GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlF in Sinorhizobium meliloti 1021

Align SmoF, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate SMc01978 SMc01978 sugar transport system permease ABC transporter protein

Query= TCDB::O30832
         (290 letters)



>FitnessBrowser__Smeli:SMc01978
          Length = 311

 Score =  153 bits (387), Expect = 4e-42
 Identities = 100/281 (35%), Positives = 152/281 (54%), Gaps = 7/281 (2%)

Query: 8   TAARLMISPAVILLFLWMIVPLSMTLYFSFLRYNLLMPGMESFTGWDNYYYFLTDPAFSA 67
           +A  L  +PA+IL+   M+VPL + + ++F    LL P    F G D++     D AF  
Sbjct: 25  SAPYLYTAPALILIVTVMLVPLVLGISYAFRDIQLLNPFSGGFVGLDHFRALAQDQAFFR 84

Query: 68  ALTNTILLVVGVLLITVVGGVLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSALVWKNMF 127
           +L NT+      + +    G++LALLLD+PF G+ I + LV  P+ V   ++ L W  +F
Sbjct: 85  SLRNTLWWTGASVFLQFAFGLILALLLDKPFHGRAIAQALVFLPWAVPSFLAGLNWAWLF 144

Query: 128 MNPVNGMFAHIARGLGL--PPFDFLSQAPLASIIGIVA--WQWLPFATLILLTALQSLDR 183
            NPV G   H    LG+   P + LS   LA    IVA  W  +PF  + LL ALQ++ R
Sbjct: 145 -NPVVGPLPHWLFALGIMSQPTNILSDPQLAMWGPIVANIWWGIPFFAITLLAALQAIPR 203

Query: 184 EQMEAAEMDGASALDRFIHITVPHLTRAITVVVLIQTIFLLGVFAEILVTTNGGPGTAST 243
           +  EAA +DGA  L RF+ IT+P L   I + +L++T+++      I+V TNGGP   + 
Sbjct: 204 DLYEAASIDGAGPLQRFLSITLPFLAPTIAITILLRTVWISNFADLIIVMTNGGPADRTQ 263

Query: 244 NITYLVYAQSLLNYDVGGGSAGGIVAVVLANIVAIFLMRMI 284
            +   ++ Q+    D G  SA  I  V+LA ++A  L+ +I
Sbjct: 264 IVASYIFTQAFKRLDFGYASA--IALVLLALLLAYSLLIVI 302


Lambda     K      H
   0.329    0.142    0.429 

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: 235
Number of extensions: 20
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: 290
Length of database: 311
Length adjustment: 27
Effective length of query: 263
Effective length of database: 284
Effective search space:    74692
Effective search space used:    74692
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 (21.8 bits)
S2: 48 (23.1 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