Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate BPHYT_RS12830 BPHYT_RS12830 dihydrolipoamide dehydrogenase
Query= BRENDA::Q0KBV8 (594 letters) >lcl|FitnessBrowser__BFirm:BPHYT_RS12830 BPHYT_RS12830 dihydrolipoamide dehydrogenase Length = 600 Score = 897 bits (2317), Expect = 0.0 Identities = 460/608 (75%), Positives = 515/608 (84%), Gaps = 22/608 (3%) Query: 1 MSVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVK 60 MS++EVKVPDIGDF V+VIEV +KAGD +E EQ+L+ LESDKAS++VPS AG V EV+ Sbjct: 1 MSLVEVKVPDIGDFKDVDVIEVNIKAGDVIENEQALMTLESDKASIEVPSDTAGTVKEVR 60 Query: 61 VKVGDKVGQGAVICTIE-------AQQAAAAPA--PAQAPAPAQA-PAPAAAAPA----P 106 VK GDKV QG VI +E A+ A APA P +APA A+A P A AAPA P Sbjct: 61 VKAGDKVSQGTVIALVETSADAAPAKDAPKAPAKEPEKAPAQAEAKPQAAQAAPAKAATP 120 Query: 107 APAAASHSGGADIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIP 166 AP A S SG ADI+C+MLVLG+GPGGYSAAFR+ADLGM TVLVERY+TLGGVCLNVGCIP Sbjct: 121 APQAGSFSGNADIECDMLVLGSGPGGYSAAFRSADLGMKTVLVERYATLGGVCLNVGCIP 180 Query: 167 SKALLHNAAVIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQV 226 SKALLH A VIDEA+AL +HGI FG+ +IDLD LR +K+ VV KLTGGLAGMAK RKV+V Sbjct: 181 SKALLHTALVIDEAEALRSHGITFGKPQIDLDKLRDFKSGVVKKLTGGLAGMAKMRKVEV 240 Query: 227 VRGIGNFLDPHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDS 286 V G G+F+DPHHMEV++ G K V++F++AIIAAGS+AVKLPFIPEDPR+VDS Sbjct: 241 VTGTGSFVDPHHMEVQVEGG--------KKVVKFKQAIIAAGSEAVKLPFIPEDPRVVDS 292 Query: 287 TGALELPEVPNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKK 346 TGALEL ++P +MLVIGGGIIGLEMATVY+TLGA IDVVEMLDGLM GADRDLVKVWEK Sbjct: 293 TGALELRQIPQRMLVIGGGIIGLEMATVYATLGAQIDVVEMLDGLMAGADRDLVKVWEKY 352 Query: 347 NKDRFGKVMLKTKTVGVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEK 406 N RF VMLKTKT EAK DGIYV FEGE APAE QRYDLVLV+VGRSPNGK+I A+K Sbjct: 353 NSKRFANVMLKTKTTAAEAKDDGIYVSFEGEKAPAEAQRYDLVLVAVGRSPNGKKIGADK 412 Query: 407 AGVAVSERGFINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDA 466 AGVAV+ERGFI+VDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAE AHGEKAYFDA Sbjct: 413 AGVAVTERGFIDVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEVAHGEKAYFDA 472 Query: 467 KQIPSVAFTDPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEE 526 QIPSVA+TDPEVAWAG TED+ K +GIKY K VFPWAASGRAIANGRDEGFTKL+FDEE Sbjct: 473 LQIPSVAYTDPEVAWAGKTEDQLKAEGIKYGKAVFPWAASGRAIANGRDEGFTKLLFDEE 532 Query: 527 THRVIGGGIVGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCT 586 THRVIGGGIVG +AGDLISEVCLA+EMGADA DIGKTIHPHPTLGESIGMAAE+YEG CT Sbjct: 533 THRVIGGGIVGLNAGDLISEVCLAVEMGADATDIGKTIHPHPTLGESIGMAAELYEGVCT 592 Query: 587 DVPPPRKR 594 D+PP +K+ Sbjct: 593 DLPPQKKK 600 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: 1111 Number of extensions: 33 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: 600 Length adjustment: 37 Effective length of query: 557 Effective length of database: 563 Effective search space: 313591 Effective search space used: 313591 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 BPHYT_RS12830 BPHYT_RS12830 (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.10893.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-149 482.7 3.6 8.3e-149 482.1 3.6 1.2 1 lcl|FitnessBrowser__BFirm:BPHYT_RS12830 BPHYT_RS12830 dihydrolipoamide d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS12830 BPHYT_RS12830 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 482.1 3.6 8.3e-149 8.3e-149 2 453 .. 135 586 .. 134 592 .. 0.97 Alignments for each domain: == domain 1 score: 482.1 bits; conditional E-value: 8.3e-149 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgiev 70 d++v+G+GpgGY aA r+a lg+k++lve+ +lGG+ClnvGCiP+KalL++a v++e++ + ++gi+ lcl|FitnessBrowser__BFirm:BPHYT_RS12830 135 CDMLVLGSGPGGYSAAFRSADLGMKTVLVERyATLGGVCLNVGCIPSKALLHTALVIDEAEALRSHGITF 204 699****************************99************************************* PP TIGR01350 71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtG 140 + ++dl+kl + k+ vvkkl+gG++++ k kvev++G+++++d++++ev+ e ++k++++k++iiA G lcl|FitnessBrowser__BFirm:BPHYT_RS12830 205 GKPQIDLDKLRDFKSGVVKKLTGGLAGMAKMRKVEVVTGTGSFVDPHHMEVQVEGGKKVVKFKQAIIAAG 274 *******************************************************9************** PP TIGR01350 141 seprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpald 210 se +lp+ + ed +v++s++alel+++p++++++GgG+iG+E+a+++a+lG+++ v+e+ld +++ d lcl|FitnessBrowser__BFirm:BPHYT_RS12830 275 SEAVKLPF-IPEDP-RVVDSTGALELRQIPQRMLVIGGGIIGLEMATVYATLGAQIDVVEMLDGLMAGAD 342 ********.77776.7****************************************************** PP TIGR01350 211 aevskvlkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleelglek 278 +++ kv +k +k+ +++ ++k t+ e+++d + v+ +++ +e +++ vLvavGr+pn +++g +k lcl|FitnessBrowser__BFirm:BPHYT_RS12830 343 RDLVKVWEKYNSKRFANVMLKTKTTAAEAKDDGIYVSFEGEkaPAEAQRYDLVLVAVGRSPNGKKIGADK 412 ********************************99987777644679999********************* PP TIGR01350 279 lgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviyt 348 gv ++erg+i vd+++rtnvp+i+aiGD++g++mLAh+A++e+ vaae + g+++ +d+ ++Psv yt lcl|FitnessBrowser__BFirm:BPHYT_RS12830 413 AGVAVTERGFIDVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEVAHGEKA-YFDALQIPSVAYT 481 *****************************************************776.9************ PP TIGR01350 349 ePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaselis 418 +Peva G+te+q+k+egi++ + fp aa+g+a+a + ++Gf k+++d++t++++G ivg +a +lis lcl|FitnessBrowser__BFirm:BPHYT_RS12830 482 DPEVAWAGKTEDQLKAEGIKYGKAVFPWAASGRAIANGRDEGFTKLLFDEETHRVIGGGIVGLNAGDLIS 551 ********************************************************************** PP TIGR01350 419 elalaveleltveelaktihpHPtlsEaikeaala 453 e+ lave+++ ++++ ktihpHPtl+E i aa+ lcl|FitnessBrowser__BFirm:BPHYT_RS12830 552 EVCLAVEMGADATDIGKTIHPHPTLGESIGMAAEL 586 *****************************999875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (600 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 12.55 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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