Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_050654705.1 C1M55_RS23120 dihydrolipoyl dehydrogenase
Query= BRENDA::P50970 (466 letters) >NCBI__GCF_002893965.1:WP_050654705.1 Length = 465 Score = 494 bits (1272), Expect = e-144 Identities = 248/461 (53%), Positives = 327/461 (70%), Gaps = 6/461 (1%) Query: 5 FDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEMQ 64 +D++V+GGGPGGYVAAIRAAQL L VALVER LGGICLNWGCIPTK++L A+V H + Sbjct: 10 YDVLVIGGGPGGYVAAIRAAQLGLSVALVERDRLGGICLNWGCIPTKAMLHGADVAHTLS 69 Query: 65 NAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQMLV 124 + YG +S FD+ K+++ SR V+ +L+ GV L++KN V+VISG +L + V Sbjct: 70 ELDTYGFSSASVQFDISKLVSFSRGVSEKLSGGVAYLMKKNGVDVISGTAKLVDKGVVSV 129 Query: 125 ETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGAI 184 E + A +IIATGAR R +P V DG +WTY AL P +PK LLVIGSGAI Sbjct: 130 EG-----QTYRADHVIIATGARPRSIPGVAPDGDRVWTYFDALVPKELPKSLLVIGSGAI 184 Query: 185 GIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPDD 244 G+EFAS Y D G EV+IVE AP I+P+ED E+SA+V K F+KRGI I T +++ +T D Sbjct: 185 GVEFASLYRDLGTEVTIVEMAPHIMPVEDEEISAFVRKQFEKRGITIHTGASVSAVTVGD 244 Query: 245 EGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTNVD 304 + V + +DG V +VA G+ NVE++GL+ LG++++RG I D + RT+ Sbjct: 245 DAVQVNVQTSDG-VESLTVDRVLVAAGITGNVEDLGLEALGVEIERGAIVTDQWCRTSAF 303 Query: 305 HVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGLTE 364 ++AIGDVAGAPCLAHKASH+ V+ E +AG VHPL+ +PGCTYARPQVAS+GLTE Sbjct: 304 GIYAIGDVAGAPCLAHKASHEAVLCVEKLAGVPDVHPLDRDYVPGCTYARPQVASLGLTE 363 Query: 365 EKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMIQG 424 ++ G +++G+F ANGKA+A G +GFVKT+FDAD+G LLGAHMVG +VTE IQG Sbjct: 364 KQCAGTGRALRVGHFDLQANGKALAIGEAEGFVKTIFDADTGELLGAHMVGPDVTEQIQG 423 Query: 425 YTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465 + +AR+LE T ++ E +F HPTLSEAMHESVL+A GR L+ Sbjct: 424 FGIARSLEATGEDLAEVVFAHPTLSEAMHESVLSALGRPLN 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: 637 Number of extensions: 26 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_050654705.1 C1M55_RS23120 (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.2802286.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-171 557.1 0.3 1.6e-171 557.0 0.3 1.0 1 NCBI__GCF_002893965.1:WP_050654705.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002893965.1:WP_050654705.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 557.0 0.3 1.6e-171 1.6e-171 1 460 [. 9 464 .. 9 465 .] 0.98 Alignments for each domain: == domain 1 score: 557.0 bits; conditional E-value: 1.6e-171 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 +ydv+viGgGpgGYvaAiraaqlgl+valve+++lGG+Cln+GCiPtKa+L+ a+v+++l+e++++g+++++v NCBI__GCF_002893965.1:WP_050654705.1 9 KYDVLVIGGGPGGYVAAIRAAQLGLSVALVERDRLGGICLNWGCIPTKAMLHGADVAHTLSELDTYGFSSASV 81 59*********************************************************************** PP TIGR01350 74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprel 146 ++d++kl+ ++ v++kl+gGv++L+kkn+v+vi+G+akl+dk+ v+v++++ ++a+++iiAtG++pr++ NCBI__GCF_002893965.1:WP_050654705.1 82 QFDISKLVSFSRGVSEKLSGGVAYLMKKNGVDVISGTAKLVDKGVVSVEGQT----YRADHVIIATGARPRSI 150 *************************************************998....56*************** PP TIGR01350 147 plkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkk 219 p+ ++ d+++v+t+ +al ke+p+sl+++G+G+iGvEfas++++lG++vt++e++++i+p++d+e+s +++k NCBI__GCF_002893965.1:WP_050654705.1 151 PG-VAPDGDRVWTYFDALVPKELPKSLLVIGSGAIGVEFASLYRDLGTEVTIVEMAPHIMPVEDEEISAFVRK 222 **.9********************************************************************* PP TIGR01350 220 klkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikv 291 +++k+g++i+t+a+v++v+ +d+v+v+ + + ve+l++++vLva G + n+e+lgle+lgve+++ gai++ NCBI__GCF_002893965.1:WP_050654705.1 223 QFEKRGITIHTGASVSAVTVGDDAVQVNVQTSdGVESLTVDRVLVAAGITGNVEDLGLEALGVEIER-GAIVT 294 *************************9777776679*****************************988.***** PP TIGR01350 292 deelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks.eidykavPsviytePevasvGlteeqak 363 d+ +rt++ giyaiGDv+g + LAh+As+e+v+++ek+ag + +d+++vP ++y++P+vas+Glte+q+ NCBI__GCF_002893965.1:WP_050654705.1 295 DQWCRTSAFGIYAIGDVAGAPCLAHKASHEAVLCVEKLAGVPDVhPLDRDYVPGCTYARPQVASLGLTEKQCA 367 ****************************************988779*************************** PP TIGR01350 364 eegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelakt 436 g +++vg+f+++angkala++e++Gfvk+i+d +tge+lGah+vg++++e i+ + +a +le+t e+la++ NCBI__GCF_002893965.1:WP_050654705.1 368 GTGRALRVGHFDLQANGKALAIGEAEGFVKTIFDADTGELLGAHMVGPDVTEQIQGFGIARSLEATGEDLAEV 440 ************************************************************************* PP TIGR01350 437 ihpHPtlsEaikeaalaalgkaih 460 +++HPtlsEa++e++l+alg++++ NCBI__GCF_002893965.1:WP_050654705.1 441 VFAHPTLSEAMHESVLSALGRPLN 464 *******************99876 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 18.83 // [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