Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate N515DRAFT_2155 N515DRAFT_2155 dihydrolipoamide dehydrogenase
Query= BRENDA::Q0KBV8 (594 letters) >FitnessBrowser__Dyella79:N515DRAFT_2155 Length = 594 Score = 766 bits (1977), Expect = 0.0 Identities = 399/602 (66%), Positives = 481/602 (79%), Gaps = 19/602 (3%) Query: 2 SVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKV 61 + IEVKVPDIG D+V VIEVLVKAGD+V +QSLI LESDKA+M++PSSAAG + EVKV Sbjct: 3 NTIEVKVPDIGGHDSVPVIEVLVKAGDSVTKDQSLITLESDKATMEIPSSAAGTIKEVKV 62 Query: 62 KVGDKVGQGAVICTIEAQQAAAAPAP-------AQAPAPAQAPAPAAAAPAPAPAAASHS 114 KVGD++ +GAVI +E AAAPA A APAPA APAPA AA APAP AA S Sbjct: 63 KVGDELSEGAVIVILEVSGDAAAPAAEAPKAAAAPAPAPASAPAPAKAA-APAPQAAGAS 121 Query: 115 GG-ADIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHN 173 G ADI+C+++VLG+GPGGY+AAFRAADLG++TVLVERY+TLGGVCLNVGCIPSKALLH Sbjct: 122 GRTADIECKLVVLGSGPGGYTAAFRAADLGVDTVLVERYATLGGVCLNVGCIPSKALLHA 181 Query: 174 AAVIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNF 233 AAVIDEA+A+AAHG+ FG+ K+DLD LR +KN+VVG+LTGGLAGM++ RKV+ V+G+G+F Sbjct: 182 AAVIDEAEAMAAHGVSFGKPKLDLDKLRSFKNKVVGQLTGGLAGMSRQRKVRTVQGVGSF 241 Query: 234 LDPHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIP-EDPRIVDSTGALEL 292 + PH +EVE EG K ++RFE AIIAAGSQ+VKLP P +D R++DSTGALEL Sbjct: 242 VSPHELEVETAEG--------KKLVRFEHAIIAAGSQSVKLPAFPWDDERVMDSTGALEL 293 Query: 293 PEVPNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFG 352 +VP K+LV+GGGIIGLEMATVY+ LG+++ VVE +D L+ GAD DL+K K+ + Sbjct: 294 KDVPGKLLVVGGGIIGLEMATVYAALGSEVTVVEFMDQLIPGADADLIKPLAKRLGGKLK 353 Query: 353 KVMLKTKTVGVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVS 412 V LKTK +A GI V +EG++ P E + +D VLV+VGRSPNG +I A+KAGVAV+ Sbjct: 354 GVHLKTKVTEAKATKKGIEVAYEGDSIP-ETKLFDRVLVAVGRSPNGGKIGADKAGVAVT 412 Query: 413 ERGFINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSV 472 ERGFINVD QMRTNVPHIFAIGD+VGQPMLAHKA HEA VAAE G K++FDA+ IPSV Sbjct: 413 ERGFINVDTQMRTNVPHIFAIGDLVGQPMLAHKATHEARVAAEVVAGMKSHFDARVIPSV 472 Query: 473 AFTDPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIG 532 AFTDPEVAW G+TE E KEKG+K G FPWAASGRAI R EGFTKLIFDEETHRV+G Sbjct: 473 AFTDPEVAWVGVTEREAKEKGLKIGVGKFPWAASGRAIGIDRTEGFTKLIFDEETHRVVG 532 Query: 533 GGIVGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPR 592 G IVG HAGDLI+E+ AIEMG++A DIG TIHPHPTL ES+GMAAE+YEGT TD+ P+ Sbjct: 533 GAIVGPHAGDLIAEITHAIEMGSEAADIGLTIHPHPTLSESVGMAAEVYEGTITDLYMPK 592 Query: 593 KR 594 ++ Sbjct: 593 RK 594 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: 1014 Number of extensions: 48 Number of successful extensions: 6 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: 594 Length of database: 594 Length adjustment: 37 Effective length of query: 557 Effective length of database: 557 Effective search space: 310249 Effective search space used: 310249 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: 53 (25.0 bits)
Align candidate N515DRAFT_2155 N515DRAFT_2155 (dihydrolipoamide 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.25742.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-154 500.0 4.3 3.8e-154 499.7 4.3 1.1 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 N515DRAFT_2155 dihydrolipoamide Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 N515DRAFT_2155 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 499.7 4.3 3.8e-154 3.8e-154 3 455 .. 130 582 .. 128 587 .. 0.97 Alignments for each domain: == domain 1 score: 499.7 bits; conditional E-value: 3.8e-154 TIGR01350 3 dvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelg 67 +vv+G+GpgGY+aA raa lg ++lve+ +lGG+ClnvGCiP+KalL++a v++e++ ++ +g lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 130 KLVVLGSGPGGYTAAFRAADLGVDTVLVERyATLGGVCLNVGCIPSKALLHAAAVIDEAEAMAAHG 195 68****************************99********************************** PP TIGR01350 68 ievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleak 133 ++ + kldl+kl k+kvv +l+gG++++ ++ kv +++G +++++++e+ev++ +++k ++++ lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 196 VSFGKPKLDLDKLRSFKNKVVGQLTGGLAGMSRQRKVRTVQGVGSFVSPHELEVETAEGKKLVRFE 261 ****************************************************************** PP TIGR01350 134 niiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvi 199 ++iiA Gs+ +lp + d ++v++s++alelk vp +l++vGgG+iG+E+a+++a lG++vtv+ lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 262 HAIIAAGSQSVKLPA-FPWDDERVMDSTGALELKDVPGKLLVVGGGIIGLEMATVYAALGSEVTVV 326 ***************.999999******************************************** PP TIGR01350 200 elldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLva 264 e++d+++p da++ k l+k+l k ++ ++kvte +++++ ++v +++ et ++vLva lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 327 EFMDQLIPGADADLIKPLAKRLGGKLKGVHLKTKVTEAKATKKGIEVAYEGDsIPETKLFDRVLVA 392 ***********************9999999****************99999944577779****** PP TIGR01350 265 vGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekia 330 vGr+pn ++g +k gv ++erg+i+vd ++rtnvp+i+aiGD++g++mLAh+A++e+ vaae +a lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 393 VGRSPNGGKIGADKAGVAVTERGFINVDTQMRTNVPHIFAIGDLVGQPMLAHKATHEARVAAEVVA 458 ****************************************************************** PP TIGR01350 331 gkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkviv 396 g ++ ++d++++Psv +t+Peva vG+te++ake+g ++ vgkfp aa+g+a+ ++ t+Gf k+i+ lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 459 GMKS-HFDARVIPSVAFTDPEVAWVGVTEREAKEKGLKIGVGKFPWAASGRAIGIDRTEGFTKLIF 523 *665.9************************************************************ PP TIGR01350 397 dkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaal 455 d++t++++G ivg++a +li+e++ a+e++ ++ ++ tihpHPtlsE + aa+ lcl|FitnessBrowser__Dyella79:N515DRAFT_2155 524 DEETHRVVGGAIVGPHAGDLIAEITHAIEMGSEAADIGLTIHPHPTLSESVGMAAEVYE 582 ***************************************************99998765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (594 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: 00:00:00.03 # Mc/sec: 8.96 // [ok]
This GapMind analysis is from Sep 17 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