Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate RR42_RS16135 RR42_RS16135 ABC transporter permease
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Cup4G11:RR42_RS16135 Length = 335 Score = 182 bits (461), Expect = 1e-50 Identities = 123/337 (36%), Positives = 186/337 (55%), Gaps = 29/337 (8%) Query: 1 MKIALVIFITLALAGCA--LLSLHMGVIPVP----WRALL--TDWQAGHEHYYVLMEYRL 52 M+ AL I++ LA AG A LLSL +G +P+ W AL D AG ++ E RL Sbjct: 4 MRRALAIWLMLAAAGVAVFLLSLAVGSVPLSGAQVWHALCGGADDTAGA----IVRELRL 59 Query: 53 PRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLP 112 PR A G LA+ G L+Q ++RNPLA P +LGV+ A+ ++ A+L+M P+ + Sbjct: 60 PRAAAAFACGGLLALTGALMQVLLRNPLAEPYVLGVSGGAATGALTAMLMM--WPLWTVQ 117 Query: 113 LLAFAGGMAGLILLKMLAKT-----------HQP-MKLALTGVALSACWASLTDYLMLSR 160 A G + ++L+ LA+ H+ +L LTGV L+A W +L ++ Sbjct: 118 AGAAGGALFSMVLVATLARRDLLHPQVQGGHHEAGSRLLLTGVILAAGWGALITLILSVA 177 Query: 161 PQD-VNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGV 219 P+ + L WLTG L G + +A+ + L + L++ R L+ + +G+ A LGV Sbjct: 178 PEARLRGMLFWLTGDLGGT--ASYGLALGALALAVLLAMPMARSLNAMLMGETVAQALGV 235 Query: 220 SVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALL 279 V R +LA + + + G I F+GLVVPH++R G R +LP SAL G L Sbjct: 236 RVGAVRLSVFVLASLAIAVAITSAGSIGFVGLVVPHLVRLAWGNDQRLMLPASALLGGTL 295 Query: 280 LVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVR 316 L+ ADL+AR + P +LPVGV+TA++G P F++LL+R Sbjct: 296 LMAADLVARTVIAPAQLPVGVITALLGVPTFLFLLLR 332 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: 321 Number of extensions: 20 Number of successful extensions: 4 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: 335 Length adjustment: 28 Effective length of query: 290 Effective length of database: 307 Effective search space: 89030 Effective search space used: 89030 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 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