Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of acetoin cleaving system (uncharacterized)
to candidate WP_035704233.1 BA79_RS17615 dihydrolipoyl dehydrogenase
Query= curated2:O34324 (458 letters) >NCBI__GCF_000691145.1:WP_035704233.1 Length = 459 Score = 553 bits (1424), Expect = e-162 Identities = 273/458 (59%), Positives = 349/458 (76%), Gaps = 1/458 (0%) Query: 1 MTLAIIGGGPAGYAAAVSAAQQGRNVLLIDKGKLGGTCLNEGCIPTKSLLESANVLDKIK 60 MTL IIGGGPAGY AA++AA+ R V+LID+G LGGTCLNEGCIPTK+LL+SA++ + +K Sbjct: 1 MTLVIIGGGPAGYVAAITAARFDREVVLIDQGLLGGTCLNEGCIPTKALLQSADMYEHVK 60 Query: 61 HADSFGIELPAGAISVDWSKMQSRKQQVVSQLVQGVQYLMKKNQIQVVKGTASFLSERKL 120 A FGIELP + W +Q RK+ VV QL GV+YLM KN+I V+ G ASFLS +L Sbjct: 61 SAGHFGIELPGKEPVIHWDAVQKRKRSVVKQLTDGVRYLMNKNKISVLNGKASFLSAHEL 120 Query: 121 LIEGENGKEIREADQVLIASGSEPIELPFAPFDGEWILDSKDALSLSEIPSSLVIVGGGV 180 LIE E EI +A Q++IASGSEP LPFAPFD EWI+DSKDA++L IP SL I+GGGV Sbjct: 121 LIESEGKSEIIQAKQIIIASGSEPAALPFAPFDREWIIDSKDAMTLPSIPDSLCIIGGGV 180 Query: 181 IGCEYAGLFARLGSQVTIIETADRLIPAEDEDIARLFQEKLEEDGVEVHTSSRLGRVDQT 240 IGCE+A +F+R+GS+V ++E A ++P ED D A ++L++ GVE+ TS+ + ++D + Sbjct: 181 IGCEFASIFSRMGSKVVMVEQAAHILPEEDYDTANCLYDQLQKAGVEILTSAAVKQLDAS 240 Query: 241 AKTAIWKSGQRE-FKTKADYVLVAIGRKPRLDGLQLEQAGVDFSPKGIPVNGHMQTNVPH 299 +K + + E ++D+ LVAIGRKPRL L LEQ G++F GI VN HMQTN+ H Sbjct: 241 SKKVVVEKDHGERCDIQSDHCLVAIGRKPRLGELNLEQIGIEFDRNGICVNEHMQTNLSH 300 Query: 300 IYACGDAIGGIQLAHAAFHEGIIAASHASGRDVKINEKHVPRCIYTSPEIACIGMTERQA 359 IYACGD GG+QLAHAAFHEG IAASHASG DVK+NE+ +PRCIYTSPEIA +G+ E A Sbjct: 301 IYACGDVTGGVQLAHAAFHEGTIAASHASGEDVKVNEQVIPRCIYTSPEIASVGLNEENA 360 Query: 360 RSIYGDVKIGEFSFSANGKALIKQQAEGKVKIMAEPEFGEIVGVSMIGPDVTELIGQAAA 419 R YG+++IG+F+FSANGKALI Q G+VK++ EP++ EI+GVS+IGP+ TELIGQAA Sbjct: 361 RKQYGEIRIGKFAFSANGKALILNQPAGQVKVIVEPQYQEILGVSIIGPNATELIGQAAV 420 Query: 420 IMNGEMTADMAEHFIAAHPTLSETLHEALLSTIGLAVH 457 +M+ E+TAD E FIAAHPTLSE +HEALL T G AVH Sbjct: 421 MMHTELTADTLEQFIAAHPTLSEAIHEALLQTNGRAVH 458 Lambda K H 0.316 0.134 0.381 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: 600 Number of extensions: 34 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 458 Length of database: 459 Length adjustment: 33 Effective length of query: 425 Effective length of database: 426 Effective search space: 181050 Effective search space used: 181050 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: 51 (24.3 bits)
Align candidate WP_035704233.1 BA79_RS17615 (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.2793283.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-173 561.5 4.5 7.7e-173 561.3 4.5 1.0 1 NCBI__GCF_000691145.1:WP_035704233.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000691145.1:WP_035704233.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 561.3 4.5 7.7e-173 7.7e-173 4 460 .. 3 458 .. 1 459 [] 0.98 Alignments for each domain: == domain 1 score: 561.3 bits; conditional E-value: 7.7e-173 TIGR01350 4 vvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgieven..vk 74 +v+iGgGp+GYvaAi+aa+ +v+l+++ lGGtCln+GCiPtKalL+sa+++e++k a ++gie+ + NCBI__GCF_000691145.1:WP_035704233.1 3 LVIIGGGPAGYVAAITAARFDREVVLIDQGLLGGTCLNEGCIPTKALLQSADMYEHVKSAGHFGIELPGkePV 75 89****************************************************************8776799 PP TIGR01350 75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelp 147 + ++++++rk++vvk+l++Gv++L++knk++v++G+a++l+++e+ +++e k++ ++ak+iiiA+Gsep++lp NCBI__GCF_000691145.1:WP_035704233.1 76 IHWDAVQKRKRSVVKQLTDGVRYLMNKNKISVLNGKASFLSAHELLIESEGKSEIIQAKQIIIASGSEPAALP 148 ***************************************************99******************** PP TIGR01350 148 lkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkk 220 + +d++ +i+s++a++l+++p+sl i+GgGviG+Efasif+++G+kv ++e + +ilp +d + ++ l ++ NCBI__GCF_000691145.1:WP_035704233.1 149 F-APFDREWIIDSKDAMTLPSIPDSLCIIGGGVIGCEFASIFSRMGSKVVMVEQAAHILPEEDYDTANCLYDQ 220 *.7777777**************************************************************** PP TIGR01350 221 lkkkgvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvde 293 l+k gv+ilt+a v+++ +++++vvve++++e +++++ Lva+Grkp+l el+le++g+e+d++g i v+e NCBI__GCF_000691145.1:WP_035704233.1 221 LQKAGVEILTSAAVKQLDASSKKVVVEKDHGERCDIQSDHCLVAIGRKPRLGELNLEQIGIEFDRNG-ICVNE 292 ***************************9999**********************************77.***** PP TIGR01350 294 elrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeeg 366 +++tn+++iya+GDv+g+++LAh A++eg++aa ++ g+ +++++++P++iyt+Pe+asvGl+ee+a++++ NCBI__GCF_000691145.1:WP_035704233.1 293 HMQTNLSHIYACGDVTGGVQLAHAAFHEGTIAASHASGED-VKVNEQVIPRCIYTSPEIASVGLNEENARKQY 364 **************************************66.59****************************** PP TIGR01350 367 ievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihp 439 e+++gkf f+angkal+l++ G vkviv+++++eilG++i+g++a+eli ++a+++++elt++ l+++i + NCBI__GCF_000691145.1:WP_035704233.1 365 GEIRIGKFAFSANGKALILNQPAGQVKVIVEPQYQEILGVSIIGPNATELIGQAAVMMHTELTADTLEQFIAA 437 ************************************************************************* PP TIGR01350 440 HPtlsEaikeaalaalgkaih 460 HPtlsEai+ea+l+++g+a+h NCBI__GCF_000691145.1:WP_035704233.1 438 HPTLSEAIHEALLQTNGRAVH 458 *******************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (459 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 14.94 // [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