GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlF in Burkholderia phytofirmans PsJN

Align SmoF, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate BPHYT_RS22775 BPHYT_RS22775 sugar ABC transporter permease

Query= TCDB::O30832
         (290 letters)



>FitnessBrowser__BFirm:BPHYT_RS22775
          Length = 325

 Score =  115 bits (289), Expect = 1e-30
 Identities = 88/289 (30%), Positives = 146/289 (50%), Gaps = 13/289 (4%)

Query: 4   QHSKTAARLMISPAVILLFLWMIVPLSMTLYFSFLRYNLLMPGME--SFTGWDNYYYFLT 61
           +  + AA L ++PA +++ ++++ P+  T+  SF  ++    GM   SF G  NY     
Sbjct: 46  RRQRRAAFLFLAPACVMVAIYVVWPILSTIRLSFFNWD----GMSEPSFVGLANYVELFH 101

Query: 62  DPAFSAALTNTILLVVGVLLITVVGGVLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSAL 121
              F  AL N ++ ++  LL   +G + +AL L+Q   G  IV+ L  APF +   V  L
Sbjct: 102 AQTFYTALKNNLIWLLLFLLAPPMG-LAVALYLNQAVAGIRIVKSLFFAPFVLSGVVVGL 160

Query: 122 VWKNMFMNPVNGMFAHIARGLGLPPFDFLSQAPLASIIGIVAWQWLPFATLILLTALQSL 181
           ++ + F +P  G+ A I  G G+P       A    I+    W    +  ++ LT L SL
Sbjct: 161 IF-SWFYDPTFGLLAVIL-GHGVPVLGDPRYATFG-IVFAALWPQTAYCMILYLTGLTSL 217

Query: 182 DREQMEAAEMDGASALDRFIHITVPHLTRAITVVVLIQTIFLLGVFAEILVTTNGGPGTA 241
           + EQ+EAA M+GA       H+ +P L     + +++  I  L  F  I V T GGP  +
Sbjct: 218 NAEQIEAARMEGARGWSMLWHVILPQLRPTTFMAIVVTIIGALRSFDLISVMTGGGPFES 277

Query: 242 STNITYLVYAQSLLNYDVGGGSAGGIVAVVLANIVAIFLMRMIGKNLDA 290
           ST + Y +Y Q++  Y +G  +A   VAVVL  I+ ++++  + + L A
Sbjct: 278 STVLAYYMYDQAIKYYRIGYSAA---VAVVLFAIMLVYIVYHLRRMLRA 323


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: 234
Number of extensions: 11
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: 325
Length adjustment: 27
Effective length of query: 263
Effective length of database: 298
Effective search space:    78374
Effective search space used:    78374
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.

Links

Downloads

Related tools

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