Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011159873.1 TX73_RS22125 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000195775.1:WP_011159873.1 Length = 263 Score = 161 bits (408), Expect = 1e-44 Identities = 101/248 (40%), Positives = 137/248 (55%), Gaps = 6/248 (2%) Query: 4 ENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTG-SEKAFA 62 E I +E R V L+TLNRP+ LNAL+ AL+D L L + D+A+ A+++TG SE+AF+ Sbjct: 3 ELIPIELRDGVALLTLNRPEKLNALSYALIDRLMQRLDAIEVDNAVRAVILTGASERAFS 62 Query: 63 AGADIGMMSTYTYM--DVYKGDYITRNWET---VRSIRKPIIAAVAGFALGGGCELAMMC 117 AGADI S D D++ R + S KP+IAAV G A GGGCE+ Sbjct: 63 AGADIAEFSASVARGADHAVRDFVRRGQTMTARLESFNKPVIAAVNGLAYGGGCEITEAV 122 Query: 118 DIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLV 177 + A+D A+F +PEIKL + P GGTQRLPR + +A++L LT A A GLV Sbjct: 123 HLAVASDRARFAKPEIKLAMPPTFGGTQRLPRLAGRKRALELLLTGEPFSPAHALAIGLV 182 Query: 178 SRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFAT 237 +RV+P L+ A A A I P AV V + R ++ EG+ ER F L Sbjct: 183 NRVVPHEELIGAADALARQIIRHPPGAVAAVITATTRGLNLSIDEGLLVERAQFAMLAGR 242 Query: 238 EDQKEGMA 245 E+ G+A Sbjct: 243 EELSHGLA 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: 163 Number of extensions: 11 Number of successful extensions: 3 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: 263 Length adjustment: 25 Effective length of query: 233 Effective length of database: 238 Effective search space: 55454 Effective search space used: 55454 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