransferase; Validated. Length = 342 Score = 27.2 bits (61), Expect = 8.7 Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 8/46 (17%) Query: 420 YLDAPILTITGRDVPMPYAANLEKLAL-PNVDEIIESVESICYKRK 464 Y + I I G D NLEK N++EI++ V+ + +KRK Sbjct: 95 YPNDEIYFIIGSD-------NLEKFKKWKNIEEILKKVQIVVFKRK 133 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.316 0.134 0.378 Gapped Lambda K H 0.267 0.0819 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 7,671,126 Number of extensions: 514252 Number of successful extensions: 1189 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1176 Number of HSP's successfully gapped: 61 Length of query: 467 Length of database: 5,994,473 Length adjustment: 97 Effective length of query: 370 Effective length of database: 3,898,497 Effective search space: 1442443890 Effective search space used: 1442443890 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 59 (26.3 bits)