Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate RR42_RS07380 RR42_RS07380 dihydrolipoamide dehydrogenase
Query= BRENDA::Q0KBV8 (594 letters) >FitnessBrowser__Cup4G11:RR42_RS07380 Length = 594 Score = 1058 bits (2737), Expect = 0.0 Identities = 535/597 (89%), Positives = 562/597 (94%), Gaps = 6/597 (1%) Query: 1 MSVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVK 60 MSVIEV+VPDIGDFDAVEVIEVLVKAGDTVE EQSLIVLESDKASMDVPSSAAGKVVEV+ Sbjct: 1 MSVIEVQVPDIGDFDAVEVIEVLVKAGDTVEQEQSLIVLESDKASMDVPSSAAGKVVEVR 60 Query: 61 VKVGDKVGQGAVICTIEAQQAA---AAPAPAQAPAPAQAPAPAAAAPAPAPAAASHSGGA 117 +KVGDKV +GAVICT+E++ AA AAP A APAPAQ APAAA PAP AA+H+G A Sbjct: 61 IKVGDKVAKGAVICTLESEAAAKPAAAPVSAPAPAPAQVSAPAAA---PAPVAAAHAGSA 117 Query: 118 DIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVI 177 DI C+MLVLGAGPGGYSAAFR+ADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVI Sbjct: 118 DITCDMLVLGAGPGGYSAAFRSADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVI 177 Query: 178 DEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLDPH 237 DEAKALAAHGILFGEAKIDLDGLRHYK VVGKLTGGLAGMAKARKVQVVRGIG FLDPH Sbjct: 178 DEAKALAAHGILFGEAKIDLDGLRHYKETVVGKLTGGLAGMAKARKVQVVRGIGTFLDPH 237 Query: 238 HMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDSTGALELPEVPN 297 H+EV+ TEG+ K +TGKKTVIRFEKA+IAAGSQAVKLPFIPEDPRIVDSTGALELPEVPN Sbjct: 238 HLEVQETEGDAKATTGKKTVIRFEKAVIAAGSQAVKLPFIPEDPRIVDSTGALELPEVPN 297 Query: 298 KMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVMLK 357 KMLVIGGGIIGLEMATVYSTLGA IDVVEMLDGLM GADRDLVKVW+K NK RF KVMLK Sbjct: 298 KMLVIGGGIIGLEMATVYSTLGASIDVVEMLDGLMQGADRDLVKVWDKMNKKRFDKVMLK 357 Query: 358 TKTVGVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERGFI 417 TKTVGVEAKPDGIYVKFEGE APAEPQRYDLVLVSVGR PNGKRI AEKAGVAV++RGFI Sbjct: 358 TKTVGVEAKPDGIYVKFEGEQAPAEPQRYDLVLVSVGRVPNGKRIGAEKAGVAVTDRGFI 417 Query: 418 NVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFTDP 477 +VDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFD KQIPSVA+TDP Sbjct: 418 DVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDVKQIPSVAYTDP 477 Query: 478 EVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVG 537 EVAWAG+TED+C+ +GIKYSK VFPWAASGRAIANGRDEGFTKLIFDEETHR+IGGGIVG Sbjct: 478 EVAWAGVTEDQCRAQGIKYSKSVFPWAASGRAIANGRDEGFTKLIFDEETHRIIGGGIVG 537 Query: 538 THAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594 THAGDLISEVCLA+EMGADAVDIGKTIHPHPTLGESIGMAAEIYEG CTDVPPPRKR Sbjct: 538 THAGDLISEVCLAVEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGVCTDVPPPRKR 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: 1224 Number of extensions: 34 Number of successful extensions: 3 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 RR42_RS07380 RR42_RS07380 (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.7944.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-146 472.8 4.7 6.8e-146 472.5 4.7 1.1 1 lcl|FitnessBrowser__Cup4G11:RR42_RS07380 RR42_RS07380 dihydrolipoamide de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS07380 RR42_RS07380 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 472.5 4.7 6.8e-146 6.8e-146 2 452 .. 121 579 .. 120 586 .. 0.97 Alignments for each domain: == domain 1 score: 472.5 bits; conditional E-value: 6.8e-146 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgie 69 d++v+G+GpgGY aA r+a lg++++lve+ ++lGG+ClnvGCiP+KalL++a v++e+k ++ +gi lcl|FitnessBrowser__Cup4G11:RR42_RS07380 121 CDMLVLGAGPGGYSAAFRSADLGMNTVLVERySTLGGVCLNVGCIPSKALLHNAAVIDEAKALAAHGIL 189 699****************************99************************************ PP TIGR01350 70 venvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke........kkl 130 + k+dl+ l + ke+vv kl+gG++++ k kv+v+ G +++ld++++ev+++++ +++ lcl|FitnessBrowser__Cup4G11:RR42_RS07380 190 FGEAKIDLDGLRHYKETVVGKLTGGLAGMAKARKVQVVRGIGTFLDPHHLEVQETEGDakattgkkTVI 258 *****************************************************9998788889987788 PP TIGR01350 131 eakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvi 199 ++++++iA Gs+ +lp+ + ed ++++s++alel+evp++++++GgG+iG+E+a+++++lG+ + v+ lcl|FitnessBrowser__Cup4G11:RR42_RS07380 259 RFEKAVIAAGSQAVKLPF-IPEDP-RIVDSTGALELPEVPNKMLVIGGGIIGLEMATVYSTLGASIDVV 325 9*****************.77776.7******************************************* PP TIGR01350 200 elldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavG 266 e+ld +++ d+++ kv k+ kk+ k++ ++k ve++ d + v+ +++ +e +++ vLv+vG lcl|FitnessBrowser__Cup4G11:RR42_RS07380 326 EMLDGLMQGADRDLVKVWDKMNKKRFDKVMLKTKTVGVEAKPDGIYVKFEGEqaPAEPQRYDLVLVSVG 394 ********************************************9988888744678999********* PP TIGR01350 267 rkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks 335 r pn + +g ek gv +++rg+i vd+++rtnvp+i+aiGD++g++mLAh+A++e+ vaae++ g+++ lcl|FitnessBrowser__Cup4G11:RR42_RS07380 395 RVPNGKRIGAEKAGVAVTDRGFIDVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKA- 462 *****************************************************************776. PP TIGR01350 336 eidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeil 404 +d k++Psv yt+Peva G+te+q++++gi++ + fp aa+g+a+a + ++Gf k+i+d++t++i+ lcl|FitnessBrowser__Cup4G11:RR42_RS07380 463 YFDVKQIPSVAYTDPEVAWAGVTEDQCRAQGIKYSKSVFPWAASGRAIANGRDEGFTKLIFDEETHRII 531 9******************************************************************** PP TIGR01350 405 GahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaal 452 G ivg++a +lise+ lave+++ + ++ ktihpHPtl+E i aa+ lcl|FitnessBrowser__Cup4G11:RR42_RS07380 532 GGGIVGTHAGDLISEVCLAVEMGADAVDIGKTIHPHPTLGESIGMAAE 579 ******************************************999887 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 14.69 // [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