Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate 14262 b0116 dihydrolipoamide dehydrogenase (NCBI)
Query= BRENDA::P0A9P0 (474 letters) >FitnessBrowser__Keio:14262 Length = 474 Score = 941 bits (2433), Expect = 0.0 Identities = 474/474 (100%), Positives = 474/474 (100%) Query: 1 MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVA 60 MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVA Sbjct: 1 MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVA 60 Query: 61 KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFT 120 KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFT Sbjct: 61 KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFT 120 Query: 121 GANTLEVEGENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLV 180 GANTLEVEGENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLV Sbjct: 121 GANTLEVEGENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLV 180 Query: 181 MGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTA 240 MGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTA Sbjct: 181 MGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTA 240 Query: 241 VEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQ 300 VEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQ Sbjct: 241 VEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQ 300 Query: 301 LRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWV 360 LRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWV Sbjct: 301 LRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWV 360 Query: 361 GLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGE 420 GLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGE Sbjct: 361 GLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGE 420 Query: 421 LLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK 474 LLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK Sbjct: 421 LLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK 474 Lambda K H 0.317 0.137 0.396 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: 943 Number of extensions: 23 Number of successful extensions: 1 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: 474 Length of database: 474 Length adjustment: 33 Effective length of query: 441 Effective length of database: 441 Effective search space: 194481 Effective search space used: 194481 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 (21.6 bits) S2: 51 (24.3 bits)
Align candidate 14262 b0116 (dihydrolipoamide dehydrogenase (NCBI))
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.2600.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-154 501.5 6.2 1.3e-154 501.2 6.2 1.0 1 lcl|FitnessBrowser__Keio:14262 b0116 dihydrolipoamide dehydroge Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:14262 b0116 dihydrolipoamide dehydrogenase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 501.2 6.2 1.3e-154 1.3e-154 2 455 .. 7 460 .. 6 465 .. 0.97 Alignments for each domain: == domain 1 score: 501.2 bits; conditional E-value: 1.3e-154 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenvkldlek 79 ++vvv+G+Gp+GY aA r+a lgl++++ve+ ++lGG+ClnvGCiP+KalL+ a+v+ee+k ++e+gi + k d++k lcl|FitnessBrowser__Keio:14262 7 TQVVVLGAGPAGYSAAFRCADLGLETVIVERyNTLGGVCLNVGCIPSKALLHVAKVIEEAKALAEHGIVFGEPKTDIDK 85 579****************************9*********************************************** PP TIGR01350 80 llerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplkleedekvvi 158 + +kekv+++l+gG++++ k kv+v++G +k+++++++ev++e+++++++++n+iiA Gs+p++lp+ + ++ +++ lcl|FitnessBrowser__Keio:14262 86 IRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFTGANTLEVEGENGKTVINFDNAIIAAGSRPIQLPF-IPHEDPRIW 163 *********************************************************************.8888889** PP TIGR01350 159 tseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtev 237 +s++alelkevpe+l+++GgG+iG+E++++++ lG+++ v+e+ d+++pa d+++ kv +k+++k + +++ ++kvt+v lcl|FitnessBrowser__Keio:14262 164 DSTDALELKEVPERLLVMGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISK-KFNLMLETKVTAV 241 **************************************************************986.58*********** PP TIGR01350 238 ekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmL 314 e++ed + v++++k +e ++++vLva+Gr pn ++l+ k gve+d+rg+i vd++lrtnvp+i+aiGD++g++mL lcl|FitnessBrowser__Keio:14262 242 EAKEDGIYVTMEGKkaPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQLRTNVPHIFAIGDIVGQPML 320 ******9988887744578999********************************************************* PP TIGR01350 315 AhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvk 393 Ah+ ++eg vaae iagk++ +d k++Ps+ ytePeva vGlte++ake+gi+++++ fp aa+g+a+a++ +dG+ k lcl|FitnessBrowser__Keio:14262 321 AHKGVHEGHVAAEVIAGKKH-YFDPKVIPSIAYTEPEVAWVGLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTK 398 *****************776.9********************************************************* PP TIGR01350 394 vivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaal 455 +i+dk++++++G ivg++ el+ e+ la+e++ +e++a tih+HPtl E + aa+ lcl|FitnessBrowser__Keio:14262 399 LIFDKESHRVIGGAIVGTNGGELLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFE 460 *****************************************************998887655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (474 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: 9.38 // [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