Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate 5208201 Shew_0713 transport system permease protein (RefSeq)
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__PV4:5208201 Length = 347 Score = 163 bits (412), Expect = 6e-45 Identities = 103/277 (37%), Positives = 160/277 (57%), Gaps = 10/277 (3%) Query: 46 VLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMP- 104 +L+E RLPR+LLA G LA+AG ++Q + RNPLA P + G++ ASL +V + L+ Sbjct: 67 ILIELRLPRILLAFIAGFGLALAGAVLQTVTRNPLADPYLFGISSGASLGAVVVITLLGG 126 Query: 105 ---SLPVMVLPLLAFAGG-MAGLILLKMLAK--THQPMKLALTGVALSACWASLTDYLM- 157 +L + LPL AF G +A L++L + + Q ++ L+GVA+S + +L ++ Sbjct: 127 VGGALASVGLPLGAFIGASLAVLMVLALCGRDLNTQIERMLLSGVAISFLFGALASLMLY 186 Query: 158 LSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTL 217 S PQ + L W GS W + + L++ + L R + + GD A TL Sbjct: 187 FSGPQSAASVLFWSLGSFAKASWQMLWLPWLLVLAASAILLLLKRQILAIQAGDETAHTL 246 Query: 218 GVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGA 277 G+ V R +LLL +T+ VA CG I F+GL+VPHM+R + GR LL +AL G Sbjct: 247 GIRVQRLRLVSLLLCSLITAVLVANCGGIGFVGLMVPHMVRLLLPGRFALLL--TALVGG 304 Query: 278 LLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLL 314 L ++ D+LAR + ELPVG++TA+IG+ +F+++L Sbjct: 305 LFMIWVDVLARCLLSYQELPVGIITAVIGSLFFLFIL 341 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: 282 Number of extensions: 12 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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