Align MtlF, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate Pf1N1B4_4849 Various polyols ABC transporter, permease component 1
Query= TCDB::O30492 (296 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4849 Length = 299 Score = 547 bits (1409), Expect = e-160 Identities = 271/290 (93%), Positives = 286/290 (98%) Query: 6 KNRLANPGWFLVTPSVALLLLWMIVPLGMTLYFSLIRYNLLYPGENQFVGLENFTYFITD 65 K+RL NPGWFLV+PSVALLLLWMIVPLGMT+YFS+IRYNLLYPGENQFVGLENF+YF++D Sbjct: 9 KSRLTNPGWFLVSPSVALLLLWMIVPLGMTVYFSMIRYNLLYPGENQFVGLENFSYFLSD 68 Query: 66 SGFLPGATNTLLLVGSVLLISVVFGVLISALLEASEFLGRGIVRVLLISPFFIMPTVGAL 125 SGFLPGATNTLLLVGSVLLISVVFGVLISALLEASEFLGRGIVRV+LISPFFIMPTVGAL Sbjct: 69 SGFLPGATNTLLLVGSVLLISVVFGVLISALLEASEFLGRGIVRVMLISPFFIMPTVGAL 128 Query: 126 IWKNLIFHPVSGILAAVWKFFGAEPVDWLAHYPLLSIIIIVSWQWLPFAILLLMTAMQSL 185 IWKNLIFHPVSGILA +WK FGA+PVDWLAHYPLLSIIIIVSWQWLPFAIL+LMTAMQSL Sbjct: 129 IWKNLIFHPVSGILAYIWKLFGAQPVDWLAHYPLLSIIIIVSWQWLPFAILILMTAMQSL 188 Query: 186 DQEQKEAARLDGAGAIAIFWHLTLPHLARPIAVVVMIETIFLLSVFAEIFTTTNGGPGYA 245 DQEQKEAARLDGAG +AIFWHLTLPHLARPIAVVVMIETIFLLSVFAEIFTTTNGGPGYA Sbjct: 189 DQEQKEAARLDGAGPVAIFWHLTLPHLARPIAVVVMIETIFLLSVFAEIFTTTNGGPGYA 248 Query: 246 STNLAYLIYNQALVQFDVGMASAGGLIAVVIANIAAIILVRMIGKNLTDK 295 STNLAYLIYNQALVQFDVGMASAGGLIAV+IAN+AAI+LVRMIGKNLTDK Sbjct: 249 STNLAYLIYNQALVQFDVGMASAGGLIAVLIANVAAIVLVRMIGKNLTDK 298 Lambda K H 0.328 0.143 0.437 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: 428 Number of extensions: 10 Number of successful extensions: 1 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: 296 Length of database: 299 Length adjustment: 26 Effective length of query: 270 Effective length of database: 273 Effective search space: 73710 Effective search space used: 73710 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 (21.7 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