Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate PP_3725 PP_3725 putative Acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >FitnessBrowser__Putida:PP_3725 Length = 386 Score = 196 bits (497), Expect = 1e-54 Identities = 134/387 (34%), Positives = 199/387 (51%), Gaps = 12/387 (3%) Query: 1 MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMG----RMGLFGLPFP 56 M+ +LT E E L V F + P E+ ++ G + P Sbjct: 1 MNFQLTQEQEMLVEAVRSFVAKELLPHEEAVDRADAVSPELAAQIRGKAIAAGFYAFNMP 60 Query: 57 EEYGGMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCS 116 EE GG G DYL+ + EL++V ++ + + I + D Q ++L Sbjct: 61 EEVGGGGLDYLSQALIERELSKVSWALHVFVAR-----PSKILMACKDEQINDYLLPCVQ 115 Query: 117 GEILGAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSG-TDITGLVTVTAV 175 GE + F LTEP GSDA A +T R +++VING+K FI+++G D + VT Sbjct: 116 GEKVDCFALTEPGAGSDANAIKT--RAVRQGDDFVINGSKHFISHAGHADFAIVFAVTDT 173 Query: 176 TGRKPDGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGR 235 + +++++V GTPG T+ V T EL F D RVPA+ +LGE G+ Sbjct: 174 YEHNGRKRNAVTALLVDRGTPGMTIRRGPKCVSNRGYHTYELFFDDCRVPASKVLGEVGK 233 Query: 236 GYAQFLRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEM 295 G+ L GR+ ++A G AQ +D S+++A +R FG+ IG+YQ + FK+ADM Sbjct: 234 GWEVANAWLTAGRVMVAANCVGQAQRALDLSLQWAADRKQFGQAIGSYQGVSFKLADMAT 293 Query: 296 KAHMARVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVA 355 + A + A ++ G EA +AKL++S V A EA QI GG G M+E PV Sbjct: 294 QIRAAEMLTLHTAWKMDQGNMTDGEAGMAKLFASEVLGKVADEAVQIFGGMGLMDEGPVE 353 Query: 356 RMWRDSKILEIGEGTSEVQRMLIAREL 382 R+WR+++I I EGTSE+QR +IAREL Sbjct: 354 RIWRNARIERIWEGTSEIQRHIIAREL 380 Lambda K H 0.318 0.136 0.402 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: 366 Number of extensions: 21 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: 386 Length of database: 386 Length adjustment: 30 Effective length of query: 356 Effective length of database: 356 Effective search space: 126736 Effective search space used: 126736 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: 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