Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate GFF3534 PS417_18100 iron ABC transporter
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__WCS417:GFF3534 Length = 329 Score = 241 bits (616), Expect = 1e-68 Identities = 133/312 (42%), Positives = 195/312 (62%), Gaps = 3/312 (0%) Query: 21 IFWLSLFCYSAIPVSGADATRALL-PGHTPTLPEALVQNLRLPRSLVAVLIGASLALAGT 79 +FWLSL+ +S ++ DA L+ G +V LR+PR+L A L+GA L LAG Sbjct: 17 LFWLSLYSWSPFTITATDAWNGLVHQGRVGGNMAYIVAQLRVPRALCAALVGACLGLAGA 76 Query: 80 LLQTLTHNPMASPSLLGINSGAALAMALTSA-LSPTPIAGYSLSFIAACGGGVSWLLVMT 138 L+Q +T N +ASPSL G+ +GAAL +AL S L P AG +L + GG ++W+ V + Sbjct: 77 LMQGITRNRLASPSLFGVTAGAALGLALFSTGLVALPFAGGAL-LMTCLGGALAWITVFS 135 Query: 139 AGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYGIFYWLAGGVSHARWQDVW 198 GG + T + +L+LAG+A++A C LTR+T++L E A + WLAG +++A V Sbjct: 136 LGGAWSPTTAQGRLVLAGVAVAALCAALTRLTVILVEAQAQSVLNWLAGSLANAGAAQVQ 195 Query: 199 QLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAG 258 L P + L A +LNL+NL + A +LGV + LRL + + LLLVGA V G Sbjct: 196 LLWPCTLIGGLWALWCAPRLNLINLGEDAARSLGVGIASLRLQVFIASLLLVGASVCAVG 255 Query: 259 PVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGDLPAGAVLAL 318 P+ F+GL+ P++ R + G D R ++P+S LGA ++L AD+L+RA+AFP + PAG V AL Sbjct: 256 PIGFVGLIAPNILRQFLGNDYRWLIPLSAALGAVIVLAADLLSRAVAFPVETPAGVVTAL 315 Query: 319 IGSPCFVWLVRR 330 IG+P F++L RR Sbjct: 316 IGAPFFLFLARR 327 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: 338 Number of extensions: 15 Number of successful extensions: 4 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: 329 Length adjustment: 28 Effective length of query: 304 Effective length of database: 301 Effective search space: 91504 Effective search space used: 91504 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