Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate Ga0059261_0623 Ga0059261_0623 ABC-type Fe3+-siderophore transport system, permease component
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Korea:Ga0059261_0623 Length = 331 Score = 139 bits (351), Expect = 8e-38 Identities = 97/297 (32%), Positives = 146/297 (49%), Gaps = 6/297 (2%) Query: 38 DATRALLPGHTPTLPEALVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGI 97 D A L G + +V LR+PR L+ +L+GA L LAG LQ NP+A PS+LG Sbjct: 35 DRVIAALLGKGDMIASTIVLELRMPRMLLGLLVGAMLGLAGAALQGFLRNPLAEPSVLGA 94 Query: 98 NSGAALAMALTSALSPTPIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGI 157 ++ AA + + L +A V+ +L+ G + LILAGI Sbjct: 95 SNAAAFGAVIALYFGIAELHPALLPLLAIAAAMVALVLLFGLSG---QSESALTLILAGI 151 Query: 158 ALSAFCMGLTRITLLLAEDH--AYGIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLA 215 A++ + L L+ + A I WL G + + Q VW LP +V ++L A Sbjct: 152 AIATLAGAGISLALNLSPNPFAAMEIMNWLLGSLENRSSQHVWIALPCIVVGAALLLWDA 211 Query: 216 NQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWA 275 L+ L L + A LG+NL +R + + V + VG V+V+G + FIGL+VPH+ R + Sbjct: 212 RALDALTLGEDGARALGINLRAVRWRLLVGVAIGVGGAVAVSGSIGFIGLIVPHIIRPFT 271 Query: 276 GFDQRNVLPVSMLLGATLMLLADVLARALAFPGDLPAGAVLALIGSPCF-VWLVRRR 331 +L S + GA L+ L+D+ R + +L G V A +G P F V L+R R Sbjct: 272 DRSPSAILWPSAIGGALLLTLSDLGVRMIPATNELKLGVVTAFLGIPVFLVHLLRER 328 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: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 332 Length of database: 331 Length adjustment: 28 Effective length of query: 304 Effective length of database: 303 Effective search space: 92112 Effective search space used: 92112 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