Align TPP-dependent acetoin dehydrogenase complex, E3 component, dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate 352713 BT3186 dihydrolipoamide dehydrogenase (NCBI ptt file)
Query= CharProtDB::CH_006552 (578 letters) >FitnessBrowser__Btheta:352713 Length = 447 Score = 333 bits (853), Expect = 1e-95 Identities = 188/449 (41%), Positives = 270/449 (60%), Gaps = 9/449 (2%) Query: 118 LVVIGGGPGGYVAAIRAAQLGAKVTLIEKESLGGTCLNVGCIPTKVLLHSSQLLTEMKEG 177 +++IGGGP GY AA A + G V LIEK +LGG CLN GCIPTK LL+S++ + Sbjct: 5 VIIIGGGPAGYTAAEAAGKAGLSVLLIEKNNLGGVCLNEGCIPTKTLLYSAKTYDSARHS 64 Query: 178 DKLGIDIEGSIVVNWKHIQKRKKIVIKKLVSGVSGLLTCNKVKVIKGTAKFESKDTILVT 237 K +++ + + I RK V++KLV GV LT N V ++ G A+ K+T+ Sbjct: 65 SKYAVNVS-EVSFDLPKIIARKSKVVRKLVLGVKAKLTSNNVAMVTGEAQIIDKNTVRCG 123 Query: 238 KEDGVAEKVNFDNAIIATGSMPFIPEIEGNKLSGVIDSTGALSLESNPESIAIIGGGVIG 297 +E N +N I+ TGS FIP I G + AL + P S+AI+GGGVIG Sbjct: 124 EET-----YNAENLILCTGSETFIPPITGVETVNYWTHRDALDSKELPASLAIVGGGVIG 178 Query: 298 VEFASIFNSLGCKVSIIEMLPHILPPMDREISEIAKAKLIRDGININNNCKVTRIEQGED 357 +EFAS FNSLG +V++IEM+ IL MD+E+S + +A+ + GI + KV + Q E+ Sbjct: 179 MEFASFFNSLGVQVTVIEMMDEILGGMDKELSALLRAEYAKRGIKFLLSTKVVALSQTEE 238 Query: 358 GLKVSFIGDKGEESIDVEKVLIAVGRRSNIEGLDVEKIGV-KTEGGSIIVNDKMETNVEG 416 G VS+ +G+ S+ EK+L++VGRR +G +E + + KT G+I VN+KM+T++ G Sbjct: 239 GAVVSYENAEGKGSVIAEKLLMSVGRRPVTKGFGLENLNLDKTGRGAIKVNEKMQTSLSG 298 Query: 417 IYAIGDCTGKIMLAHVASDQGVVAAENIMGQNKKMDYKTVPACVYTKPELASVGLTEEQA 476 +Y GD TG +LAH A + VA +I+G+ M Y+ +P VYT PE+A VG TEE A Sbjct: 299 VYVCGDLTGFSLLAHTAVREAEVAVHSILGKEDAMSYRAIPGVVYTNPEIAGVGETEESA 358 Query: 477 KEKGIDYKVGKFQLAANGKSLIMNE-TGGVIKIITDKKYEEILGVHILGPRATDLITEAA 535 KGI YKV K +A +G+ + NE GV K++ D++ E I+G H+LG A+++IT A Sbjct: 359 SAKGITYKVVKLPMAYSGRFVAENEGVNGVCKVLLDEQ-ERIIGAHVLGNPASEIITLAG 417 Query: 536 LALRLEATLEEIITTVHAHPTVGEAMKEA 564 A+ L T V HPTVGE +EA Sbjct: 418 TAIELGLTAAAWKKVVFPHPTVGEIFREA 446 Lambda K H 0.313 0.134 0.365 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: 610 Number of extensions: 29 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: 578 Length of database: 447 Length adjustment: 34 Effective length of query: 544 Effective length of database: 413 Effective search space: 224672 Effective search space used: 224672 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 52 (24.6 bits)
Align candidate 352713 BT3186 (dihydrolipoamide dehydrogenase (NCBI ptt file))
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.1907680.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-145 469.4 8.1 6.7e-145 469.2 8.1 1.0 1 FitnessBrowser__Btheta:352713 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Btheta:352713 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 469.2 8.1 6.7e-145 6.7e-145 1 450 [. 2 446 .. 2 447 .] 0.96 Alignments for each domain: == domain 1 score: 469.2 bits; conditional E-value: 6.7e-145 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvkldlekl 80 +y+v++iGgGp+GY+aA a+++gl+v+l+ek++lGG+Cln+GCiPtK+lL sa++++++++ +++ ++v++v++dl k+ FitnessBrowser__Btheta:352713 2 KYQVIIIGGGPAGYTAAEAAGKAGLSVLLIEKNNLGGVCLNEGCIPTKTLLYSAKTYDSARHSSKYAVNVSEVSFDLPKI 81 599***************************************************************************** PP TIGR01350 81 lerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplkleedekvvits 160 +rk+kvv+klv Gvka l++n+v +++Gea++ dk++v+ +e+ ++a+n+i+ tGse +p++ +++ +t FitnessBrowser__Btheta:352713 82 IARKSKVVRKLVLGVKAKLTSNNVAMVTGEAQIIDKNTVRCGEET----YNAENLILCTGSETFIPPIT-GVETVNYWTH 156 ***************************************998887....67*****************5.4444458*** PP TIGR01350 161 eealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvteveke 240 ++al ke+p sl+ivGgGviG+Efas+f++lGv+vtvie++d+il +d+e+s +l+ ++ k+g+k+l ++kv +++++ FitnessBrowser__Btheta:352713 157 RDALDSKELPASLAIVGGGVIGMEFASFFNSLGVQVTVIEMMDEILGGMDKELSALLRAEYAKRGIKFLLSTKVVALSQT 236 ***************************************************************************99999 PP TIGR01350 241 edevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAs 319 e+ vv+ ++ + ++ aek+L++vGr+p ++++gle+l+++ + rgaikv+e+++t+++g+y++GD++g LAh+A+ FitnessBrowser__Btheta:352713 237 EEGAVVSYENAeGKGSVIAEKLLMSVGRRPVTKGFGLENLNLDKTGRGAIKVNEKMQTSLSGVYVCGDLTGFSLLAHTAV 316 9888876666646799**************************************************************** PP TIGR01350 320 kegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalalee.tdGfvkvivdk 398 +e+ va++ i+gke+ ++ y+a+P v+yt+Pe+a vG tee a ++gi +kv+k+p+a +g+ +a +e +G+ kv++d+ FitnessBrowser__Btheta:352713 317 REAEVAVHSILGKED-AMSYRAIPGVVYTNPEIAGVGETEESASAKGITYKVVKLPMAYSGRFVAENEgVNGVCKVLLDE 395 ************887.9************************************************99978********97 PP TIGR01350 399 ktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikea 450 + ++i+Gah++g+ ase+i+ + a+el+lt+ +k+++pHPt++E++ ea FitnessBrowser__Btheta:352713 396 Q-ERIIGAHVLGNPASEIITLAGTAIELGLTAAAWKKVVFPHPTVGEIFREA 446 5.79*********************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (447 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 15.66 // [ok]
This GapMind analysis is from Apr 09 2024. 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