Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate AO356_16120 AO356_16120 ABC transporter permease
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_16120 Length = 345 Score = 173 bits (439), Expect = 5e-48 Identities = 131/345 (37%), Positives = 185/345 (53%), Gaps = 18/345 (5%) Query: 1 MTAIKHPVLLW-GLPVAALIIIFWLSLFCYSAIPVSGADATRALL-----PGHTPTLPEA 54 MT++ P L+ GL + L+ WLSL + + D RA L P L +A Sbjct: 1 MTSLVKPRTLFIGLGLLCLLAT-WLSL-ALGPVSLPLLDTLRAALRLLGLPVAADGLEQA 58 Query: 55 --LVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALT---- 108 ++ +RLPR+L+ + +G LAL+G +Q L NP+A P L+G++SGAAL A+ Sbjct: 59 ELILGQIRLPRTLLGLAVGGVLALSGVAMQGLFRNPLADPGLVGVSSGAALGAAVAIVGG 118 Query: 109 SALSPTPIA--GYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGL 166 SAL P A Y LS A GG LV G TH ++LAGIAL+A Sbjct: 119 SALGGLPEAFGPYVLSLCAFLGGLGVTALVYRLGRRNGQTHVAT-MLLAGIALTALSGSA 177 Query: 167 TRITLLLAEDHAYG-IFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSD 225 + LA+D + +W G ++ A + +W LL V + A +LN L L + Sbjct: 178 VGLFTYLADDATLRTLTFWNLGSLNGASYARLWPLLLVSAGVALWLPRRARELNALLLGE 237 Query: 226 STAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPV 285 S A LGVN+ L+ + L VGA V+ AG + F+GL+VPHL R AG D R +LP Sbjct: 238 SEAAHLGVNVEALKRELVFCTALGVGAAVAAAGMIGFVGLVVPHLVRLVAGPDHRVLLPA 297 Query: 286 SMLLGATLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRR 330 S+L GA+L+LLAD++AR P +LP G V A IG+P F++L+ R Sbjct: 298 SVLAGASLLLLADLVARLALAPAELPIGIVTAFIGAPFFLYLLVR 342 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: 30 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: 345 Length adjustment: 28 Effective length of query: 304 Effective length of database: 317 Effective search space: 96368 Effective search space used: 96368 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