Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate AZOBR_RS14390 AZOBR_RS14390 dihydrolipoamide dehydrogenase
Query= BRENDA::P50970 (466 letters) >FitnessBrowser__azobra:AZOBR_RS14390 Length = 465 Score = 544 bits (1401), Expect = e-159 Identities = 280/467 (59%), Positives = 343/467 (73%), Gaps = 3/467 (0%) Query: 1 MAD-HFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEV 59 MAD ++DLIV+GGGPGGYVAAIRAAQL L A+VER +LGGICLNWGCIPTK+LLRSAEV Sbjct: 1 MADMNYDLIVIGGGPGGYVAAIRAAQLGLSTAVVERENLGGICLNWGCIPTKALLRSAEV 60 Query: 60 YHEMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGN 119 ++A YGL P FDLDK++ RSR+VA +L GVK LL+KNKV VI G +L G Sbjct: 61 LRNAKHASEYGLVIQNPSFDLDKVVQRSRKVAGQLNGGVKHLLKKNKVAVIEGEAKLLGK 120 Query: 120 QQMLVETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVI 179 Q+ V AK+IIIATGARAR LP + DG +WTY A+ P PK LLVI Sbjct: 121 GQVAVTKGGAAVGTFGAKNIIIATGARARTLPGLEDDGNLVWTYRKAMTPNTTPKSLLVI 180 Query: 180 GSGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQN 239 GSGAIGIEFASFY + GA+V++VE +ILP+ED E+SA+ K F+K+G+RI+T N Sbjct: 181 GSGAIGIEFASFYNELGAKVTVVEVMDRILPVEDEEISAFARKQFEKQGMRIITNGKAGN 240 Query: 240 LTPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFG 299 L + VT + A+GK I+A+G+ N EN+GL+ ++ DRG I + Sbjct: 241 LRKGADSVTVAVE-ANGKTEDITVDRVILAVGIAPNTENLGLENTKVQTDRGHIKTNANC 299 Query: 300 RTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVAS 359 +T+ V+AIGDV GAP LAHKASH+GVIA E IAG H H L+ +NIPGCTY+ PQ+AS Sbjct: 300 QTDEPGVYAIGDVTGAPWLAHKASHEGVIAVEHIAG-KHPHALDVRNIPGCTYSHPQIAS 358 Query: 360 VGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVT 419 VGLTE+KA++ GY V++G FPFI NGKAIA G DG VKTVFDA +G LLGAHMVGAEVT Sbjct: 359 VGLTEKKAKEAGYEVRVGRFPFIGNGKAIALGEADGMVKTVFDAKTGELLGAHMVGAEVT 418 Query: 420 EMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALHF 466 E+IQGYTVA+T+ETTE E+M+T+FPHPTLSE MHESVL AYGRA+HF Sbjct: 419 ELIQGYTVAKTMETTEQELMQTVFPHPTLSEMMHESVLDAYGRAIHF 465 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: 669 Number of extensions: 31 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 AZOBR_RS14390 AZOBR_RS14390 (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.6905.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-183 596.6 8.1 1.7e-183 596.4 8.1 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS14390 AZOBR_RS14390 dihydrolipoamide d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS14390 AZOBR_RS14390 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 596.4 8.1 1.7e-183 1.7e-183 1 461 [] 5 465 .] 5 465 .] 0.99 Alignments for each domain: == domain 1 score: 596.4 bits; conditional E-value: 1.7e-183 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgie 69 +yd++viGgGpgGYvaAiraaqlgl++a+ve+e+lGG+Cln+GCiPtKalL+saev++++k+a+e+g+ lcl|FitnessBrowser__azobra:AZOBR_RS14390 5 NYDLIVIGGGPGGYVAAIRAAQLGLSTAVVERENLGGICLNWGCIPTKALLRSAEVLRNAKHASEYGLV 73 69******************************************************************* PP TIGR01350 70 venvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniii 137 ++n ++dl+k+++r++kv +l+gGvk+Llkknkv vi+Geakll+k++v v+k ++ + akniii lcl|FitnessBrowser__azobra:AZOBR_RS14390 74 IQNPSFDLDKVVQRSRKVAGQLNGGVKHLLKKNKVAVIEGEAKLLGKGQVAVTKGGAAvGTFGAKNIII 142 ******************************************************998878999****** PP TIGR01350 138 AtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldril 206 AtG++ r+lp+ le d+++v+t+++a++ +++p+sl+++G+G+iG+Efas++++lG+kvtv+e++dril lcl|FitnessBrowser__azobra:AZOBR_RS14390 143 ATGARARTLPG-LEDDGNLVWTYRKAMTPNTTPKSLLVIGSGAIGIEFASFYNELGAKVTVVEVMDRIL 210 ***********.********************************************************* PP TIGR01350 207 paldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleel 274 p++d+e+s +++k+++k+g++i+tn k +++k +d+v+v + + ++e +++++v++avG pn+e+l lcl|FitnessBrowser__azobra:AZOBR_RS14390 211 PVEDEEISAFARKQFEKQGMRIITNGKAGNLRKGADSVTVAVEANgKTEDITVDRVILAVGIAPNTENL 279 ***************************************877777789********************* PP TIGR01350 275 gleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavP 343 gle++ v++d+ g ik++++++t pg+yaiGDv+g + LAh+As+egv+a+e+iagk+++++d + +P lcl|FitnessBrowser__azobra:AZOBR_RS14390 280 GLENTKVQTDR-GHIKTNANCQTDEPGVYAIGDVTGAPWLAHKASHEGVIAVEHIAGKHPHALDVRNIP 347 ********776.********************************************************* PP TIGR01350 344 sviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgae 412 ++y++P++asvGlte++ake+g+ev+vg+fpf ngka+al+e+dG+vk+++d ktge+lGah+vgae lcl|FitnessBrowser__azobra:AZOBR_RS14390 348 GCTYSHPQIASVGLTEKKAKEAGYEVRVGRFPFIGNGKAIALGEADGMVKTVFDAKTGELLGAHMVGAE 416 ********************************************************************* PP TIGR01350 413 aseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461 ++eli+ ++a ++e+t++el++t++pHPtlsE+++e++l+a+g+aih+ lcl|FitnessBrowser__azobra:AZOBR_RS14390 417 VTELIQGYTVAKTMETTEQELMQTVFPHPTLSEMMHESVLDAYGRAIHF 465 ***********************************************96 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 8.44 // [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