GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlF in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate H281DRAFT_05891 H281DRAFT_05891 carbohydrate ABC transporter membrane protein 1, CUT1 family

Query= reanno::Phaeo:GFF1304
         (288 letters)



>FitnessBrowser__Burk376:H281DRAFT_05891
          Length = 318

 Score =  109 bits (272), Expect = 9e-29
 Identities = 85/292 (29%), Positives = 135/292 (46%), Gaps = 23/292 (7%)

Query: 7   RSAARIMMAPAVILLLGWMLVPLTMTLYFSFKKY------LPLRGGDLGWVGFDNYARFL 60
           R+ A + + P ++LLL   + PL   L  SF  +      +P R     +VG DNY   L
Sbjct: 30  RTIAWLFILPTILLLLAINIFPLIWALRLSFTNFKSNMPSVPAR-----FVGIDNYVDIL 84

Query: 61  SSSAFWPSVQATLVIVGGVLAITVILGVFLALLLNQPMWGQGIVRILVIAPFFVMPTVSA 120
           +    W ++Q T   V   + + V+LG  LALL+N+   G      L++ P  + P V  
Sbjct: 85  TDEDIWYAMQVTARFVFWSVGLEVLLGFGLALLINRQFRGHSFWTTLILLPMMLSPAVVG 144

Query: 121 LVWKNMFMDPVNGLFAHLWKAF-GAEPVSW--LSEASLQ--SIILIVSWQWLPFATLILL 175
             W    + P  GLF  +   F G  P S+  + + SL   +I+++ +W W P+  LI L
Sbjct: 145 NFW-TFLLQPQTGLFNDIVGFFTGIAPGSFQMIGDVSLAPWTIVMVDTWMWTPYVMLICL 203

Query: 176 TAIQSLDSEQLEAAEMDGAPPVARFGYITLPHLSRAITVVVLIQTIFLLSIFAEIFVTTQ 235
             ++S+     EAAE+D A P  +F  ITLP     + + VL + I    +F  + + T 
Sbjct: 204 AGLRSIPDYIYEAAEVDRATPWRQFWSITLPMTLPFLMLAVLFRGIENFKMFDMVNLLTS 263

Query: 236 GSFG--TKTLTYLIYQRVLESQNVGLGSAGGVYAII----LANIVAIFLMRI 281
           G  G  T+T++  + +   E    G  SA  +   +     ANI    L R+
Sbjct: 264 GGPGSVTETVSITLKRAAFEKWQTGYSSALAIILFVTVFGAANIYVKALNRV 315


Lambda     K      H
   0.328    0.140    0.430 

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: 259
Number of extensions: 16
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: 288
Length of database: 318
Length adjustment: 27
Effective length of query: 261
Effective length of database: 291
Effective search space:    75951
Effective search space used:    75951
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