Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate SMa1745 SMa1745 ABC transporter permease, Fe3+-siderophore transport system
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Smeli:SMa1745 Length = 366 Score = 191 bits (485), Expect = 2e-53 Identities = 110/272 (40%), Positives = 153/272 (56%), Gaps = 4/272 (1%) Query: 51 RLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMV 110 R+PR +LAL G AL +AG ++QG+ RNPLA P ILGVN ASLA V + + Sbjct: 91 RIPRTVLALLAGGALGLAGAIMQGVTRNPLADPGILGVNMGASLAVVVGVAWFGMSSLYA 150 Query: 111 LPLLAFAGGMAGLILLKMLAKTHQ----PMKLALTGVALSACWASLTDYLMLSRPQDVNN 166 +A G I + + + P+K+AL G A S +AS+ ++L R Sbjct: 151 YIWVAILGAGCAAIFVYAIGSLGRGGATPLKMALAGAATSVAFASMVIAVVLPRGDIAGG 210 Query: 167 ALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRF 226 W G + G + + +P +++ +SL R L+ LALGD AT LG SV R Sbjct: 211 IHSWQIGGVGGATYERILPVLPFLLVGFVISLLSARKLNSLALGDELATGLGESVATARA 270 Query: 227 WALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLL 286 A L A+ + A CGPI F+GLVVPH+ R + G HR LLP S L GA LL+ AD+L Sbjct: 271 VASLGAILLCGATTAICGPIGFLGLVVPHLCRLLVGVDHRWLLPFSTLAGACLLLAADVL 330 Query: 287 ARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 RI+ P E+ VG++TA+IGAP+F+W++ R R Sbjct: 331 GRIVARPAEIDVGIVTAMIGAPFFIWIVRRQR 362 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: 295 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: 366 Length adjustment: 29 Effective length of query: 289 Effective length of database: 337 Effective search space: 97393 Effective search space used: 97393 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