Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate WP_254914180.1 BZY95_RS08605 iron ABC transporter permease
Query= SwissProt::P15030 (332 letters) >NCBI__GCF_002151265.1:WP_254914180.1 Length = 339 Score = 178 bits (452), Expect = 1e-49 Identities = 115/315 (36%), Positives = 179/315 (56%), Gaps = 4/315 (1%) Query: 17 ALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLVAVLIGASLAL 76 AL+++ L+ + A V A A A+ G + +V +LRLPR+LV +++G +L + Sbjct: 24 ALLVLVCLASLLWGAGDVGPARAWAAIT-GQGDAEAQFVVGSLRLPRTLVGLVVGLALGV 82 Query: 77 AGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSLSFIAACGGGVSWLLV 136 AG LLQ +T NP+A P LLG+++GAA A+A+ L T A +A G V L V Sbjct: 83 AGALLQAVTRNPLAEPGLLGVSAGAAFAVAVALVLGAT--ATTMRIGVAQLGAMVGCLCV 140 Query: 137 MTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYGIFYWLAGGVSHARWQD 196 + +D +L+LAG AL+ + LT + LL + A I +W+ G ++ R + Sbjct: 141 LGVARVSGAGNDPVRLVLAGAALTGLLLSLTSL-LLFDQRAADEIRFWIVGSLAGRRLEH 199 Query: 197 VWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSV 256 + +LP ++ A +VL +A L L+L + A LG +RL++ + V LLVGA + Sbjct: 200 LLAILPSLLLAGAIVLAVARPLAALSLGERVASGLGHRPGLIRLLVIVAVALLVGAATAT 259 Query: 257 AGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGDLPAGAVL 316 AGP+AF+GL+VP AR AG D R L + + LG +++ AD+++R L P +LP G + Sbjct: 260 AGPIAFVGLVVPFAARALAGPDIRRTLWLCLPLGPLMVITADIVSRLLVAPSELPLGVLT 319 Query: 317 ALIGSPCFVWLVRRR 331 AL G+P V +VR R Sbjct: 320 ALCGAPVLVAVVRAR 334 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: 309 Number of extensions: 11 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: 339 Length adjustment: 28 Effective length of query: 304 Effective length of database: 311 Effective search space: 94544 Effective search space used: 94544 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