Align butyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate BPHYT_RS28040 BPHYT_RS28040 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-13470 (379 letters) >FitnessBrowser__BFirm:BPHYT_RS28040 Length = 377 Score = 348 bits (894), Expect = e-100 Identities = 174/377 (46%), Positives = 253/377 (67%) Query: 1 MDFTLTNEQKFVEQMVSEFTENEVKPIAAEIDETERFPLETVEKFAKYGMMGMPFPVEYG 60 MD T+EQ+ + +F ++ P A + D + P E V + + G +GM P E+G Sbjct: 1 MDSFYTDEQRMIRDAARDFATEQLAPHAGQWDREAQLPAEVVRQMGELGFLGMIVPAEWG 60 Query: 61 GSGTDYLSYIIAVEGLAKSCTSSSTILSAHTSLCAAPIYDWGTEEQKQKYLVPLAKGEKL 120 GS TDY++Y +A+E +A C + +T++S H S+ PI ++GTE QK +YL LA G ++ Sbjct: 61 GSYTDYVAYALALEEIAAGCAACATLMSVHNSVGCGPILNFGTEAQKDRYLQDLATGRRI 120 Query: 121 GAFGLTEPNAGTDAAGQQTTAVLEGDHYVLNGQKIFITNGAYADTFVIFAMTDRSKGTRG 180 GAF LTEP AG++A +T AVL ++LNG K F+TNG+ AD ++FA+TD +G RG Sbjct: 121 GAFCLTEPQAGSEANNLRTRAVLRDGKWILNGSKQFVTNGSRADLAIVFAVTDPDRGKRG 180 Query: 181 ITAFIVEKDFPGFSIGKSEDKLGIRASSTTELIFENCIVPKENMLGKEGKGFTVAMHTLD 240 +TAFIV D PGF++GK E KLGIRAS T + ++C VP+ N+LG+ G+G +A+ L+ Sbjct: 181 LTAFIVPTDTPGFNVGKPEHKLGIRASDTCPISLDDCAVPEANLLGEPGEGLRIALSNLE 240 Query: 241 GGRIGIAAQALGLAEGALAEALNYMKERKQFGKALYKFQGLAWMVAELDTKIEAVKQLVY 300 GGRIGIAAQA+G+A A A Y ER QFGKAL + Q +A M+A++ T++ A + LV+ Sbjct: 241 GGRIGIAAQAVGIARAAFDAARLYANERIQFGKALKEHQTIANMLADMATRLNAARLLVH 300 Query: 301 KAAVNKQMGLPYSVEAARAKLAAATVAMETTTKVVQIFGGYGFTKDYPVERMMRDAKITE 360 AA + G P EA++AKL A+ +A E + +QI GGYG+ +DY VER RDA+IT+ Sbjct: 301 HAARLRTAGKPCLSEASQAKLFASELAEEICSNAIQIHGGYGYLEDYAVERHYRDARITQ 360 Query: 361 IYEGTSQVQKMVISANL 377 IYEGTS+VQ+M+I+ ++ Sbjct: 361 IYEGTSEVQRMLIARHV 377 Lambda K H 0.316 0.132 0.372 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: 288 Number of extensions: 3 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: 379 Length of database: 377 Length adjustment: 30 Effective length of query: 349 Effective length of database: 347 Effective search space: 121103 Effective search space used: 121103 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