Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_036138918.1 N800_RS12045 dihydrolipoyl dehydrogenase
Query= BRENDA::Q0KBV8 (594 letters) >NCBI__GCF_000768355.1:WP_036138918.1 Length = 614 Score = 703 bits (1814), Expect = 0.0 Identities = 378/623 (60%), Positives = 453/623 (72%), Gaps = 38/623 (6%) Query: 1 MSVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVK 60 M IE+KVPDIG +D V VIE+LV GDTV +Q L+ LESDKA+M+VP+S AG + E+K Sbjct: 1 MPTIEIKVPDIGGYDDVPVIELLVAVGDTVAKDQGLVTLESDKATMEVPASHAGVIRELK 60 Query: 61 VKVGDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAPAAAAPAPA------------- 107 VK+GD V +G+VI IEA+ AAPA A APA APA AA A PA Sbjct: 61 VKLGDAVSEGSVIALIEAEGEGAAPAATPATAPAAAPASAAPAATPAATGAASAPIAPVA 120 Query: 108 ----------PAAASHSGGA-DIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLG 156 PA A+ SG DI+C MLVLGAGPGGY+AAFR+ADLGM+TVL+ERY++LG Sbjct: 121 PVAQPASPAGPAPAAASGRKPDIECRMLVLGAGPGGYTAAFRSADLGMDTVLIERYASLG 180 Query: 157 GVCLNVGCIPSKALLHNAAVIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLA 216 GVCLNVGCIPSKALLH AAVIDEA +GI FG+ KI LD LR YK +VVG+LT GL+ Sbjct: 181 GVCLNVGCIPSKALLHAAAVIDEAAHAKDYGIDFGKPKITLDALRAYKEKVVGQLTKGLS 240 Query: 217 GMAKARKVQVVRGIGNFLDPHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPF 276 GMAK RKV+VV G+G F+ PH +EV G +IRFE+ IIAAGSQAVKLP Sbjct: 241 GMAKQRKVRVVEGVGKFVSPHEVEVAGPNGT--------QLIRFEQCIIAAGSQAVKLPG 292 Query: 277 IP-EDPRIVDSTGALELPEVPNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGA 335 P D R++DST ALEL EVP ++LV+GGGIIGLEMATVY LG+++ VVE D +M GA Sbjct: 293 FPWGDARVMDSTDALELAEVPKRLLVVGGGIIGLEMATVYRALGSEVTVVEFADQIMPGA 352 Query: 336 DRDLVKVWEKKNKDRFGKVMLKTKTVGVEAKPDGIYVKFE----GEAAPAEPQRYDLVLV 391 D DL+K + K + V K K G EA G+ V+FE G +AP EPQ +D VLV Sbjct: 353 DTDLIKPLADRLKKQGVIVHTKVKAAGTEALKGGLKVRFEPAQEGGSAP-EPQTFDRVLV 411 Query: 392 SVGRSPNGKRISAEKAGVAVSERGFINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAH 451 +VGRSPNG ++ A KAGV+V++RGFI VD+QMRTNVPHIFAIGD+VGQPMLAHKA HE Sbjct: 412 AVGRSPNGGKLDANKAGVSVTDRGFIPVDRQMRTNVPHIFAIGDLVGQPMLAHKATHEGK 471 Query: 452 VAAEAAHGEKAYFDAKQIPSVAFTDPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIA 511 +AAE A GEK + A+ IPSVA+TDPE+AW G+TE E K KG+K G FPWAASGRAI Sbjct: 472 LAAEVAFGEKKEWVARVIPSVAYTDPEIAWVGVTETEAKAKGLKVGVGKFPWAASGRAIG 531 Query: 512 NGRDEGFTKLIFDEETHRVIGGGIVGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLG 571 GR EGFTKL+FDE THR+IGGGIVG HAGDLI+E+ LAIEMG + DIG TIHPHPTL Sbjct: 532 LGRTEGFTKLVFDEATHRIIGGGIVGVHAGDLIAEIGLAIEMGCEVHDIGATIHPHPTLS 591 Query: 572 ESIGMAAEIYEGTCTDVPPPRKR 594 ES+GMAAE+Y+GT TD+ P+K+ Sbjct: 592 ESVGMAAEVYDGTITDLYLPKKK 614 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: 1051 Number of extensions: 49 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: 614 Length adjustment: 37 Effective length of query: 557 Effective length of database: 577 Effective search space: 321389 Effective search space used: 321389 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 WP_036138918.1 N800_RS12045 (dihydrolipoyl 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.2166604.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-154 501.2 1.3 1.7e-154 500.8 1.3 1.1 1 NCBI__GCF_000768355.1:WP_036138918.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000768355.1:WP_036138918.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 500.8 1.3 1.7e-154 1.7e-154 3 454 .. 146 601 .. 144 607 .. 0.96 Alignments for each domain: == domain 1 score: 500.8 bits; conditional E-value: 1.7e-154 TIGR01350 3 dvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenvk 74 ++v+G+GpgGY+aA r+a lg+ ++l+e+ +lGG+ClnvGCiP+KalL++a v++e+ +ak++gi+ + k NCBI__GCF_000768355.1:WP_036138918.1 146 RMLVLGAGPGGYTAAFRSADLGMDTVLIERyASLGGVCLNVGCIPSKALLHAAAVIDEAAHAKDYGIDFGKPK 218 578***************************99***************************************** PP TIGR01350 75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelp 147 + l++l + kekvv +l++G++++ k+ kv v++G +k+++++evev++ ++++ ++++++iiA Gs+ +lp NCBI__GCF_000768355.1:WP_036138918.1 219 ITLDALRAYKEKVVGQLTKGLSGMAKQRKVRVVEGVGKFVSPHEVEVAGPNGTQLIRFEQCIIAAGSQAVKLP 291 ************************************************************************* PP TIGR01350 148 lkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkk 220 + + +v++s++alel evp++l++vGgG+iG+E+a++++ lG++vtv+e++d+i+p d+++ k l+++ NCBI__GCF_000768355.1:WP_036138918.1 292 G-FPWGDARVMDSTDALELAEVPKRLLVVGGGIIGLEMATVYRALGSEVTVVEFADQIMPGADTDLIKPLADR 363 *.9999999**************************************************************** PP TIGR01350 221 lkkkgvkiltnakvtevekeedevv.....veakkkevetleaekvLvavGrkpnleelgleklgvelderga 288 lkk+gv ++t+ k +e+ + ++ +++ ++ e + ++vLvavGr+pn +l+ +k gv++++rg+ NCBI__GCF_000768355.1:WP_036138918.1 364 LKKQGVIVHTKVKAAGTEALKGGLKvrfepAQEGGSAPEPQTFDRVLVAVGRSPNGGKLDANKAGVSVTDRGF 436 ***********999966666665553355444444477899******************************** PP TIGR01350 289 ikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeq 361 i+vd+++rtnvp+i+aiGD++g++mLAh+A++eg +aae ++g++k e ++++Psv yt+Pe+a vG+te++ NCBI__GCF_000768355.1:WP_036138918.1 437 IPVDRQMRTNVPHIFAIGDLVGQPMLAHKATHEGKLAAEVAFGEKK-EWVARVIPSVAYTDPEIAWVGVTETE 508 *******************************************887.899*********************** PP TIGR01350 362 akeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveela 434 ak++g +v vgkfp aa+g+a+ l+ t+Gf k+++d+ t++i+G ivg +a +li+e+ la+e++ +v+++ NCBI__GCF_000768355.1:WP_036138918.1 509 AKAKGLKVGVGKFPWAASGRAIGLGRTEGFTKLVFDEATHRIIGGGIVGVHAGDLIAEIGLAIEMGCEVHDIG 581 ************************************************************************* PP TIGR01350 435 ktihpHPtlsEaikeaalaa 454 +tihpHPtlsE + aa+ NCBI__GCF_000768355.1:WP_036138918.1 582 ATIHPHPTLSESVGMAAEVY 601 *************9999875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (614 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 40.43 // [ok]
This GapMind analysis is from Sep 24 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