Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate RR42_RS26115 RR42_RS26115 dihydrolipoamide dehydrogenase
Query= BRENDA::Q0KBV8 (594 letters) >FitnessBrowser__Cup4G11:RR42_RS26115 Length = 589 Score = 857 bits (2215), Expect = 0.0 Identities = 438/593 (73%), Positives = 495/593 (83%), Gaps = 10/593 (1%) Query: 4 IEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKVKV 63 +EVKVPDIGDF V VIEV+VK G+ + V+ SLI +ESDKASM++PS+ AG V E+ VKV Sbjct: 5 VEVKVPDIGDFKDVTVIEVMVKPGEIIAVDTSLIAVESDKASMEIPSTHAGVVKEITVKV 64 Query: 64 GDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAPAAAAPA--PAPAAASHSGGADIQC 121 DKV +G+VI +EA AAA A APAPA AP APA P P AAS++G AD +C Sbjct: 65 NDKVSEGSVILVVEAAAAAATVAAPAAPAPAAPSAPPGPAPAAAPVPNAASYTGKADQEC 124 Query: 122 EMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVIDEAK 181 EMLVLGAGPGGYSAAFR+ADLGM TVLVERY TLGGVCLNVGCIPSKALLH A+V+DE Sbjct: 125 EMLVLGAGPGGYSAAFRSADLGMKTVLVERYDTLGGVCLNVGCIPSKALLHTASVMDEVA 184 Query: 182 ALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLDPHHMEV 241 L HGI +G +IDLD LR +K+ V+ KLTGGLAGMAKARKV+VV G+G+FLDP+H+EV Sbjct: 185 TLPDHGIRYGAPEIDLDKLRGFKDSVIKKLTGGLAGMAKARKVEVVTGVGSFLDPYHLEV 244 Query: 242 ELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDSTGALELPEVPNKMLV 301 +G GKR VI+F KAIIAAGSQAVKLPF+P+D R+VDSTGAL L +P +MLV Sbjct: 245 VAADG-GKR------VIKFAKAIIAAGSQAVKLPFMPDDERVVDSTGALLLKSIPKRMLV 297 Query: 302 IGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVMLKTKTV 361 +GGGIIGLEMATVYSTLG IDVVEMLDGLM GADRDLVKVWEKKN RF VMLKT+T+ Sbjct: 298 VGGGIIGLEMATVYSTLGTRIDVVEMLDGLMQGADRDLVKVWEKKNTHRFDHVMLKTRTI 357 Query: 362 GVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERGFINVDK 421 G +A P GI V FEGE APA PQ YDLVLV+VGRSPNG+ I AEKAGVAV+ERGFI+VD+ Sbjct: 358 GAKATPAGIEVSFEGEKAPA-PQVYDLVLVAVGRSPNGRAIGAEKAGVAVTERGFIDVDR 416 Query: 422 QMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFTDPEVAW 481 QMRTNV HI AIGDIVGQPMLAHKAVHEAHVAAEAAHGE AYFDA+QIPSVA+TDPEVAW Sbjct: 417 QMRTNVAHIHAIGDIVGQPMLAHKAVHEAHVAAEAAHGEAAYFDARQIPSVAYTDPEVAW 476 Query: 482 AGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVGTHAG 541 AG TE++CK +GIK K VFPWAASGRAIANGRDEGFTKL+FDE THRVIGGGIVGTHAG Sbjct: 477 AGKTEEQCKAEGIKIGKAVFPWAASGRAIANGRDEGFTKLLFDEATHRVIGGGIVGTHAG 536 Query: 542 DLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594 DLISEVCLAIEMG + DIGKTIHPHPTLGESIGMAAE++EG CTD+PP +K+ Sbjct: 537 DLISEVCLAIEMGCEPADIGKTIHPHPTLGESIGMAAEVFEGHCTDLPPVKKK 589 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: 1126 Number of extensions: 41 Number of successful extensions: 7 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: 589 Length adjustment: 37 Effective length of query: 557 Effective length of database: 552 Effective search space: 307464 Effective search space used: 307464 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_RS26115 RR42_RS26115 (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.17890.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-142 461.3 2.0 2.8e-142 460.6 2.0 1.2 1 lcl|FitnessBrowser__Cup4G11:RR42_RS26115 RR42_RS26115 dihydrolipoamide de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS26115 RR42_RS26115 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 460.6 2.0 2.8e-142 2.8e-142 3 456 .. 125 578 .. 123 582 .. 0.96 Alignments for each domain: == domain 1 score: 460.6 bits; conditional E-value: 2.8e-142 TIGR01350 3 dvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgiev 70 +++v+G+GpgGY aA r+a lg+k++lve+ ++lGG+ClnvGCiP+KalL++a v++e+ ++ ++gi+ lcl|FitnessBrowser__Cup4G11:RR42_RS26115 125 EMLVLGAGPGGYSAAFRSADLGMKTVLVERyDTLGGVCLNVGCIPSKALLHTASVMDEVATLPDHGIRY 193 789***************************9************************************** PP TIGR01350 71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiA 138 ++dl+kl k++v+kkl+gG++++ k kvev++G +++ld+ ++ev + ++ +++++ ++iiA lcl|FitnessBrowser__Cup4G11:RR42_RS26115 194 GAPEIDLDKLRGFKDSVIKKLTGGLAGMAKARKVEVVTGVGSFLDPYHLEVVAADGGkRVIKFAKAIIA 262 ************************************************9987776554899******** PP TIGR01350 139 tGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilp 207 Gs+ +lp+ + de +v++s++al lk++p+++++vGgG+iG+E+a+++++lG+ + v+e+ld +++ lcl|FitnessBrowser__Cup4G11:RR42_RS26115 263 AGSQAVKLPF-MPDDE-RVVDSTGALLLKSIPKRMLVVGGGIIGLEMATVYSTLGTRIDVVEMLDGLMQ 329 **********.66665.7*************************************************** PP TIGR01350 208 aldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelg 275 d+++ kv +kk +++ +++ +++ +++ + ++v+ +++ ++ vLvavGr+pn + +g lcl|FitnessBrowser__Cup4G11:RR42_RS26115 330 GADRDLVKVWEKKNTHRFDHVMLKTRTIGAKATPAGIEVSFEGEkAPAPQVYDLVLVAVGRSPNGRAIG 398 ****************************9*********99999945566789***************** PP TIGR01350 276 leklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPs 344 ek gv ++erg+i vd+++rtnv++i+aiGD++g++mLAh+A++e+ vaae++ g+++ +d++++Ps lcl|FitnessBrowser__Cup4G11:RR42_RS26115 399 AEKAGVAVTERGFIDVDRQMRTNVAHIHAIGDIVGQPMLAHKAVHEAHVAAEAAHGEAA-YFDARQIPS 466 ********************************************************877.9******** PP TIGR01350 345 viytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaea 413 v yt+Peva G+teeq+k+egi++ + fp aa+g+a+a + ++Gf k+++d+ t++++G ivg++a lcl|FitnessBrowser__Cup4G11:RR42_RS26115 467 VAYTDPEVAWAGKTEEQCKAEGIKIGKAVFPWAASGRAIANGRDEGFTKLLFDEATHRVIGGGIVGTHA 535 ********************************************************************* PP TIGR01350 414 seliselalaveleltveelaktihpHPtlsEaikeaalaalg 456 +lise+ la+e++ + ++ ktihpHPtl+E i aa+ g lcl|FitnessBrowser__Cup4G11:RR42_RS26115 536 GDLISEVCLAIEMGCEPADIGKTIHPHPTLGESIGMAAEVFEG 578 **********************************999988766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (589 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: 14.89 // [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