Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of branched-chain alpha-keto acid dehydrogenase complex; LPD-Val (uncharacterized)
to candidate WP_050655902.1 C1M55_RS30485 dihydrolipoyl dehydrogenase
Query= curated2:P54533 (474 letters) >NCBI__GCF_002893965.1:WP_050655902.1 Length = 459 Score = 326 bits (836), Expect = 9e-94 Identities = 179/468 (38%), Positives = 275/468 (58%), Gaps = 20/468 (4%) Query: 6 DVVILGGGTGGYVAAIRAAQLGLKTAVVEKEKLGGTCLHKGCIPSKALLRSAEVYRTARE 65 DVVILGGG+GGY AIRAAQLGL ++E +K+GGTCLH+GCIP+KALL SAEV +AR Sbjct: 9 DVVILGGGSGGYACAIRAAQLGLSVTLIEADKVGGTCLHRGCIPTKALLHSAEVADSART 68 Query: 66 ADQFGVETAGVSLNFEKVQQRKQAVVDKLAAGVNHLMKKGKIDVYTGYGRILGPSIFSPL 125 ++QFGV + ++ +V K V++L +G+ L+ + KI + GYG +G Sbjct: 69 SEQFGVRASFAGIDVAQVHDYKNGTVERLYSGLQGLLAQHKITIVNGYGTYVG------- 121 Query: 126 PGTISVERGNGEENDMLIPKQVIIATGSRPRMLPGLEVDGKSVLTSDEALQMEELPQSII 185 R + +++ATGS PR LPG+E+ G+ ++TSD+AL+++ +P S Sbjct: 122 ------GRSIDVDGTRYTGTSLVLATGSYPRELPGIEL-GRRIVTSDQALELDRVPTSAT 174 Query: 186 IVGGGVIGIEWASMLHDFGVKVTVIEYADRILPTEDLEISKEMESLLKKKGIQFITGAKV 245 ++GGGVIG+E+AS+ FG +VT++E R++ ED SK++E +K+GI T KV Sbjct: 175 VLGGGVIGVEFASLWRSFGAEVTIVEALPRLIAAEDPWSSKQLERAYRKRGIVCKTDTKV 234 Query: 246 LPDTMTKTSDDISIQAEKDGETVTYSAEKMLVSIGRQANIEGIGLENTDIVTENGMISVN 305 D+ + + + I+ DG + + +LV++GR +G G I + G + + Sbjct: 235 --DSAKEAAGSVRIEL-SDGTIL--DTDLLLVAVGRGPRTDGNGFAENGISLDKGFVVTD 289 Query: 306 ESCQTKESHIYAIGDVIGGLQLAHVASHEGIIAVEHFAGLNPHPLDPTLVPKCIYSSPEA 365 E +T +YA+GD++ GL LAH +GI E AG +P P+ L+P+ YS PE Sbjct: 290 ERLRTSVDGVYAVGDIVPGLALAHRGFQQGIFVAEQIAGKDPIPVAEHLIPRVTYSHPEV 349 Query: 366 ASVGLTEDEAKANGHNVKIGKFPFMAIGKALVYGESDGFVKIVADRDTDDILGVHMIGPH 425 ASVGL E+ A+ +V + GK+ + + G +K++ ++GVH++G Sbjct: 350 ASVGLGEEVARTQYADVSTVIYDLAGNGKSQIL-RTTGGIKVIRSGTKGPVVGVHLVGDR 408 Query: 426 VTDMISEAGLAKVLDATPWEVGQTIHPHPTLSEAIGEAALAADGKAIH 473 V ++I EA LA +A P EVG+ IH HP+ +EA+GEA LA G +H Sbjct: 409 VGELIGEAQLAVAWEALPDEVGRFIHAHPSQNEALGEAMLALAGTPLH 456 Lambda K H 0.315 0.135 0.382 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: 630 Number of extensions: 42 Number of successful extensions: 5 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: 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: 42 (22.0 bits) S2: 51 (24.3 bits)
Align candidate WP_050655902.1 C1M55_RS30485 (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.2485630.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-141 457.2 0.0 3.3e-141 457.0 0.0 1.0 1 NCBI__GCF_002893965.1:WP_050655902.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002893965.1:WP_050655902.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 457.0 0.0 3.3e-141 3.3e-141 2 460 .. 8 456 .. 7 457 .. 0.98 Alignments for each domain: == domain 1 score: 457.0 bits; conditional E-value: 3.3e-141 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvk 74 dvv++GgG gGY +Airaaqlgl+v+l+e +k+GGtCl++GCiPtKalL+saev++++++ +++g++++ NCBI__GCF_002893965.1:WP_050655902.1 8 SDVVILGGGSGGYACAIRAAQLGLSVTLIEADKVGGTCLHRGCIPTKALLHSAEVADSARTSEQFGVRASFAG 80 69******************************************************************999** PP TIGR01350 75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelp 147 +d++++++ k+ +v++l +G+++Ll ++k++ ++G+++ ++ +++ v+++++ + ++++AtGs prelp NCBI__GCF_002893965.1:WP_050655902.1 81 IDVAQVHDYKNGTVERLYSGLQGLLAQHKITIVNGYGTYVGGRSIDVDGTRY----TGTSLVLATGSYPRELP 149 **************************************************95....699************** PP TIGR01350 148 lkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkk 220 + +e + +++ts++alel++vp+s ++GgGviGvEfas+++++G++vt++e+l+r+++a+d sk+l+++ NCBI__GCF_002893965.1:WP_050655902.1 150 G-IELGR-RIVTSDQALELDRVPTSATVLGGGVIGVEFASLWRSFGAEVTIVEALPRLIAAEDPWSSKQLERA 220 *.99998.7**************************************************************** PP TIGR01350 221 lkkkgvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvde 293 ++k+g+ +t++kv + ++ + +v++e +++ + l+++ +LvavGr p++++ g+++ g++ld+ g++++de NCBI__GCF_002893965.1:WP_050655902.1 221 YRKRGIVCKTDTKVDSAKEAAGSVRIELSDG--TILDTDLLLVAVGRGPRTDGNGFAENGISLDK-GFVVTDE 290 ***************************9999..89******************************.******* PP TIGR01350 294 elrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeeg 366 +lrt+v+g+ya+GD++ +l LAh+ +++g+ +ae+iagk + + ++++P+v+y++PevasvGl ee a+ ++ NCBI__GCF_002893965.1:WP_050655902.1 291 RLRTSVDGVYAVGDIVPGLALAHRGFQQGIFVAEQIAGKDPIPVAEHLIPRVTYSHPEVASVGLGEEVARTQY 363 ************************************************************************* PP TIGR01350 367 ievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihp 439 +v ++ +++a ngk+ +l +G +kvi ++g ++G+h+vg ++ eli e+ lav++e+ +e+ ++ih+ NCBI__GCF_002893965.1:WP_050655902.1 364 ADVSTVIYDLAGNGKSQILRT-TGGIKVIRSGTKGPVVGVHLVGDRVGELIGEAQLAVAWEALPDEVGRFIHA 435 ****************98875.5779*********************************************** PP TIGR01350 440 HPtlsEaikeaalaalgkaih 460 HP+ +Ea+ ea+la+ g+++h NCBI__GCF_002893965.1:WP_050655902.1 436 HPSQNEALGEAMLALAGTPLH 456 ****************99998 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: 00:00:00.01 # Mc/sec: 14.84 // [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