Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate 200217 SO1034 iron-compound ABC transporter, permease protein (NCBI ptt file)
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__MR1:200217 Length = 380 Score = 155 bits (392), Expect = 1e-42 Identities = 105/301 (34%), Positives = 157/301 (52%), Gaps = 30/301 (9%) Query: 46 VLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLL--- 102 ++ME RLPR+LLA GA L++AG ++Q + RNPLA P + G++ AS +V L L Sbjct: 79 IVMELRLPRILLAFVAGAGLSLAGSVLQTVTRNPLADPYLFGISSGASFGAVVMLTLFSG 138 Query: 103 ---------------------MPSLPVMVLPLLAFAGGMAGLIL---LKMLAKTHQPMKL 138 + L LP AF G +++ L L Q ++ Sbjct: 139 SGFFANAGVIANSGIFSGAEILAGLQWFSLPFGAFIGASLSVLIVLALSGLGLNSQVERM 198 Query: 139 ALTGVALSACWASLTDYLM-LSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLS 197 L+GVA S + +LT L+ + PQ + L W GS WS + + ++++ + Sbjct: 199 LLSGVATSFMFGALTSLLLYFASPQATASVLFWSLGSFAKASWSLLILPTIVVLVSFFII 258 Query: 198 LSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMM 257 L + R + L GD A TLGV+VP R LLL +T+ VA CG I F+GL++PH + Sbjct: 259 LGWKRQIMALQAGDETAHTLGVNVPKLRLNMLLLCSLITAILVATCGGIGFVGLMIPHTV 318 Query: 258 RSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVRM 317 R + GR LL +AL G L +V D+LAR + ELPVG++TA IG+ +F+ +L R Sbjct: 319 RLLFPGRQPILL--TALVGGLFMVWIDVLARCLLGNQELPVGIITASIGSFFFLLILRRR 376 Query: 318 R 318 + Sbjct: 377 K 377 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: 262 Number of extensions: 10 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: 380 Length adjustment: 29 Effective length of query: 289 Effective length of database: 351 Effective search space: 101439 Effective search space used: 101439 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