Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_111392326.1 CLV31_RS07900 dihydrolipoyl dehydrogenase
Query= BRENDA::P50970 (466 letters) >NCBI__GCF_003253485.1:WP_111392326.1 Length = 465 Score = 444 bits (1141), Expect = e-129 Identities = 230/461 (49%), Positives = 316/461 (68%), Gaps = 2/461 (0%) Query: 5 FDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEMQ 64 FDLIVLG GPGGYVAAIRA+QL LK A+VE LGGICLNWGCIPTK+LL+SA+V+ + Sbjct: 6 FDLIVLGSGPGGYVAAIRASQLGLKTAIVEAAELGGICLNWGCIPTKALLKSAQVFEYIS 65 Query: 65 NAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQMLV 124 +A+ YG++ + D ++ RSR VA ++ GV+ L++KNK+E+I+G G++ +++ V Sbjct: 66 HAKDYGISVQGAEADFAGMVKRSRGVADGMSKGVQFLMKKNKIEIITGWGKVQPGKKVEV 125 Query: 125 ETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGAI 184 EG++ ++ A +IIIATGAR+R+LP++ D K I Y A+ PKK++V+GSGAI Sbjct: 126 NDAEGKKSVITADNIIIATGARSRELPSMKIDDKKIIGYRKAMTLEKQPKKMVVVGSGAI 185 Query: 185 GIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPDD 244 G+EFA FY G EV+IVE +I+P+ED EVS + K +KK G++I+T S + + Sbjct: 186 GVEFAYFYNSIGTEVTIVEFMDRIVPVEDEEVSKALEKIYKKSGMKIMTSSEVTGVDTKG 245 Query: 245 EGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTNVD 304 EG + A G+ E + A GVV+N+ENIGL+ +GI +D+G I V+ + +TN+ Sbjct: 246 EGCKVTVKTAKGEEILE-CDVVLSAAGVVSNLENIGLEDVGILVDKGKIQVNEYYQTNMP 304 Query: 305 HVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGLTE 364 +AIGDV P LAH AS +G+I E IAG H L+ NIPGCTY P++ASVG+TE Sbjct: 305 GYYAIGDVVPGPALAHVASAEGIICVEKIAG-HHPEALDYGNIPGCTYCSPEIASVGMTE 363 Query: 365 EKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMIQG 424 KA+ G+ V++G FPF A+GKA A GA DGFVK VFD G LLGAHM+GA VTEMI Sbjct: 364 AKAKAAGHEVRVGKFPFSASGKASAAGAKDGFVKLVFDKKYGELLGAHMIGANVTEMIAE 423 Query: 425 YTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465 R LETT E+++T+ PHPT+SEA+ E+ AAY +H Sbjct: 424 IVAIRKLETTGHELIKTVHPHPTMSEAIMEAAAAAYDEVIH 464 Lambda K H 0.319 0.135 0.393 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: 592 Number of extensions: 24 Number of successful extensions: 4 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: 466 Length of database: 465 Length adjustment: 33 Effective length of query: 433 Effective length of database: 432 Effective search space: 187056 Effective search space used: 187056 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_111392326.1 CLV31_RS07900 (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.2831899.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-176 572.2 17.2 4.5e-176 572.0 17.2 1.0 1 NCBI__GCF_003253485.1:WP_111392326.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003253485.1:WP_111392326.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 572.0 17.2 4.5e-176 4.5e-176 1 460 [. 5 464 .. 5 465 .] 0.97 Alignments for each domain: == domain 1 score: 572.0 bits; conditional E-value: 4.5e-176 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 ++d++v+G+GpgGYvaAira+qlglk+a+ve +lGG+Cln+GCiPtKalLksa+v+e++++ak++gi+v++ NCBI__GCF_003253485.1:WP_111392326.1 5 KFDLIVLGSGPGGYVAAIRASQLGLKTAIVEAAELGGICLNWGCIPTKALLKSAQVFEYISHAKDYGISVQGA 77 59*********************************************************************** PP TIGR01350 74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGsepre 145 + d++ +++r++ v + +++Gv++L+kknk+e i+G +k++ k+vev++ +++ ++++a+niiiAtG++ re NCBI__GCF_003253485.1:WP_111392326.1 78 EADFAGMVKRSRGVADGMSKGVQFLMKKNKIEIITGWGKVQPGKKVEVNDAEGKkSVITADNIIIATGARSRE 150 *************************************************9998867899************** PP TIGR01350 146 lplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlk 218 lp ++ d k +i +++a++l+++p+++v+vG+G+iGvEfa++++++G++vt++e++dri+p++d+evsk+l+ NCBI__GCF_003253485.1:WP_111392326.1 151 LPS-MKIDDKKIIGYRKAMTLEKQPKKMVVVGSGAIGVEFAYFYNSIGTEVTIVEFMDRIVPVEDEEVSKALE 222 ***.9******************************************************************** PP TIGR01350 219 kklkkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleelgleklgveldergai 289 k +kk+g+ki+t+++vt v ++ + + v++ k+ +e le + vL a G+ +nle++gle +g+ +d+ g+i NCBI__GCF_003253485.1:WP_111392326.1 223 KIYKKSGMKIMTSSEVTGVDTKGEGCKvtVKTAKG-EEILECDVVLSAAGVVSNLENIGLEDVGILVDK-GKI 293 *****************887777766621555555.69******************************9.99* PP TIGR01350 290 kvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqa 362 +v+e+++tn+pg yaiGDv+ ++ LAhvAs+eg++++ekiag++++++dy +P ++y++Pe+asvG+te++a NCBI__GCF_003253485.1:WP_111392326.1 294 QVNEYYQTNMPGYYAIGDVVPGPALAHVASAEGIICVEKIAGHHPEALDYGNIPGCTYCSPEIASVGMTEAKA 366 ************************************************************************* PP TIGR01350 363 keegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelak 435 k++g+ev+vgkfpf+a+gka a++ +dGfvk+++dkk+ge+lGah++ga+++e+i+e++++ +le+t +el k NCBI__GCF_003253485.1:WP_111392326.1 367 KAAGHEVRVGKFPFSASGKASAAGAKDGFVKLVFDKKYGELLGAHMIGANVTEMIAEIVAIRKLETTGHELIK 439 ************************************************************************* PP TIGR01350 436 tihpHPtlsEaikeaalaalgkaih 460 t+hpHPt+sEai+eaa+aa+++ ih NCBI__GCF_003253485.1:WP_111392326.1 440 TVHPHPTMSEAIMEAAAAAYDEVIH 464 **********************999 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (465 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: 17.01 // [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