Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate GFF2287 PGA1_c23190 dihydrolipoyl dehydrogenase LpdA
Query= BRENDA::P0A9P0 (474 letters) >FitnessBrowser__Phaeo:GFF2287 Length = 459 Score = 464 bits (1194), Expect = e-135 Identities = 238/459 (51%), Positives = 314/459 (68%), Gaps = 8/459 (1%) Query: 9 VVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVAKVIEEAKA 68 ++VLGAGP GY+ AFR ADLG +IV+ TLGGVCLNVGCIPSKALLH A++I E + Sbjct: 8 LIVLGAGPGGYACAFRAADLGRSVIIVDPRATLGGVCLNVGCIPSKALLHAAEMIRETRH 67 Query: 69 LAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFTGANTLEVE 128 GI+ G D++K+R K+ ++ QLT GL G+AK RKV+ + G +FT +LE++ Sbjct: 68 GGGWGILTGNVSVDLNKLRAKKDSIVEQLTTGLVGLAKRRKVQTIRGSAQFTSDKSLEID 127 Query: 129 GENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLVMGGGIIGL 188 GE+ FD A+IA GS P++LP P ED RIWDSTDALEL+E+P+RL ++GGGIIGL Sbjct: 128 GESW----TFDQAVIAVGSAPVRLPGWP-EDDRIWDSTDALELREIPKRLSIVGGGIIGL 182 Query: 189 EMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRI-SKKFNLMLETKVTAVEAKEDG 247 EM TVY ALGS++ V+E DQ+ P AD D V + + ++ + TKVT V+A + Sbjct: 183 EMATVYAALGSKVTVIEFMDQIAPGADADAVTILRAALETEDVTIHTGTKVTEVKASKTA 242 Query: 248 IYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQLRTNVPH 307 + +T EG + DA + A+GR NG +D AGVE DDRG I VD RTNV Sbjct: 243 LTLTCEGGFEGTI--KADAAIQAVGRRSNGSLVDPAAAGVEADDRGIIPVDASCRTNVAT 300 Query: 308 IFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWVGLTEKEA 367 +FAIGD+ G PMLAH+ H+GHVAAEV +G D +IPS+AYT PE+AW GLT+ +A Sbjct: 301 VFAIGDVTGNPMLAHRATHQGHVAAEVASGHATALDTDLIPSVAYTAPELAWAGLTQAKA 360 Query: 368 KEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGELLGEIGL 427 E+GI + A FPWAASGR ++S +G+TKL++ +SHR++G IVG N GELL E L Sbjct: 361 TERGIPHRVANFPWAASGRNLSSGGGEGLTKLVYCPDSHRLLGATIVGRNAGELLAECVL 420 Query: 428 AIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDL 466 A+EMG ED++L +HAHPTL E+VG AAE G++TDL Sbjct: 421 AMEMGATLEDMSLAVHAHPTLSETVGFAAERALGTLTDL 459 Lambda K H 0.317 0.137 0.396 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: 562 Number of extensions: 18 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: 1 Length of query: 474 Length of database: 459 Length adjustment: 33 Effective length of query: 441 Effective length of database: 426 Effective search space: 187866 Effective search space used: 187866 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 GFF2287 PGA1_c23190 (dihydrolipoyl dehydrogenase LpdA)
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.22766.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-149 483.1 0.1 4.9e-149 482.8 0.1 1.0 1 lcl|FitnessBrowser__Phaeo:GFF2287 PGA1_c23190 dihydrolipoyl dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF2287 PGA1_c23190 dihydrolipoyl dehydrogenase LpdA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 482.8 0.1 4.9e-149 4.9e-149 2 457 .. 6 455 .. 5 458 .. 0.98 Alignments for each domain: == domain 1 score: 482.8 bits; conditional E-value: 4.9e-149 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenvkld 76 d++v+G+GpgGY +A raa lg +v++v+ +lGG+ClnvGCiP+KalL++ae+++e ++ +gi + nv++d lcl|FitnessBrowser__Phaeo:GFF2287 6 ADLIVLGAGPGGYACAFRAADLGRSVIIVDPrATLGGVCLNVGCIPSKALLHAAEMIRETRHGGGWGILTGNVSVD 81 69****************************8799****************************************** PP TIGR01350 77 lekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplklee 152 l+kl ++k+++v++l++G+ +L k+ kv++i G+a+++++k++e+++e+ ++++++iA Gs p +lp+ e lcl|FitnessBrowser__Phaeo:GFF2287 82 LNKLRAKKDSIVEQLTTGLVGLAKRRKVQTIRGSAQFTSDKSLEIDGES----WTFDQAVIAVGSAPVRLPG-WPE 152 ***********************************************98....68*****************.555 PP TIGR01350 153 dekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvki 228 d ++++s++alel+e+p++l+ivGgG+iG+E+a+++a lG+kvtvie++d+i p da+ +l+ +l+++ v+i lcl|FitnessBrowser__Phaeo:GFF2287 153 DD-RIWDSTDALELREIPKRLSIVGGGIIGLEMATVYAALGSKVTVIEFMDQIAPGADADAVTILRAALETEDVTI 227 54.6************************************************************************ PP TIGR01350 229 ltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiya 304 +t++kvtev++++ +++++ +++ + t++a++ + avGr++n + ++ ++ gve d+rg+i+vd+++rtnv+ ++a lcl|FitnessBrowser__Phaeo:GFF2287 228 HTGTKVTEVKASKTALTLTCEGGFEGTIKADAAIQAVGRRSNGSLVDPAAAGVEADDRGIIPVDASCRTNVATVFA 303 *****************99999966*************************************************** PP TIGR01350 305 iGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaang 380 iGDv+g++mLAh+A+++g vaae + g+++ ++d++++Psv yt Pe+a Glt+++a e+gi +v++fp aa+g lcl|FitnessBrowser__Phaeo:GFF2287 304 IGDVTGNPMLAHRATHQGHVAAEVASGHAT-ALDTDLIPSVAYTAPELAWAGLTQAKATERGIPHRVANFPWAASG 378 ***************************776.9******************************************** PP TIGR01350 381 kalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalg 456 + l+++ +G+ k+++ ++++++lGa+ivg +a el++e +la+e+++t+e+++ ++h+HPtlsE++ aa+ alg lcl|FitnessBrowser__Phaeo:GFF2287 379 RNLSSGGGEGLTKLVYCPDSHRLLGATIVGRNAGELLAECVLAMEMGATLEDMSLAVHAHPTLSETVGFAAERALG 454 ***********************************************************************99987 PP TIGR01350 457 k 457 + lcl|FitnessBrowser__Phaeo:GFF2287 455 T 455 5 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 9.63 // [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