Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate GFF3432 PS417_17560 dihydrolipoamide dehydrogenase
Query= reanno::WCS417:GFF3432 (459 letters) >FitnessBrowser__WCS417:GFF3432 Length = 459 Score = 905 bits (2338), Expect = 0.0 Identities = 459/459 (100%), Positives = 459/459 (100%) Query: 1 MTQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE 60 MTQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE Sbjct: 1 MTQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE 60 Query: 61 QFQQTIHHSQGSHLGIEVDVPTLDIRKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120 QFQQTIHHSQGSHLGIEVDVPTLDIRKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK Sbjct: 61 QFQQTIHHSQGSHLGIEVDVPTLDIRKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120 Query: 121 VVDGKTVEVGDQRIQCEHLLLATGSKSVNLPMLPIGGPIISSTEALAPTRVPKRLIVVGG 180 VVDGKTVEVGDQRIQCEHLLLATGSKSVNLPMLPIGGPIISSTEALAPTRVPKRLIVVGG Sbjct: 121 VVDGKTVEVGDQRIQCEHLLLATGSKSVNLPMLPIGGPIISSTEALAPTRVPKRLIVVGG 180 Query: 181 GYIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTQPVNESLKHLGVKLYLKHSVTGFT 240 GYIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTQPVNESLKHLGVKLYLKHSVTGFT Sbjct: 181 GYIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTQPVNESLKHLGVKLYLKHSVTGFT 240 Query: 241 DGSLQVRDPNGDTVSLATDQVLVAVGRKPNTQGWNLEALNLEMNGAAIKIDSRCQTSMRN 300 DGSLQVRDPNGDTVSLATDQVLVAVGRKPNTQGWNLEALNLEMNGAAIKIDSRCQTSMRN Sbjct: 241 DGSLQVRDPNGDTVSLATDQVLVAVGRKPNTQGWNLEALNLEMNGAAIKIDSRCQTSMRN 300 Query: 301 VYAIGDLSGEPMLAHRAMAQGEMVAELISGKHREFNPAAIPAVCFTDPELVVVGKTPDEA 360 VYAIGDLSGEPMLAHRAMAQGEMVAELISGKHREFNPAAIPAVCFTDPELVVVGKTPDEA Sbjct: 301 VYAIGDLSGEPMLAHRAMAQGEMVAELISGKHREFNPAAIPAVCFTDPELVVVGKTPDEA 360 Query: 361 KAAGLDCIVSSFPFAANGRAMTLESKTGFVRVVARRDNHLIVGWQAVGVGVSELSTAFGL 420 KAAGLDCIVSSFPFAANGRAMTLESKTGFVRVVARRDNHLIVGWQAVGVGVSELSTAFGL Sbjct: 361 KAAGLDCIVSSFPFAANGRAMTLESKTGFVRVVARRDNHLIVGWQAVGVGVSELSTAFGL 420 Query: 421 SLEMGSRLEDVAGTIHAHPTLGEAVQEAALRALGHALHL 459 SLEMGSRLEDVAGTIHAHPTLGEAVQEAALRALGHALHL Sbjct: 421 SLEMGSRLEDVAGTIHAHPTLGEAVQEAALRALGHALHL 459 Lambda K H 0.318 0.136 0.395 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: 808 Number of extensions: 13 Number of successful extensions: 2 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: 459 Length of database: 459 Length adjustment: 33 Effective length of query: 426 Effective length of database: 426 Effective search space: 181476 Effective search space used: 181476 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 GFF3432 PS417_17560 (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.6990.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-151 489.2 0.5 6.4e-151 489.0 0.5 1.0 1 lcl|FitnessBrowser__WCS417:GFF3432 PS417_17560 dihydrolipoamide deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF3432 PS417_17560 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 489.0 0.5 6.4e-151 6.4e-151 3 460 .. 8 458 .. 6 459 .] 0.96 Alignments for each domain: == domain 1 score: 489.0 bits; conditional E-value: 6.4e-151 TIGR01350 3 dvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke...akelgievenvk 74 +++iGgGpgGYvaAira+qlg ++lve + lGGtCln GCiP+Kal++ ae +++ + ++lgiev+ + lcl|FitnessBrowser__WCS417:GFF3432 8 TLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAEQFQQTIHhsqGSHLGIEVDVPT 82 578***************************************************9987653445789******** PP TIGR01350 75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplk 149 ld++k +e+k+ +v++l++Gv+aLlkk+kv+vi+G ak++d k+vev +++ ++ +++++AtGs+ +lp+ lcl|FitnessBrowser__WCS417:GFF3432 83 LDIRKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAKVVDGKTVEVGDQR----IQCEHLLLATGSKSVNLPM- 152 ***********************************************9997....89*****************. PP TIGR01350 150 leedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkk 224 l + +i+s+eal+ ++vp++l++vGgG+iG+E++ +++klG++v+v+e++drilpa dae+++ ++++lk+ lcl|FitnessBrowser__WCS417:GFF3432 153 LPIGG-PIISSTEALAPTRVPKRLIVVGGGYIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTQPVNESLKHL 226 99998.69******************************************************************* PP TIGR01350 225 gvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnv 299 gvk++ +++vt ++ + +v+ ++++ +l +++vLvavGrkpn+++ +le+l++e++ aik+d++++t++ lcl|FitnessBrowser__WCS417:GFF3432 227 GVKLYLKHSVTGFTDGSLQVR--DPNGDTVSLATDQVLVAVGRKPNTQGWNLEALNLEMNG-AAIKIDSRCQTSM 298 ***********6666655555..5566689******************************9.78*********** PP TIGR01350 300 pgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkf 374 ++yaiGD+ g++mLAh+A+++g ++ae i gk++ e++ a+P+v +t+Pe+ +vG+t ++ak++g ++ v++f lcl|FitnessBrowser__WCS417:GFF3432 299 RNVYAIGDLSGEPMLAHRAMAQGEMVAELISGKHR-EFNPAAIPAVCFTDPELVVVGKTPDEAKAAGLDCIVSSF 372 ********************************998.9************************************** PP TIGR01350 375 pfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaike 449 pfaang+a++le ++Gfv+v++ ++ + i+G + vg +sel + + l +e++ ++e++a tih+HPtl+Ea++e lcl|FitnessBrowser__WCS417:GFF3432 373 PFAANGRAMTLESKTGFVRVVARRDNHLIVGWQAVGVGVSELSTAFGLSLEMGSRLEDVAGTIHAHPTLGEAVQE 447 *************************************************************************** PP TIGR01350 450 aalaalgkaih 460 aal alg+a+h lcl|FitnessBrowser__WCS417:GFF3432 448 AALRALGHALH 458 ********999 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.98 // [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