Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_083709731.1 BW971_RS10800 crotonase/enoyl-CoA hydratase family protein
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_900156495.1:WP_083709731.1 Length = 266 Score = 122 bits (305), Expect = 1e-32 Identities = 86/246 (34%), Positives = 122/246 (49%), Gaps = 4/246 (1%) Query: 4 ENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAA 63 E + VE G V + +NRP NA++ + L A R FD D V+ G F A Sbjct: 8 ETVTVERHGPVTAIGINRPSVRNAVDRPTAEALAEAFRTFDDDPNASVAVLFGHGDTFCA 67 Query: 64 GADIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFAA 123 GAD+ ++T T V D T + KP+IAAV+G+A+ GG ELA+ D+ + Sbjct: 68 GADLTAVATGTPNRVAP-DGDGPMGPTRLRLGKPVIAAVSGYAVAGGLELAVWADLRVCS 126 Query: 124 DTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPA 183 D A FG + G+ GGT RLPR + + +A+DL LT R +DA EA GL RV+P Sbjct: 127 DDAVFGVFCRRWGVPLIDGGTVRLPRLIGEGRALDLILTGRAVDADEALSMGLADRVVPR 186 Query: 184 ASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFA-TEDQKE 242 + +D AIA IA FP + + S + T + + E H + + + D Sbjct: 187 GTALDAAIALGEQIAGFPQTCLRHDRLSTMDSAGLTEEQALAVEHE--HGMISLSADAVS 244 Query: 243 GMAAFV 248 G AFV Sbjct: 245 GATAFV 250 Lambda K H 0.321 0.134 0.380 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: 161 Number of extensions: 6 Number of successful extensions: 2 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: 258 Length of database: 266 Length adjustment: 25 Effective length of query: 233 Effective length of database: 241 Effective search space: 56153 Effective search space used: 56153 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 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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