Align MtlF, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate Ac3H11_2943 Various polyols ABC transporter, permease component 1
Query= TCDB::O30492 (296 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2943 Length = 316 Score = 361 bits (926), Expect = e-104 Identities = 177/277 (63%), Positives = 221/277 (79%), Gaps = 1/277 (0%) Query: 16 LVTPSVALLLLWMIVPLGMTLYFSLIRYNLLYPGENQFVGLENFTYFITDSGFLPGATNT 75 L+TP++A L LWMIVPL MT+YFSLIRYNL+ P + F GLENF +F+TD F NT Sbjct: 39 LLTPAMATLFLWMIVPLVMTIYFSLIRYNLMQPDQTGFAGLENFEFFVTDPSFGTAVVNT 98 Query: 76 LLLVGSVLLISVVFGVLISALLEASEFLGRGIVRVLLISPFFIMPTVGALIWKNLIFHPV 135 +LL+GSV+LI+VV GV I ALL F GRGIVRVLLISPFF+MPTV AL+WKN++ +P+ Sbjct: 99 ILLLGSVILITVVLGVAI-ALLINEPFPGRGIVRVLLISPFFVMPTVNALMWKNMMMNPI 157 Query: 136 SGILAAVWKFFGAEPVDWLAHYPLLSIIIIVSWQWLPFAILLLMTAMQSLDQEQKEAARL 195 G+LA VW FFGA PVDWL +PL S+I++VSWQWLPFA L+ MTA+QS++ EQ EA+R+ Sbjct: 158 YGVLAQVWIFFGAAPVDWLTDHPLFSVIVMVSWQWLPFATLIFMTALQSMNHEQLEASRM 217 Query: 196 DGAGAIAIFWHLTLPHLARPIAVVVMIETIFLLSVFAEIFTTTNGGPGYASTNLAYLIYN 255 DGA + +L +PHL R +AVVVMIE IFLLS+FAEI+TTT GGPG ASTN+ +LI+ Sbjct: 218 DGANYLQQLRYLYVPHLGRSVAVVVMIELIFLLSIFAEIYTTTAGGPGDASTNVTFLIFK 277 Query: 256 QALVQFDVGMASAGGLIAVVIANIAAIILVRMIGKNL 292 QAL+ FD G+ASAG L AVV+ANIAA+ L+RM+GKNL Sbjct: 278 QALLNFDAGVASAGALFAVVLANIAAVFLIRMVGKNL 314 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: 319 Number of extensions: 11 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: 296 Length of database: 316 Length adjustment: 27 Effective length of query: 269 Effective length of database: 289 Effective search space: 77741 Effective search space used: 77741 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