Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate 18312 b4288 KpLE2 phage-like element; iron-dicitrate transporter subunit (NCBI)
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Keio:18312 Length = 318 Score = 178 bits (452), Expect = 1e-49 Identities = 105/277 (37%), Positives = 157/277 (56%), Gaps = 7/277 (2%) Query: 55 LVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPT 114 ++ RLPR L+A+ +GA+LA+AG L+Q + NP+ASP +LG+N A+LA L P+ Sbjct: 46 VLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPS 105 Query: 115 -PIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLL 173 P+ L A GG++ L+++ TH KL L G+ALSA LT +L Sbjct: 106 LPVMVLPL---LAFAGGMAGLILLKM---LAKTHQPMKLALTGVALSACWASLTDYLMLS 159 Query: 174 AEDHAYGIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGV 233 WL G + W V +P+++ +P+ L L+LL L D+ A TLGV Sbjct: 160 RPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGV 219 Query: 234 NLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATL 293 ++ R +L + + V+ GP++FIGL+VPH+ R G R +LPVS L GA L Sbjct: 220 SVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALL 279 Query: 294 MLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRR 330 +++AD+LAR + P +LP G + A+IG+P FVWL+ R Sbjct: 280 LVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVR 316 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: 357 Number of extensions: 18 Number of successful extensions: 2 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: 318 Length adjustment: 28 Effective length of query: 304 Effective length of database: 290 Effective search space: 88160 Effective search space used: 88160 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: 48 (23.1 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