Align Enoyl-CoA isomerase/hydratase fer4; Fe-regulated protein 4; Ferrichrome A biosynthesis protein fer4; EC 4.2.1.17 (characterized)
to candidate WP_015798784.1 AFER_RS07075 enoyl-CoA hydratase/isomerase family protein
Query= SwissProt::Q4PEN0 (274 letters) >NCBI__GCF_000023265.1:WP_015798784.1 Length = 262 Score = 119 bits (299), Expect = 5e-32 Identities = 83/249 (33%), Positives = 135/249 (54%), Gaps = 23/249 (9%) Query: 23 LVLDRPEARNAISRSLLQDVLQCLQVLVCKITQPKQDEPLPRVLILRANGPC-FCAGADL 81 L +DRPEA NA+S L+ +V + L L P +L++ + P F AGAD+ Sbjct: 19 LAIDRPEAANALSLELVNEVHRALDDL----------RDAPHLLVVTSAVPGRFVAGADI 68 Query: 82 KERREMSEAEVIEFLQDLRHMLEQVEKLPIPTLAAIDGPALGGGLELALACDFRIAAETV 141 E E + + + + +++ + PT+AAIDGPA+GGGLELA+ACD R+A+ T Sbjct: 69 AELLARGEEDALRAINV--DLFDRIARWRWPTVAAIDGPAVGGGLELAMACDLRVAS-TR 125 Query: 142 SKIGFPEVKLGIIPGAGGTQRAPRIIGMQRAKELIYTGTQLNATQAKDLGLIDHV--APG 199 S PEV LGI+ GAG +R ++G+ RA+ ++ G ++ A +A + GL+D V P Sbjct: 126 SWFRQPEVGLGIVAGAGAHRRLVDLVGLGRARRMLLAGVRVEAAEAYEWGLVDVVDDDPV 185 Query: 200 STCLKLCQELAQQMMPSAPLALRAAKMAISMGANVELARGLDLEWACYEPLLESKDRREA 259 + + L + +A Q +LRA + + A+VE ++ L ES ++R Sbjct: 186 GSAVALARSMASQ-------SLRALEFTKLVLASVERPSTRTVDILAQAVLFESDEKRAR 238 Query: 260 LDAFQQKRK 268 + AF ++R+ Sbjct: 239 MGAFLEQRQ 247 Lambda K H 0.320 0.136 0.394 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: 153 Number of extensions: 7 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: 274 Length of database: 262 Length adjustment: 25 Effective length of query: 249 Effective length of database: 237 Effective search space: 59013 Effective search space used: 59013 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 (21.8 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