Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate BWI76_RS16820 BWI76_RS16820 iron ABC transporter
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Koxy:BWI76_RS16820 Length = 350 Score = 178 bits (452), Expect = 1e-49 Identities = 114/328 (34%), Positives = 168/328 (51%), Gaps = 17/328 (5%) Query: 1 MKIALVIFITLALAGCALLSLHMGVIPVP----WRALLTDWQAGHEHYYVLMEYRLPRLL 56 +KIA + + + L AL L G P+P +RALL + ++L + RLPRLL Sbjct: 27 LKIAAGMLLVILLL--ALFGLTRGSFPMPSGTLFRALLGAENVAEQPRFILFDIRLPRLL 84 Query: 57 LALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLLAF 116 +AL GA L +AG +Q I RN LA P ++GV AS+ + +L P++ V+ PL Sbjct: 85 MALLCGAMLGLAGAAMQSITRNGLADPGLIGVKEGASIVVLALVLFFPAVGVIWRPLAGM 144 Query: 117 AGGMAGLILLKMLAKTHQPMKLALTGVALSACWASLTDYLMLSRP-QDVNNALLWLTGSL 175 GG+ +L+ LA+ + L G+ +S A+ M + +DV A++WL GSL Sbjct: 145 LGGVLVALLVLALARDCSRPRFILIGIGVSWTLAAAVGIFMTTADVRDVQTAMIWLAGSL 204 Query: 176 WGRDWSFVKIAI-----PLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALL 230 W + +A MILFL R D LGD A LGV + Sbjct: 205 HAATWPLLAVAFCWALPGAMILFLT-----ARAADAALLGDRTAIGLGVRLQQLTLLRFF 259 Query: 231 LAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARII 290 V +TS V+ G + F+GL+ PHM R + G LL SAL GALL++ D + R+ Sbjct: 260 APVLLTSASVSCVGSLGFVGLMAPHMARFLLRGGQVALLCGSALIGALLVLATDTIGRLA 319 Query: 291 HPPLELPVGVLTAIIGAPWFVWLLVRMR 318 PL++P G++ A++G P+F+ LL R R Sbjct: 320 FAPLQIPAGIVIALVGCPFFIVLLWRRR 347 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: 292 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: 350 Length adjustment: 28 Effective length of query: 290 Effective length of database: 322 Effective search space: 93380 Effective search space used: 93380 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