Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate WP_086511917.1 BZY95_RS21415 iron ABC transporter permease
Query= SwissProt::P15030 (332 letters) >NCBI__GCF_002151265.1:WP_086511917.1 Length = 352 Score = 176 bits (447), Expect = 6e-49 Identities = 116/321 (36%), Positives = 173/321 (53%), Gaps = 4/321 (1%) Query: 15 VAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLVAVLIGASL 74 V AL+ + L +A+ S + R LL L + LRLPR ++A L+GA L Sbjct: 28 VLALLALAVLVALLAAAMSGSVGLSPRVLLGEWPSPLAWQVWWQLRLPRLILAALVGAML 87 Query: 75 ALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSL--SFIAACGGGVS 132 A +G +Q L NP+A P+LLG+ SGA LA+AL L L F+A G + Sbjct: 88 AGSGAAMQGLFRNPLADPTLLGLASGAGLAVALWIVLLDGAAGSLGLYGQFLAGFLGALG 147 Query: 133 WLLVMTAGGGFRHTHDRN-KLILAGIALSAFCMGLTRITLLLAEDHAYG-IFYWLAGGVS 190 +++ A G +H + L+LAG+A++ + + +A D + W G +S Sbjct: 148 VCVLVFALGQRQHGQEALFTLLLAGLAINTLAGAMGGVMAFIASDEQLRQLSLWGMGSLS 207 Query: 191 HARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLV 250 HA W L + A+ +L A L+LL L + TAH G++ RL+ + + L V Sbjct: 208 HALWSATLGALVGIPPALWWLLRCARGLDLLQLGELTAHGAGLDAPRLKRHVVVATALGV 267 Query: 251 GACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGDL 310 G CV++AG + F+GLLVPH R W G R +LP SML GA L+++AD LAR LA P ++ Sbjct: 268 GLCVALAGIIGFLGLLVPHCLRLWLGPGHRLLLPASMLGGALLLIVADTLARTLASPAEV 327 Query: 311 PAGAVLALIGSPCFVWLVRRR 331 P G + +L+G P F+WL+ +R Sbjct: 328 PVGLLTSLLGGPYFLWLLLKR 348 Lambda K H 0.327 0.140 0.436 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: 400 Number of extensions: 26 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: 332 Length of database: 352 Length adjustment: 29 Effective length of query: 303 Effective length of database: 323 Effective search space: 97869 Effective search space used: 97869 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 (21.7 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