Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate 18313 b4289 KpLE2 phage-like element; iron-dicitrate transporter subunit (NCBI)
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Keio:18313 Length = 332 Score = 178 bits (452), Expect = 1e-49 Identities = 105/277 (37%), Positives = 157/277 (56%), Gaps = 7/277 (2%) Query: 46 VLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPS 105 ++ RLPR L+A+ +GA+LA+AG L+Q + NP+ASP +LG+N A+LA L P+ Sbjct: 55 LVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPT 114 Query: 106 LPVMVLPL---LAFAGGMAGLILLKM---LAKTHQPMKLALTGVALSACWASLTDYLMLS 159 P+ L A GG++ L+++ TH KL L G+ALSA LT +L Sbjct: 115 -PIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLL 173 Query: 160 RPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGV 219 WL G + W V +P+++ +P+ L L+LL L D+ A TLGV Sbjct: 174 AEDHAYGIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGV 233 Query: 220 SVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALL 279 ++ R +L + + V+ GP++FIGL+VPH+ R G R +LPVS L GA L Sbjct: 234 NLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATL 293 Query: 280 LVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVR 316 +++AD+LAR + P +LP G + A+IG+P FVWL+ R Sbjct: 294 MLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRR 330 Lambda K H 0.330 0.142 0.447 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: 319 Number of extensions: 11 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: 318 Length of database: 332 Length adjustment: 28 Effective length of query: 290 Effective length of database: 304 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 (21.8 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