Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate PP_4688 PP_4688 Heme/hemin ABC transporter, permease protein
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Putida:PP_4688 Length = 345 Score = 157 bits (398), Expect = 3e-43 Identities = 118/343 (34%), Positives = 181/343 (52%), Gaps = 39/343 (11%) Query: 7 IFITLALAGCAL---LSLHMGVIPVPWRALLTDWQAG-------------HEHYYVLMEY 50 +FI+L+L C L LSL +G + +P + +AG + +L + Sbjct: 10 LFISLSLL-CLLAIWLSLALGPVSLP---MFDTLRAGLRLLGLPVSEDGLQQAEMILGQI 65 Query: 51 RLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALL-------LM 103 RLPR LL L VGA LA++GV +QG+ RNPLA P ++GV A++ + A++ + Sbjct: 66 RLPRTLLGLAVGAVLALSGVAMQGLFRNPLADPGLVGVAAGAAVGAAVAIVGGAWFGGMP 125 Query: 104 PSLPVMVLPLLAFAGGMAGLILLKMLAKTHQPMKLA---LTGVALSACW-ASLTDYLMLS 159 + +L AF GG+ L+ L + +A L GVA++A A++ + L+ Sbjct: 126 DAFAPYLLSFCAFVGGLGVTALVYRLGRRDGQTNVATMLLAGVAMTALGGAAVGLFSYLA 185 Query: 160 RPQDVNNALLWLTGSLWG----RDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARAT 215 + W GSL G R W + +A + + +LP + L+ L LG++ A Sbjct: 186 DDATLRTLTFWNLGSLNGASYERLWPLLLVATGVAV-WLPRR---AKALNALLLGESEAR 241 Query: 216 TLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALT 275 LGV V + + VAA G I FIGLVVPH++R + G HR +LP S L Sbjct: 242 HLGVDVERLKRELVFCTALGVGAAVAAAGLIGFIGLVVPHLVRLLAGPDHRVVLPASLLA 301 Query: 276 GALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 G +L++ ADL AR++ P ELP+G++TA IGAP+F++LL+R R Sbjct: 302 GGVLMLFADLAARLLLAPAELPIGIVTAFIGAPFFLFLLMRGR 344 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: 300 Number of extensions: 15 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: 345 Length adjustment: 28 Effective length of query: 290 Effective length of database: 317 Effective search space: 91930 Effective search space used: 91930 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