Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_086511849.1 BZY95_RS21050 dihydrolipoyl dehydrogenase
Query= BRENDA::Q0KBV8 (594 letters) >NCBI__GCF_002151265.1:WP_086511849.1 Length = 701 Score = 873 bits (2256), Expect = 0.0 Identities = 442/590 (74%), Positives = 494/590 (83%), Gaps = 7/590 (1%) Query: 5 EVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKVKVG 64 EV+VPDIGDF V VIEVLV+ GDT+ E SLI LESDKA+MDVP+ AG+V EV V VG Sbjct: 119 EVRVPDIGDFGDVPVIEVLVRPGDTIRAEDSLITLESDKAAMDVPAPKAGRVAEVLVTVG 178 Query: 65 DKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAPAAAAPAPAPAAASHSGGADIQCEML 124 DKV QG+ I +EA+ +A A APAQ A PAP PAP AAS+ GGAD++C ML Sbjct: 179 DKVSQGSPILMLEAEGSAHAAAPAQV---AGQPAPVT----PAPKAASYGGGADLECAML 231 Query: 125 VLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVIDEAKALA 184 VLGAGPGGYSAAFRAADLGM TVLVERY+TLGGVCLNVGCIPSKALLH AAV D A A+A Sbjct: 232 VLGAGPGGYSAAFRAADLGMKTVLVERYATLGGVCLNVGCIPSKALLHVAAVTDAANAMA 291 Query: 185 AHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLDPHHMEVELT 244 HGI FG+ KIDLD LR +K +VV KLTGGLAGMAKARKV+VVRG+G FLDPHH+EV LT Sbjct: 292 DHGIAFGKPKIDLDKLRGWKEKVVDKLTGGLAGMAKARKVEVVRGVGTFLDPHHLEVALT 351 Query: 245 EGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDSTGALELPEVPNKMLVIGG 304 G+G+ TG K VI+F K IIAAGSQ+VKLPFIP+DPR+VDSTGAL+L +P +MLVIGG Sbjct: 352 GGDGQEPTGAKQVIKFGKCIIAAGSQSVKLPFIPDDPRVVDSTGALKLTTIPKRMLVIGG 411 Query: 305 GIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVMLKTKTVGVE 364 GIIGLEMATVYSTLG IDVVEMLDGLM GADRDLVKVWEK N+ RF KVML T+T V+ Sbjct: 412 GIIGLEMATVYSTLGTRIDVVEMLDGLMAGADRDLVKVWEKVNQPRFDKVMLNTRTTAVK 471 Query: 365 AKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERGFINVDKQMR 424 A+ +G+ V FEGE APAEPQ YD++L +VGRSPNG +I AE AGVAV ERGFI DKQMR Sbjct: 472 AQKNGLKVSFEGEGAPAEPQLYDMILQAVGRSPNGHKIGAENAGVAVDERGFIATDKQMR 531 Query: 425 TNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFTDPEVAWAGL 484 TNV HIFAIGDIVGQPMLAHKAVHEAHVAAEAA G K++FDA+Q PSVA+TDPEVAWAG Sbjct: 532 TNVGHIFAIGDIVGQPMLAHKAVHEAHVAAEAAAGHKSFFDARQNPSVAYTDPEVAWAGK 591 Query: 485 TEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVGTHAGDLI 544 TE ECK +GIKY K VFPWAASGRAIANGRDEGFTKLIFDEETHR+IGG IVGT AGDLI Sbjct: 592 TEAECKAEGIKYGKAVFPWAASGRAIANGRDEGFTKLIFDEETHRIIGGAIVGTQAGDLI 651 Query: 545 SEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594 E+CLAIEMG D VDIGKTIHPHPTLGES+GMAAE++EG CTD+PP +KR Sbjct: 652 GELCLAIEMGCDPVDIGKTIHPHPTLGESVGMAAELFEGVCTDLPPQKKR 701 Score = 102 bits (255), Expect = 4e-26 Identities = 56/121 (46%), Positives = 74/121 (61%), Gaps = 12/121 (9%) Query: 2 SVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKV 61 + IEVKVPDIGDF VE+IEVLVK GD ++++ LI LE+DKASMDVPS +G V ++V Sbjct: 3 NAIEVKVPDIGDFKDVEIIEVLVKPGDAIDIDTPLITLETDKASMDVPSPVSGTVAALRV 62 Query: 62 KVGDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAP-----AAAAPAPAPAAASHSGG 116 K GD+V +G++I +E PA A + P P +PAP A + GG Sbjct: 63 KEGDRVSEGSLILMLE-------PAEAGSRVMDHEPQPVVHERGVGSPAPGDAGGGYGGG 115 Query: 117 A 117 A Sbjct: 116 A 116 Lambda K H 0.316 0.134 0.387 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1277 Number of extensions: 53 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 594 Length of database: 701 Length adjustment: 38 Effective length of query: 556 Effective length of database: 663 Effective search space: 368628 Effective search space used: 368628 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: 54 (25.4 bits)
Align candidate WP_086511849.1 BZY95_RS21050 (dihydrolipoyl dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01350.hmm # target sequence database: /tmp/gapView.9900.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01350 [M=461] Accession: TIGR01350 Description: lipoamide_DH: dihydrolipoyl dehydrogenase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-142 459.2 2.0 9.1e-142 458.9 2.0 1.1 1 lcl|NCBI__GCF_002151265.1:WP_086511849.1 BZY95_RS21050 dihydrolipoyl dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086511849.1 BZY95_RS21050 dihydrolipoyl dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 458.9 2.0 9.1e-142 9.1e-142 4 453 .. 230 687 .. 227 693 .. 0.96 Alignments for each domain: == domain 1 score: 458.9 bits; conditional E-value: 9.1e-142 TIGR01350 4 vvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgieve 71 ++v+G+GpgGY aA raa lg+k++lve+ +lGG+ClnvGCiP+KalL+ a v + ++ ++++gi lcl|NCBI__GCF_002151265.1:WP_086511849.1 230 MLVLGAGPGGYSAAFRAADLGMKTVLVERyATLGGVCLNVGCIPSKALLHVAAVTDAANAMADHGIAFG 298 68***************************99************************************** PP TIGR01350 72 nvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke........kklea 132 + k+dl+kl +kekvv+kl+gG++++ k kvev+ G +++ld++++ev+ + + +++++ lcl|NCBI__GCF_002151265.1:WP_086511849.1 299 KPKIDLDKLRGWKEKVVDKLTGGLAGMAKARKVEVVRGVGTFLDPHHLEVALTGGDgqeptgakQVIKF 367 ***********************************************9998776656689999999*** PP TIGR01350 133 kniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtviel 201 ++iiA Gs+ +lp+ + d +v++s++al+l+++p++++++GgG+iG+E+a+++++lG+ + v+e+ lcl|NCBI__GCF_002151265.1:WP_086511849.1 368 GKCIIAAGSQSVKLPF-IPDDP-RVVDSTGALKLTTIPKRMLVIGGGIIGLEMATVYSTLGTRIDVVEM 434 ****************.55554.7********************************************* PP TIGR01350 202 ldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrk 268 ld +++ d+++ kv +k + + k++ n++ t+v+++++ ++v+ +++ +e ++ +L avGr+ lcl|NCBI__GCF_002151265.1:WP_086511849.1 435 LDGLMAGADRDLVKVWEKVNQPRFDKVMLNTRTTAVKAQKNGLKVSFEGEgaPAEPQLYDMILQAVGRS 503 ******************9999999999999999999998888877666644778899*********** PP TIGR01350 269 pnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeksei 337 pn +++g e+ gv +derg+i +d+++rtnv +i+aiGD++g++mLAh+A++e+ vaae++ag++ s + lcl|NCBI__GCF_002151265.1:WP_086511849.1 504 PNGHKIGAENAGVAVDERGFIATDKQMRTNVGHIFAIGDIVGQPMLAHKAVHEAHVAAEAAAGHK-SFF 571 ***************************************************************55.59* PP TIGR01350 338 dykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGa 406 d+++ Psv yt+Peva G+te+++k+egi++ + fp aa+g+a+a + ++Gf k+i+d++t++i+G lcl|NCBI__GCF_002151265.1:WP_086511849.1 572 DARQNPSVAYTDPEVAWAGKTEAECKAEGIKYGKAVFPWAASGRAIANGRDEGFTKLIFDEETHRIIGG 640 ********************************************************************* PP TIGR01350 407 hivgaeaseliselalaveleltveelaktihpHPtlsEaikeaala 453 ivg++a +li el la+e++ ++ ktihpHPtl+E + aa+ lcl|NCBI__GCF_002151265.1:WP_086511849.1 641 AIVGTQAGDLIGELCLAIEMGCDPVDIGKTIHPHPTLGESVGMAAEL 687 ****************************************9999875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (701 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 13.13 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory