Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_011426504.1 RHE_RS16730 iron ABC transporter permease
Query= CharProtDB::CH_004160 (318 letters) >NCBI__GCF_000092045.1:WP_011426504.1 Length = 370 Score = 196 bits (498), Expect = 7e-55 Identities = 108/285 (37%), Positives = 165/285 (57%), Gaps = 12/285 (4%) Query: 46 VLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPS 105 ++ + RLPR +L +GA+LAV+G ++QG+ RNPLA P ++GV+ AS +V ++L Sbjct: 81 IIFDIRLPRTILGFLIGASLAVSGTVMQGLFRNPLADPGLVGVSSGASFGAVAMIVLGGG 140 Query: 106 LP--------VMVLPLLAFAGGMAGLILLKMLAKTHQPMKLA---LTGVALSACWASLTD 154 L + LP AF GG+A +LL +A H +A L G+AL A +LT Sbjct: 141 LAAPFEAPLGIYALPAAAFGGGLATTLLLYRIATRHGQTSVATMLLAGIALGALALALTG 200 Query: 155 YLM-LSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDAR 213 L+ ++ Q + + W GSL G W+ + A P+++L R L+ + LG+A Sbjct: 201 LLIYMANDQQLRDLTFWSMGSLAGATWTKIAAAGPIVLLSFTALPFMARGLNAITLGEAA 260 Query: 214 ATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSA 273 A +GV V + A++ A T VA G I F+G+VVPH++R G HR LLP +A Sbjct: 261 AFHMGVPVQRLKNVAIVGVAAATGASVAVSGGIGFVGIVVPHILRMAIGPDHRFLLPAAA 320 Query: 274 LTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 L G LL+ AD+LAR + P ELP+G++TA +G P+F+W+L++ R Sbjct: 321 LLGGSLLIFADVLARTLVAPAELPIGIITAAVGGPFFLWILLKQR 365 Lambda K H 0.330 0.142 0.447 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: 281 Number of extensions: 19 Number of successful extensions: 4 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: 318 Length of database: 370 Length adjustment: 29 Effective length of query: 289 Effective length of database: 341 Effective search space: 98549 Effective search space used: 98549 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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