Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate H281DRAFT_00468 H281DRAFT_00468 dihydrolipoamide dehydrogenase
Query= BRENDA::Q0KBV8 (594 letters) >FitnessBrowser__Burk376:H281DRAFT_00468 Length = 590 Score = 887 bits (2291), Expect = 0.0 Identities = 455/599 (75%), Positives = 509/599 (84%), Gaps = 14/599 (2%) Query: 1 MSVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVK 60 MS++EVKVPDIGDF V+VIEV +K GD +E EQ+L+ LESDKAS++VPS AG V EV+ Sbjct: 1 MSLVEVKVPDIGDFKDVDVIEVNIKPGDVIENEQALMTLESDKASIEVPSDTAGTVKEVR 60 Query: 61 VKVGDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAP--APAAAAP---APAPAAASHSG 115 VK GDKV QG +I +E A AAPA APA+ P AP A P APAP A S SG Sbjct: 61 VKAGDKVSQGTIIALVETS-ADAAPAKDAPKAPAKEPEKAPTEAKPQAAAPAPQAGSFSG 119 Query: 116 GADIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAA 175 ADI+C+MLVLG+GPGGYSAAFR+ADLGM TVLVERY+TLGGVCLNVGCIPSKALLH A Sbjct: 120 SADIECDMLVLGSGPGGYSAAFRSADLGMKTVLVERYATLGGVCLNVGCIPSKALLHTAL 179 Query: 176 VIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLD 235 VIDEA+AL AHGI F + +IDLD LR +K+ VV KLTGGLAGMAK RKV+VV G G+F+D Sbjct: 180 VIDEAEALGAHGITFAKPQIDLDKLRDFKSGVVKKLTGGLAGMAKMRKVEVVTGTGSFVD 239 Query: 236 PHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDSTGALELPEV 295 P+HMEV+ TEG GKK V++F++AIIAAGS+AVKLPFIPEDPR+VDSTGALEL ++ Sbjct: 240 PNHMEVQ-TEG------GKK-VVKFKQAIIAAGSEAVKLPFIPEDPRVVDSTGALELRQI 291 Query: 296 PNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVM 355 P +MLVIGGGIIGLEMATVY+TLGA IDVVEMLDGLM GADRDLVKVWEK N RF VM Sbjct: 292 PQRMLVIGGGIIGLEMATVYATLGAKIDVVEMLDGLMAGADRDLVKVWEKYNSKRFANVM 351 Query: 356 LKTKTVGVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERG 415 LKTKT EAK DGIYV FEGE AP E QRYDLVLV+VGRSPNGK+I A+KAGV V++RG Sbjct: 352 LKTKTTAAEAKDDGIYVSFEGEKAPPEAQRYDLVLVAVGRSPNGKKIGADKAGVTVTDRG 411 Query: 416 FINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFT 475 FI+VDKQMRTNVPHIFAIGDIVGQPMLAHKAVHE HVAAEAAHGEKAYFDA QIPSVA+T Sbjct: 412 FIDVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEGHVAAEAAHGEKAYFDALQIPSVAYT 471 Query: 476 DPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGI 535 DPEVAWAG TED+ K +G+KY K VFPWAASGRAIANGRDEGFTKL+FDEETHRVIGGGI Sbjct: 472 DPEVAWAGKTEDQLKAEGVKYGKAVFPWAASGRAIANGRDEGFTKLLFDEETHRVIGGGI 531 Query: 536 VGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594 VG +AGDLISEVCLAIEMGADA DIGKTIHPHPTLGESIGMAAE+YEG CTD+PP +K+ Sbjct: 532 VGLNAGDLISEVCLAIEMGADATDIGKTIHPHPTLGESIGMAAELYEGVCTDLPPQKKK 590 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: 1101 Number of extensions: 35 Number of successful extensions: 4 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: 590 Length adjustment: 37 Effective length of query: 557 Effective length of database: 553 Effective search space: 308021 Effective search space used: 308021 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 H281DRAFT_00468 H281DRAFT_00468 (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.5394.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-150 485.5 2.8 1.1e-149 485.0 2.8 1.1 1 lcl|FitnessBrowser__Burk376:H281DRAFT_00468 H281DRAFT_00468 dihydrolipoamide Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_00468 H281DRAFT_00468 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 485.0 2.8 1.1e-149 1.1e-149 2 453 .. 125 576 .. 124 582 .. 0.97 Alignments for each domain: == domain 1 score: 485.0 bits; conditional E-value: 1.1e-149 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakel 66 d++v+G+GpgGY aA r+a lg+k++lve+ +lGG+ClnvGCiP+KalL++a v++e++ + + lcl|FitnessBrowser__Burk376:H281DRAFT_00468 125 CDMLVLGSGPGGYSAAFRSADLGMKTVLVERyATLGGVCLNVGCIPSKALLHTALVIDEAEALGAH 190 699****************************99********************************* PP TIGR01350 67 gievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekklea 132 gi+ ++ ++dl+kl + k+ vvkkl+gG++++ k kvev++G+++++d++++ev++e ++k++++ lcl|FitnessBrowser__Burk376:H281DRAFT_00468 191 GITFAKPQIDLDKLRDFKSGVVKKLTGGLAGMAKMRKVEVVTGTGSFVDPNHMEVQTEGGKKVVKF 256 ****************************************************************** PP TIGR01350 133 kniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtv 198 k++iiA Gse +lp+ + ed +v++s++alel+++p++++++GgG+iG+E+a+++a+lG+k+ v lcl|FitnessBrowser__Burk376:H281DRAFT_00468 257 KQAIIAAGSEAVKLPF-IPEDP-RVVDSTGALELRQIPQRMLVIGGGIIGLEMATVYATLGAKIDV 320 ****************.77776.7****************************************** PP TIGR01350 199 ielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvL 262 +e+ld +++ d+++ kv +k +k+ +++ ++k t+ e+++d + v+ +++ e +++ vL lcl|FitnessBrowser__Burk376:H281DRAFT_00468 321 VEMLDGLMAGADRDLVKVWEKYNSKRFANVMLKTKTTAAEAKDDGIYVSFEGEkaPPEAQRYDLVL 386 ********************************************99988887733568999***** PP TIGR01350 263 vavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaek 328 vavGr+pn +++g +k gv++++rg+i vd+++rtnvp+i+aiGD++g++mLAh+A++eg vaae+ lcl|FitnessBrowser__Burk376:H281DRAFT_00468 387 VAVGRSPNGKKIGADKAGVTVTDRGFIDVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEGHVAAEA 452 ****************************************************************** PP TIGR01350 329 iagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkv 394 + g+++ +d+ ++Psv yt+Peva G+te+q+k+eg+++ + fp aa+g+a+a + ++Gf k+ lcl|FitnessBrowser__Burk376:H281DRAFT_00468 453 AHGEKA-YFDALQIPSVAYTDPEVAWAGKTEDQLKAEGVKYGKAVFPWAASGRAIANGRDEGFTKL 517 ***776.9********************************************************** PP TIGR01350 395 ivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaala 453 ++d++t++++G ivg +a +lise+ la+e+++ ++++ ktihpHPtl+E i aa+ lcl|FitnessBrowser__Burk376:H281DRAFT_00468 518 LFDEETHRVIGGGIVGLNAGDLISEVCLAIEMGADATDIGKTIHPHPTLGESIGMAAEL 576 *****************************************************999875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (590 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: 00:00:00.02 # Mc/sec: 11.35 // [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