Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate GFF3533 PS417_18095 iron-dicitrate transporter subunit FecD
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__WCS417:GFF3533 Length = 322 Score = 174 bits (441), Expect = 3e-48 Identities = 105/276 (38%), Positives = 148/276 (53%), Gaps = 6/276 (2%) Query: 56 VQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSP-T 114 V N RLPRSL+A+L G + LAG ++Q + NP+ASP +LG+ GA LA+ + P Sbjct: 49 VWNHRLPRSLIAILAGCAFGLAGAIVQGVIRNPLASPEILGVTQGAGLALTVAIISWPHM 108 Query: 115 PIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLA 174 PIA L GG L + AG F + L+G+A++ +T +L Sbjct: 109 PIAWLPLVACLGGAGGALLLALYNAGVSFSGV----RFALSGVAIAVTLSSVTEFLILSH 164 Query: 175 EDHAYGIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVN 234 L G + W V +LP +V +PV L LA LNL+ L D AH+LG Sbjct: 165 PLDINTALLALTGSLWSRNWHHVALVLPFLVL-IPVGLCLAKPLNLIALGDEAAHSLGTA 223 Query: 235 LTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLM 294 L R R + ++L V V GP+ FIGL+ PH+AR G + +LP +ML GA L+ Sbjct: 224 LGRTRWLAMACAVVLTSLGVGVIGPIGFIGLVAPHMARRLVGGHHQYLLPAAMLTGALLL 283 Query: 295 LLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRR 330 +LAD L R L P ++PAG + A+IG+P F+WL+ R Sbjct: 284 VLADTLGRTLIAPSEIPAGVLTAVIGAPYFLWLLAR 319 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: 358 Number of extensions: 15 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: 322 Length adjustment: 28 Effective length of query: 304 Effective length of database: 294 Effective search space: 89376 Effective search space used: 89376 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: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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