Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate Dsui_0530 Dsui_0530 ABC-type Fe3+-siderophore transport system, permease component
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__PS:Dsui_0530 Length = 326 Score = 182 bits (461), Expect = 1e-50 Identities = 131/321 (40%), Positives = 180/321 (56%), Gaps = 15/321 (4%) Query: 5 LVIFITLALAGCALL-SLHMGVIPVPWRALLTDWQAGHEH--YYVLMEYRLPRLLLALFV 61 +VI + + LAG +L+ +L +G I +P A+L E Y V+ RLPR L A Sbjct: 9 IVIALLVLLAGVSLVVALAVGSISIPPGAVLQGLLGDAEAPGYAVVHNLRLPRALAAFAC 68 Query: 62 GAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLLAFAGGMA 121 G LAVAG L+Q ++RNPLA P +LG++ A + ++ A+LL L + LAF+G +A Sbjct: 69 GGLLAVAGCLMQVLLRNPLADPYVLGISGGAGVGALVAILL--GLSAFGINGLAFSGALA 126 Query: 122 GLILLKMLAK---THQPMKLALTGVALSA-CWASLTDYLMLSRPQDVNNALLWLTGSLWG 177 L+ LA + +L LTGV ++A C A + L L+ ++ L WL G L Sbjct: 127 ATFLVFGLAHGDGSWTQTRLLLTGVIVAAGCGALVALMLSLAPEHKLHGMLYWLMGDLS- 185 Query: 178 RDWSFVKIAIPLMILF--LPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAM 235 PL+ L L L+L F R+L+LLA G A A LGV+V R ++A Sbjct: 186 ---QATDARPPLLALAAALLLALPFARELNLLARGLATAQALGVAVVRLRRLVYVVASLA 242 Query: 236 TSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLE 295 T+T V G I F+GLVVPH++R G R LLP SAL G LL +AD LAR + P + Sbjct: 243 TATAVTTAGSIGFVGLVVPHLVRLAVGNDQRLLLPASALAGGALLALADTLARTVAAPQQ 302 Query: 296 LPVGVLTAIIGAPWFVWLLVR 316 LPVGVLTA+IG P F++LL R Sbjct: 303 LPVGVLTALIGVPVFLFLLTR 323 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: 269 Number of extensions: 11 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: 326 Length adjustment: 28 Effective length of query: 290 Effective length of database: 298 Effective search space: 86420 Effective search space used: 86420 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 Apr 09 2024. 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