GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TM1748 in Klebsiella michiganensis M5al

Align TM1748, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate BWI76_RS09110 BWI76_RS09110 glutathione ABC transporter permease GsiD

Query= TCDB::Q9X270
         (289 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS09110 BWI76_RS09110 glutathione
           ABC transporter permease GsiD
          Length = 303

 Score =  223 bits (567), Expect = 5e-63
 Identities = 108/274 (39%), Positives = 168/274 (61%), Gaps = 1/274 (0%)

Query: 13  WKAFWLRFKKNKMAVIGGVFVLILIALAILAPYIAPYPYDEPH-YIRAFEGPSKDFIFGT 71
           W  FW RF++  +A+  G+FVL+LIA+AI+AP+IAP+  +    Y R  +GPS    FG 
Sbjct: 27  WHEFWRRFRRQPVAMGAGIFVLLLIAVAIVAPWIAPFDAENYFDYDRLNDGPSMMHWFGV 86

Query: 72  DALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVDIMFA 131
           D+LGRD+FSR+L   + +   G  + F+   IG +LG +AG+  GW D+ IM I D++FA
Sbjct: 87  DSLGRDIFSRVLVGAQISLAAGVLAVFIGAAIGTVLGLLAGYYEGWWDRIIMRICDVLFA 146

Query: 132 FPTFLFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAAGAST 191
           FP  L  + +V  +G G+  + +A+ +      ARLVRG  L LK   F+E+A++ GAS 
Sbjct: 147 FPGILLAIAVVAVMGSGMSNVIIAVAIFSIPAFARLVRGNTLVLKQQTFIESARSIGASD 206

Query: 192 FYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGIGMMM 251
             I+  HILP  +  I+V     +  ++++ + L+ +G+G +PP P WG ++ E    M+
Sbjct: 207 ANILFNHILPGTVSSIVVYFTMRIGVSIISAASLSFLGLGAQPPTPEWGAMLNEARADMV 266

Query: 252 AFPHLLIFPAVTFAFTLISFTFLADGLRDAFNPR 285
             PH+ +FPA+    T+++F  L DGLRDA +PR
Sbjct: 267 MAPHVALFPAIAIFLTVLAFNLLGDGLRDALDPR 300


Lambda     K      H
   0.331    0.147    0.457 

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: 244
Number of extensions: 13
Number of successful extensions: 3
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: 289
Length of database: 303
Length adjustment: 26
Effective length of query: 263
Effective length of database: 277
Effective search space:    72851
Effective search space used:    72851
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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