GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Sinorhizobium meliloti 1021

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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