Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate GFF4015 HP15_3955 bacterial transport system permease protein
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Marino:GFF4015 Length = 324 Score = 169 bits (428), Expect = 9e-47 Identities = 118/321 (36%), Positives = 175/321 (54%), Gaps = 17/321 (5%) Query: 19 IIIFWLSLFCYSAIPVS------GADATRALLPGHTPTLPEALVQNLRLPRSLVAVLIGA 72 ++I L+ F + + VS G T ++ G L + L+ LRLPR+L A G Sbjct: 10 LLILLLAGFLAALLSVSIGSTSIGFGDTLRVITGSGTELQQTLILELRLPRTLSAFATGG 69 Query: 73 SLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSLSFIAACGGGVS 132 LA+AG L+Q L NP+A P +LG++ GAA+ AL + L+ AG+ +S A G ++ Sbjct: 70 LLAVAGALMQVLLRNPLADPYVLGLSGGAAVG-ALLAMLAGA--AGFLISGSAFAGAMLA 126 Query: 133 WLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAY---GIFYWLAGGV 189 LLV G + ++L+L G+ ++A + ITL+L+ A G+ YWL G + Sbjct: 127 TLLVFGLAHG-SGSWTPSRLLLTGVVVAAGWGAM--ITLILSMTPASRLPGMLYWLMGDL 183 Query: 190 SHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLL 249 SHA W L ++V +V L LN+L A LGV++ L I ++ LL Sbjct: 184 SHAATP--WPGLIILVLVCLMVFPLGRALNVLARGSLQAAALGVSVRPLEWSIYLMASLL 241 Query: 250 VGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGD 309 A V++AG V F+GL++PH+ R G DQR +LP L G TL++LAD LAR + P Sbjct: 242 TAAAVTMAGSVGFVGLVIPHMLRLVLGNDQRLILPACALAGGTLLVLADTLARVVIAPEQ 301 Query: 310 LPAGAVLALIGSPCFVWLVRR 330 LP G + ALIG P F++L+ R Sbjct: 302 LPVGVITALIGVPTFLYLLYR 322 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: 312 Number of extensions: 21 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: 324 Length adjustment: 28 Effective length of query: 304 Effective length of database: 296 Effective search space: 89984 Effective search space used: 89984 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 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