Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate 6936573 Sama_0761 iron-compound ABC transporter, permease protein (RefSeq)
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__SB2B:6936573 Length = 347 Score = 159 bits (401), Expect = 1e-43 Identities = 103/280 (36%), Positives = 157/280 (56%), Gaps = 9/280 (3%) Query: 46 VLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPS 105 +L+E RLPR+LLA GA LA++G +Q + RNPLA P + G++ ASL ++ L L + Sbjct: 68 ILLELRLPRILLAFVCGAGLALSGWALQLVTRNPLADPYLFGISAGASLGAIVVLSLGIT 127 Query: 106 LPVMV---LPLLAFAGGMAGLILLKMLA---KTHQPMKLALTGVALSACWASLTDYLM-L 158 V++ LPL AF G A ++++ L+ Q ++ L+GVA S + +L L+ Sbjct: 128 HGVLLAIGLPLGAFIGASASVLVVLTLSGFGLQSQVERMLLSGVATSFLFGALGSLLLYF 187 Query: 159 SRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLG 218 S PQ + + W GS W + + + F+ L R L L+ GD A LG Sbjct: 188 SSPQVTASVIFWSLGSFARAAWDLLWLPWLVFGGFVAFLLLVRRQLFALSAGDETAHALG 247 Query: 219 VSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGAL 278 VSV R +LL+ MT+ VA+CG I F+GL++PH+ R + G L + A+ G L Sbjct: 248 VSVAKLRIISLLMCSLMTAVLVASCGGIGFVGLMIPHIARLLFPGSQSLL--IVAMLGGL 305 Query: 279 LLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 +V D++ R + PP ELPVGV+TA++G+ +F+ LL R Sbjct: 306 FMVWVDVMTRSLLPPQELPVGVITAVVGSVFFLMLLFGRR 345 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: 264 Number of extensions: 14 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: 318 Length of database: 347 Length adjustment: 28 Effective length of query: 290 Effective length of database: 319 Effective search space: 92510 Effective search space used: 92510 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: 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