Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate WP_013404169.1 CALHY_RS11790 iron ABC transporter permease
Query= SwissProt::P15030 (332 letters) >NCBI__GCF_000166355.1:WP_013404169.1 Length = 358 Score = 142 bits (357), Expect = 2e-38 Identities = 102/329 (31%), Positives = 164/329 (49%), Gaps = 16/329 (4%) Query: 15 VAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLVAVLIGASL 74 VA L I+ + + +S +D +A L G + +V ++RL R + A+L G L Sbjct: 29 VAILTILLSIYAISSGSSDLSFSDVLKAFL-GKSDERTALIVFDIRLVRVVAAILAGIGL 87 Query: 75 ALAGTLLQTLTHNPMASPSLLGINSGAALAMAL---------TSALSPTPIAGYSLSFIA 125 A+ G +Q+L HNP+ASP LGI+ GAA A+ S+ + + S + Sbjct: 88 AIGGAAIQSLFHNPLASPFTLGISQGAAFGAAIGIIVLGGGVASSAASDSVTILHPSRVV 147 Query: 126 AC---GGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAED-HAYGI 181 AC G +S +V+ R + + ++L+G+ALS+ T I A D + Sbjct: 148 ACAFLGSMLSTAVVLALAQIKRFSPEA--VVLSGVALSSLFSAATTIIQYFASDVKIAAL 205 Query: 182 FYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLV 241 +W G + A W DV + V+ A L + N + + A +LGVN+ + R Sbjct: 206 VFWTFGDIGRATWDDVKIMAVFVILAWLYFLANSWNYNAIASGEDVAKSLGVNVEKARFF 265 Query: 242 INMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLA 301 ++ + VS G + FI L+ PH+AR + G DQR + S L+GA L+LL+D +A Sbjct: 266 GILVSSFITSVIVSFLGIIGFICLVAPHIARRFIGNDQRFLTLASGLVGAFLLLLSDTVA 325 Query: 302 RALAFPGDLPAGAVLALIGSPCFVWLVRR 330 R + P LP GAV + +G+P F++L+ R Sbjct: 326 RLIVSPVVLPVGAVTSFLGAPLFMYLLIR 354 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: 244 Number of extensions: 14 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: 332 Length of database: 358 Length adjustment: 29 Effective length of query: 303 Effective length of database: 329 Effective search space: 99687 Effective search space used: 99687 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 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