Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate Ga0059261_0839 Ga0059261_0839 Acyl-CoA dehydrogenases
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__Korea:Ga0059261_0839 Length = 393 Score = 263 bits (671), Expect = 8e-75 Identities = 156/396 (39%), Positives = 219/396 (55%), Gaps = 22/396 (5%) Query: 12 FRDEVRQFFKDNVPAKTRQKLIE-------GRHNTK--EEMVEWYRILNKKGWAVTHWPK 62 FR E R + ++N PA R+ + GR + + W + +GW V WPK Sbjct: 7 FRAETRAWLEENCPASMREPVRSEKDTVWGGRDQSALTPDQKTWMDRMAARGWTVPDWPK 66 Query: 63 EYGGTGWSSVQHYIFNEELQAAPAPQPLA-FGVSMVGPVIYTFGSEEQKKRFLPRIANVD 121 YGG G S + I EE++A PL+ FG+SM+GP + +G+EEQK LPRIA + Sbjct: 67 AYGGGGLSPAESKILREEMRALGCRNPLSSFGISMLGPALLKYGNEEQKLEHLPRIARGE 126 Query: 122 DWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAKK 181 WCQG+SEP +GSDLA+L T AE GD +++NGQK WT+ A ADWIFCL RTD + K Sbjct: 127 IRWCQGYSEPNAGSDLAALATSAEDMGDHYLVNGQKVWTSYADKADWIFCLVRTDKSV-K 185 Query: 182 QEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFLL 241 Q GISF+L DM + G++ +PI I G E FFDDV+VP NLVG+ NKGWD AK+LL Sbjct: 186 QAGISFLLFDMASPGVSTKPILLISGYSPFCETFFDDVKVPKANLVGELNKGWDVAKYLL 245 Query: 242 GNERTGIARVGMS-KERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQL 300 G+ER I+ +G+ I A++ G + DP R ++A E+ +A Sbjct: 246 GHEREMISGMGLGLSSGGTLIGNAVARMGLGDDGRLADPLLRGQIALHEVRARAFAAMSE 305 Query: 301 RVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSNETMD 360 R + DE K G+ P S++K G+E+ +A EL M G + ++ ++ Sbjct: 306 RFL-DELKTGRAHP-AQPSMMKYYGTELNKARHELEMAAGGSDSLEWESAASNNGAAPRA 363 Query: 361 WTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 W + SI GG++E+Q NII K +L L Sbjct: 364 W--------LRTKANSIEGGTSEVQLNIIAKRILEL 391 Lambda K H 0.317 0.135 0.411 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: 441 Number of extensions: 24 Number of successful extensions: 5 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: 396 Length of database: 393 Length adjustment: 31 Effective length of query: 365 Effective length of database: 362 Effective search space: 132130 Effective search space used: 132130 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: 50 (23.9 bits)
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