Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_053412606.1 CLAC_RS08855 iron ABC transporter permease
Query= CharProtDB::CH_004160 (318 letters) >NCBI__GCF_001274895.1:WP_053412606.1 Length = 327 Score = 196 bits (499), Expect = 5e-55 Identities = 115/319 (36%), Positives = 180/319 (56%), Gaps = 6/319 (1%) Query: 2 KIALVIFITLA-LAGCALLSLHMGVIPVPWRALLTDWQAGHEHYYVLMEYRLPRLLLALF 60 + ALV+ ++ A L LL + +G + +++ AG Y+ YR+PR+++ + Sbjct: 6 RFALVLVVSTAFLVLACLLGMGIGAVQKSLPDVISGLLAGENLYW---RYRMPRIVVGVL 62 Query: 61 VGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLLAFAGGM 120 G +AVAG L+Q +RNPLA+PD LG+ LA+V ALL SLP + L +AF G + Sbjct: 63 AGVGMAVAGSLLQTALRNPLAAPDTLGITAGGGLAAVVALLGFGSLPPLALTPIAFVGSL 122 Query: 121 AGLILLKMLA--KTHQPMKLALTGVALSACWASLTDYLMLSRPQDVNNALLWLTGSLWGR 178 G + + A P +LALTGVA+S A++T L++ + A+ WL GSL+ R Sbjct: 123 LGALAVFATAGRAVADPARLALTGVAVSVGLAAVTQLLLVRVAPEAGAAMTWLKGSLYAR 182 Query: 179 DWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAMTST 238 S P+++ ++++ R + L L D+ ++GV R AL++AVA S Sbjct: 183 TMSDALTVAPVVVAGAVVAMAVARHFNTLVLDDSTMASIGVRSNVLRILALIIAVACGSA 242 Query: 239 GVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLELPV 298 VAA G + F+GL++PH + + G R +PV A+ GA L+V AD + R P E+PV Sbjct: 243 AVAAAGVLGFVGLIIPHAAKLLVGQNLARQIPVGAVAGAALVVAADAVGRWAFAPTEIPV 302 Query: 299 GVLTAIIGAPWFVWLLVRM 317 G L AI GAP+F++L+ R+ Sbjct: 303 GALIAIAGAPYFIYLVHRV 321 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: 245 Number of extensions: 9 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: 327 Length adjustment: 28 Effective length of query: 290 Effective length of database: 299 Effective search space: 86710 Effective search space used: 86710 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 24 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