Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate PP_2417 PP_2417 putative Iron ABC transporter, permease protein
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Putida:PP_2417 Length = 339 Score = 174 bits (441), Expect = 3e-48 Identities = 116/326 (35%), Positives = 172/326 (52%), Gaps = 10/326 (3%) Query: 3 IALVIFITLALAGCALLSLHMGVIPVPWRALLTDWQAGHE----HYYVLMEYRLPRLLLA 58 +AL + LAG A+ ++ V WQA + ++ YRL R L+A Sbjct: 11 VALAALLAALLAGTAIGETNLSPSVVGQVLANHLWQAAYPVDPIDAGIVWNYRLTRTLVA 70 Query: 59 LFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLLAFAG 118 GA LA GV++Q ++RNPLA P +LG++ AS +V LL + + AF G Sbjct: 71 AACGAGLATCGVILQAMLRNPLAEPYLLGLSAGASTGAVLVGLLGLGSLALSMSAGAFIG 130 Query: 119 GMAGLILLKMLAKTHQPM----KLALTGVALSACWASLTDYLML--SRPQDVNNALLWLT 172 A L+ +LA+ P ++ L G+A S + +LT +L+ + + L WL Sbjct: 131 AGAAFALVLVLARAAGPSSNNAQVILAGIAGSQLFNALTAFLITKSATAEQARGILFWLL 190 Query: 173 GSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLA 232 G+L G W V +A+P+ + L + L R LD G A +LG+ V T+ + A Sbjct: 191 GNLSGVRWPSVWLAVPVAVFGLLVCLWHRRALDAFTFGADSAASLGIPVRRTQLLLISCA 250 Query: 233 VAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHP 292 +T+ V+ G I F+GLV+PH +R + G H RLLP SAL GAL L+VAD+L+R + Sbjct: 251 ALVTAVMVSIVGAIGFVGLVIPHALRLLLGPGHSRLLPASALGGALFLIVADILSRTLIT 310 Query: 293 PLELPVGVLTAIIGAPWFVWLLVRMR 318 +PVGV+TA+IGAP F +LV R Sbjct: 311 GQVIPVGVVTALIGAPVFALILVSRR 336 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: 272 Number of extensions: 16 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: 339 Length adjustment: 28 Effective length of query: 290 Effective length of database: 311 Effective search space: 90190 Effective search space used: 90190 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