Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate SMc04140 SMc04140 ABC transporter ATP-binding protein
Query= TCDB::O30494 (367 letters) >FitnessBrowser__Smeli:SMc04140 Length = 360 Score = 399 bits (1025), Expect = e-116 Identities = 202/354 (57%), Positives = 256/354 (72%), Gaps = 1/354 (0%) Query: 6 IKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIELDGR 65 ++ ++K + +I GIDL ++ EF VFVGPSGCGKSTLLR+IAGLEE+S GT+ LD Sbjct: 7 LQKVEKRYGALDVIHGIDLTIDPGEFAVFVGPSGCGKSTLLRMIAGLEEISGGTLMLDSD 66 Query: 66 DITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAARILELGP 125 + EV PA+R +AMVFQ+YALYPHMSV KN++F L+ AG K +E KV AA IL++ Sbjct: 67 RMNEVAPARRGIAMVFQSYALYPHMSVYKNLAFGLETAGFKKAEIEPKVRRAAEILQIEK 126 Query: 126 LLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKELQA 185 LL+RKPK LSGGQRQRVAIGRAIVR P+IFLFDEPLSNLDA LRVQMR+E++RLH++L Sbjct: 127 LLDRKPKALSGGQRQRVAIGRAIVREPRIFLFDEPLSNLDAELRVQMRVEISRLHRDLGN 186 Query: 186 TMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMGFLKGK 245 TMIYVTHDQVEAMT+ADK+VVLNSGRIEQVG+PL+LY+ P N FVAGF+G+PKM FLK + Sbjct: 187 TMIYVTHDQVEAMTMADKIVVLNSGRIEQVGAPLDLYNNPVNRFVAGFIGSPKMNFLKAR 246 Query: 246 VTRVDGQGCEVQLDAGTLISLPLSGASLSVGSAVTLGIRPEHLEIASPGQTTLTVTADVG 305 + V G +++ GT I LP + G VT GIRPEHL G TV ++ Sbjct: 247 IADVTGSETAIEVCGGT-IRLPRRLNGATQGQDVTFGIRPEHLSAREGGIELATVNVEIV 305 Query: 306 ERLGSDTFCHVITSNGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFDTDGVAV 359 E LG +T + IT + + LT+ + G + G L +H DP+ CH+F DG A+ Sbjct: 306 ENLGGETMLYGITPDRQQLTVALEGQQKVERGSNLAVHFDPSRCHVFGADGRAM 359 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: 399 Number of extensions: 7 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: 367 Length of database: 360 Length adjustment: 29 Effective length of query: 338 Effective length of database: 331 Effective search space: 111878 Effective search space used: 111878 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: 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