Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate GFF65 HP15_65 dihydrolipoamide dehydrogenase
Query= BRENDA::A0A0H2ZB32 (464 letters) >FitnessBrowser__Marino:GFF65 Length = 461 Score = 514 bits (1324), Expect = e-150 Identities = 268/466 (57%), Positives = 337/466 (72%), Gaps = 9/466 (1%) Query: 1 MSQILKTSLLIVGGGPGGYVAAIRAGQLGIPTVLVEGAALGGTCLNVGCIPSKALIHAAE 60 MS+++KT +L+VGGGPGGYVAAIR GQLG+ TVLVE LGGTCL GCIPSKA+IHAA Sbjct: 1 MSEVIKTKVLVVGGGPGGYVAAIRCGQLGLDTVLVEADQLGGTCLTRGCIPSKAMIHAAS 60 Query: 61 EYLKARHYAGRSALGIQV-QAPSIDIARTVEWKDAIVDRLTSGVAALLKKHGVDVVQGWA 119 E+ A + LGI + + P +D+A TV+WKD+IV RL +GVAALLK+ V VV+GW Sbjct: 61 EFSAMMKAASKPHLGISLSEPPKVDLAATVDWKDSIVKRLNTGVAALLKRAKVKVVKGWG 120 Query: 120 RILDGKSVAVELAGGGSQRIECEHLLLAAGSQSVELPILPLGGKVISSTEALAPGSLPKR 179 D K+ VE A G I+ EH++LA GS VELP LPLGGKVISSTEAL+ +P + Sbjct: 121 TFSDAKTCNVETADGVIT-IQSEHVILATGSAPVELPFLPLGGKVISSTEALSLPDVPSK 179 Query: 180 LVVVGGGYIGLELGTAYRKLGVEVAVVEAQPRILPGYDEELTKPVAQALRKLGVELYLGH 239 LVV+G GYIGLELG AY KLG +V +VE+ RILP YDE L +PV + L + V+L+L Sbjct: 180 LVVIGAGYIGLELGIAYAKLGSDVTIVESSDRILPLYDEALVEPVRRWLDESAVKLHLNA 239 Query: 240 SLLGPSENGVRVRDGAGEEREIAADQVLVAVGRKPRSEGWNLESLGLDMNGRAVKVDDQC 299 LG + G+ V G E + AD +LV VGRKP ++GW LE++ LDM+GR V+VD+QC Sbjct: 240 RALGERDGGLAVELEGGSETVLPADNILVTVGRKPVTQGWGLENMALDMDGRYVRVDEQC 299 Query: 300 RTSMRNVWAIGDLAGEPMLAHRAMAQGEMVAELIAGKRRQFAPVAIPAVCFTDPEVVVAG 359 TSM+NVWAIGDL GEPMLAH+A AQGE+VAE+IAGKRR+F PVAIPAVCFT+PE+V G Sbjct: 300 ATSMKNVWAIGDLVGEPMLAHKASAQGEVVAEVIAGKRRRFDPVAIPAVCFTEPEIVSVG 359 Query: 360 LSPEQAKDAGLDCLVASFPFAANGRAMTLEA--NEGFVRVVARRDNHLVVGWQAVGKAVS 417 P A + FP AANGRA++++A N GFVRVVA + H ++G QAVG +S Sbjct: 360 AEPSLA-----GTVTGVFPVAANGRALSMDAGDNGGFVRVVAHSETHRILGVQAVGTHIS 414 Query: 418 ELSTAFAQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALH 463 EL+ AF ++EMGA ++DI G I AHPTLGE EA+L+ LGHA+H Sbjct: 415 ELTAAFVTAVEMGATVDDIEGMIQAHPTLGEMFHEASLKILGHAIH 460 Lambda K H 0.318 0.136 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: 670 Number of extensions: 36 Number of successful extensions: 8 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: 464 Length of database: 461 Length adjustment: 33 Effective length of query: 431 Effective length of database: 428 Effective search space: 184468 Effective search space used: 184468 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 (21.7 bits) S2: 51 (24.3 bits)
Align candidate GFF65 HP15_65 (dihydrolipoamide 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.16745.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.3e-142 459.4 1.2 7.1e-142 459.2 1.2 1.0 1 lcl|FitnessBrowser__Marino:GFF65 HP15_65 dihydrolipoamide dehydro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF65 HP15_65 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.2 1.2 7.1e-142 7.1e-142 3 460 .. 8 460 .. 6 461 .] 0.95 Alignments for each domain: == domain 1 score: 459.2 bits; conditional E-value: 7.1e-142 TIGR01350 3 dvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke.ak..elgieven.vkl 75 v+v+GgGpgGYvaAir++qlgl ++lve ++lGGtCl +GCiP+Ka++++a ++ + + a+ +lgi++++ k+ lcl|FitnessBrowser__Marino:GFF65 8 KVLVVGGGPGGYVAAIRCGQLGLDTVLVEADQLGGTCLTRGCIPSKAMIHAASEFSAMMKaASkpHLGISLSEpPKV 84 799************************************************9988877664432269***9998*** PP TIGR01350 76 dlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplklee 152 dl++ +++k+++vk+l++Gv+aLlk++kv+v+kG ++++d+k+ +v++ ++ +++ +++i+AtGs p elp+ l lcl|FitnessBrowser__Marino:GFF65 85 DLAATVDWKDSIVKRLNTGVAALLKRAKVKVVKGWGTFSDAKTCNVETADGVITIQSEHVILATGSAPVELPF-LPL 160 **************************************************99*********************.999 PP TIGR01350 153 dekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkil 229 + vi+s+eal+l+ vp++lv++G+G+iG+E++ ++aklG++vt++e +drilp d+ + + +++ l ++ vk++ lcl|FitnessBrowser__Marino:GFF65 161 GG-KVISSTEALSLPDVPSKLVVIGAGYIGLELGIAYAKLGSDVTIVESSDRILPLYDEALVEPVRRWLDESAVKLH 236 88.59************************************************************************ PP TIGR01350 230 tnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiG 306 na+ +++ + ve +++ +++l a+++Lv+vGrkp +++ gle++ +++d ++ vde++ t++++++aiG lcl|FitnessBrowser__Marino:GFF65 237 LNARAL--GERDGGLAVELEGGSETVLPADNILVTVGRKPVTQGWGLENMALDMDG-RYVRVDEQCATSMKNVWAIG 310 ***988..78888888888899889*******************************.67****************** PP TIGR01350 307 DvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkal 383 D++g++mLAh+As++g v+ae iagk++ +d a+P+v +tePe+ svG + a ++g fp+aang+al lcl|FitnessBrowser__Marino:GFF65 311 DLVGEPMLAHKASAQGEVVAEVIAGKRR-RFDPVAIPAVCFTEPEIVSVGAEPSLA-----GTVTGVFPVAANGRAL 381 *************************887.9********************877655.....45799*********** PP TIGR01350 384 alee..tdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgka 458 +++ + Gfv+v+++ +t++ilG++ vg++ sel + ++ ave+++tv++++ +i++HPtl+E+++ea l++lg+a lcl|FitnessBrowser__Marino:GFF65 382 SMDAgdNGGFVRVVAHSETHRILGVQAVGTHISELTAAFVTAVEMGATVDDIEGMIQAHPTLGEMFHEASLKILGHA 458 99754388********************************************************************* PP TIGR01350 459 ih 460 ih lcl|FitnessBrowser__Marino:GFF65 459 IH 460 *9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (461 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8.32 // [ok]
This GapMind analysis is from Sep 17 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