Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_017601334.1 D471_RS0126060 iron chelate uptake ABC transporter family permease subunit
Query= CharProtDB::CH_004160 (318 letters) >NCBI__GCF_000341125.1:WP_017601334.1 Length = 366 Score = 196 bits (499), Expect = 5e-55 Identities = 119/318 (37%), Positives = 171/318 (53%), Gaps = 6/318 (1%) Query: 5 LVIFITLALAGCALLSLHMGVIPVPWRALLTDWQAGHEHYYVLMEYRLPRLLLALFVGAA 64 L + + LA L M W+AL A E ++ E RLPR L L G + Sbjct: 47 LAVLLGLAALSSVLFGARMLDPATVWQAL--SHAASDEANIIVNEIRLPRTALGLLAGLS 104 Query: 65 LAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLLAFAGGMAGLI 124 L + G L+QG RNPL P ILGV A+ V + + + LAF G A + Sbjct: 105 LGLGGALMQGHTRNPLGDPSILGVTFGAAFVVVLGIHFLAIDDLRTQAWLAFVGAGAAAV 164 Query: 125 LLKMLAKTH----QPMKLALTGVALSACWASLTDYLMLSRPQDVNNALLWLTGSLWGRDW 180 ++ ++ P+ LAL G A+S SL ++L ++N W GSL GRD Sbjct: 165 VVYLIGSVPGRGPTPITLALAGTAVSWLMYSLVSGIVLLDQDTMDNFRFWRVGSLTGRDP 224 Query: 181 SFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAMTSTGV 240 S + +P +++ + L+L+ R L+ LALGD A LG + R LL +T V Sbjct: 225 SVIGQMLPFVVVGVVLALANTRALNALALGDDTARALGFRIGWARATGLLAITLLTGVTV 284 Query: 241 AACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLELPVGV 300 AACGPI+F+GL+VPH+ R++ G HR LLP S L GA+LL+ AD+L R + PP EL VGV Sbjct: 285 AACGPIAFVGLIVPHLARAMVGSDHRWLLPYSGLLGAILLMAADVLGRFLAPPGELQVGV 344 Query: 301 LTAIIGAPWFVWLLVRMR 318 + AI+GAP+F++++ R + Sbjct: 345 VLAILGAPFFIYVVRRRK 362 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: 287 Number of extensions: 8 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: 318 Length of database: 366 Length adjustment: 29 Effective length of query: 289 Effective length of database: 337 Effective search space: 97393 Effective search space used: 97393 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