Align Enoyl-CoA isomerase/hydratase fer4; Fe-regulated protein 4; Ferrichrome A biosynthesis protein fer4; EC 4.2.1.17 (characterized)
to candidate WP_035704417.1 BA79_RS18210 enoyl-CoA hydratase
Query= SwissProt::Q4PEN0 (274 letters) >NCBI__GCF_000691145.1:WP_035704417.1 Length = 260 Score = 202 bits (513), Expect = 8e-57 Identities = 109/252 (43%), Positives = 157/252 (62%), Gaps = 8/252 (3%) Query: 23 LVLDRPEARNAISRSLLQDVLQCLQVLVCKITQPKQDEPLPRVLILRANGPCFCAGADLK 82 + L+RP NA+S ++L+++ Q +Q + K D + +L+ A FCAGADLK Sbjct: 17 MTLNRPAQANALSAAMLEEINQTIQEI-------KHDANIRCLLMTGAGAKVFCAGADLK 69 Query: 83 ERREMSEAEVIEFLQDLRHMLEQVEKLPIPTLAAIDGPALGGGLELALACDFRIAAETVS 142 ERR M+E E E + ++ +E LP+P +A I+G ALGGGLELALACD RIA + Sbjct: 70 ERRLMTEQEAKEAVLTIQQTFTDIESLPVPVIAVINGHALGGGLELALACDLRIARAGAA 129 Query: 143 KIGFPEVKLGIIPGAGGTQRAPRIIGMQRAKELIYTGTQLNATQAKDLGLIDHVAPGSTC 202 +G PE L I+PGAGGTQR PR+IG +AKE+I+TGT L A +A +GLI+ ++ + Sbjct: 130 -LGLPETGLAILPGAGGTQRLPRLIGPGKAKEMIFTGTSLRAEEAVQIGLIERISTADSL 188 Query: 203 LKLCQELAQQMMPSAPLALRAAKMAISMGANVELARGLDLEWACYEPLLESKDRREALDA 262 + LA+Q+ + P+AL+ AK AI + +L GL E+ Y L+ ++DR E L A Sbjct: 189 MNDAITLAKQITKNGPIALKEAKQAIQSSLDHDLQTGLTKEYEAYLRLIHTEDRLEGLKA 248 Query: 263 FQQKRKPIFTGK 274 FQ+KR P + GK Sbjct: 249 FQEKRTPHYRGK 260 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: 169 Number of extensions: 8 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: 260 Length adjustment: 25 Effective length of query: 249 Effective length of database: 235 Effective search space: 58515 Effective search space used: 58515 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