Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate GFF3640 HP15_3582 transport system permease protein
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Marino:GFF3640 Length = 326 Score = 169 bits (428), Expect = 9e-47 Identities = 102/313 (32%), Positives = 173/313 (55%), Gaps = 10/313 (3%) Query: 24 LSLFCYSAIPVSGADATR----ALLPGHTPTLPEALVQNLRLPRSLVAVLIGASLALAGT 79 L+L + A+ + + T A L G T + +V N+RLPR A+L+GA+LA AG Sbjct: 12 LTLLAFGAVMIGPYNLTPGQTLAALLGQGDTQAQIVVWNIRLPRVAAALLVGAALAAAGA 71 Query: 80 LLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSLSFIAACGGGVSWLLVMTA 139 Q L NP+ SP +LG+++GA L A+ P+A S A GG ++ V+ Sbjct: 72 SYQALFRNPLVSPDILGVSAGAGLG-AVAGIFLSLPVAAIQAS--AFVGGMLAVGFVILV 128 Query: 140 GGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAE--DHAYGIFYWLAGGVSHARWQDV 197 R+T L+L G+ + A T + ++A+ D I +WL G ++ +D+ Sbjct: 129 ASLVRNTDRTLTLVLIGVVIGALAGAATSLLKVMADPYDQLPAITFWLLGSLAATTTEDI 188 Query: 198 WQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSVA 257 LP+V+ + + LL ++N+L+L D A LG+++++ R ++ + L+ + ++A Sbjct: 189 LPTLPMVLIGLVPLALLRWRINVLSLGDEEARALGIDVSKTRFLVIVAATLITASVTALA 248 Query: 258 GPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGDLPAGAVLA 317 G V ++GL++PH+AR G +LP S+L+GA +L+ D LAR +A ++P G + A Sbjct: 249 GVVGWVGLVIPHIARMLVGPGFGRLLPTSVLIGAGYLLVVDTLARTMA-QVEVPLGILTA 307 Query: 318 LIGSPCFVWLVRR 330 +IG+P FVWL+ R Sbjct: 308 VIGAPFFVWLLAR 320 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: 332 Number of extensions: 21 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: 326 Length adjustment: 28 Effective length of query: 304 Effective length of database: 298 Effective search space: 90592 Effective search space used: 90592 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