Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate HSERO_RS01355 HSERO_RS01355 sugar ABC transporter ATP-binding protein
Query= TCDB::O30494 (367 letters) >FitnessBrowser__HerbieS:HSERO_RS01355 Length = 381 Score = 363 bits (931), Expect = e-105 Identities = 189/368 (51%), Positives = 258/368 (70%), Gaps = 9/368 (2%) Query: 1 MANLKIKNLQKGF-EGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGT 59 MA++ ++ QK + + +I+ +DL++ + EF VF+GPSGCGKSTLLR IAGLE+++ G Sbjct: 1 MASITLRAAQKAYGDAPPVIRNVDLDIGEHEFCVFLGPSGCGKSTLLRSIAGLEDLTSGD 60 Query: 60 IELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAAR 119 + + G+ + +V A+R +AMVFQ+YAL+PHM+V +NMSF L LA + K +E KV EAAR Sbjct: 61 LFIGGKRVNDVPSAQRSVAMVFQSYALFPHMTVYENMSFGLTLAKLPKAEIEQKVREAAR 120 Query: 120 ILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARL 179 IL+L LL+RKPK+LSGGQRQRVAIGRAIVR P +FLFDEPLSNLDA LR Q R+E+ARL Sbjct: 121 ILQLEELLQRKPKELSGGQRQRVAIGRAIVRRPGVFLFDEPLSNLDATLRSQTRIEIARL 180 Query: 180 HKEL-QATMIYVTHDQVEAMTLADKVVVLNS-------GRIEQVGSPLELYHQPANLFVA 231 H++ QA+++YVTHDQVEAMTLAD++V+L++ G I QVG+P+ELYH P N FVA Sbjct: 181 HRQFEQASVVYVTHDQVEAMTLADRIVLLHAGADTQRFGSIAQVGTPMELYHHPRNRFVA 240 Query: 232 GFLGTPKMGFLKGKVTRVDGQGCEVQLDAGTLISLPLSGASLSVGSAVTLGIRPEHLEIA 291 GF+G+P+M FL +V V G V+L L + +L G VT+G+RPEH+EI Sbjct: 241 GFIGSPRMNFLPAQVAGVQENGILVRLSGSEETLLVAAQGALQPGQMVTVGVRPEHMEIG 300 Query: 292 SPGQTTLTVTADVGERLGSDTFCHVITSNGEPLTMRIRGDMASQYGETLHLHLDPAHCHL 351 S GQ + + ERLG T+ H+ G+PL + GD GE + + + PA +L Sbjct: 301 SQGQYGIHREVVLVERLGEQTYVHLDEPAGQPLVAKAAGDARITRGERVRVAIAPACAYL 360 Query: 352 FDTDGVAV 359 FD DG+A+ Sbjct: 361 FDQDGLAL 368 Lambda K H 0.319 0.137 0.387 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: 410 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: 367 Length of database: 381 Length adjustment: 30 Effective length of query: 337 Effective length of database: 351 Effective search space: 118287 Effective search space used: 118287 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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