GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TM1748 in Desulfovibrio vulgaris Miyazaki F

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 8500163 DvMF_0921 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= TCDB::Q9X270
         (289 letters)



>lcl|FitnessBrowser__Miya:8500163 DvMF_0921
           binding-protein-dependent transport systems inner
           membrane component (RefSeq)
          Length = 284

 Score =  216 bits (551), Expect = 4e-61
 Identities = 113/273 (41%), Positives = 160/273 (58%), Gaps = 3/273 (1%)

Query: 13  WKAFWLRFKKNKMAVIGGVFVLILIALAILAPYIAPYPYDEPHYIRAFEGPSKDFIFGTD 72
           W  FW R   + M   G   VL + A A+LAP+IAP+     +     + PS     GTD
Sbjct: 12  WLLFWTR---HPMLATGLSLVLAMSAAALLAPWIAPHDPTALNLTAILQPPSSAHPLGTD 68

Query: 73  ALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVDIMFAF 132
           ALGRD+ SR+L+  R +  +GF S  + + IG  LG  AG+ GG  D+ IM  VDIM  F
Sbjct: 69  ALGRDVLSRMLHGARVSLWVGFVSVGISVAIGLALGLAAGYFGGLADELIMRCVDIMLCF 128

Query: 133 PTFLFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAAGASTF 192
           P+F   + ++  L   L  I   IGLT W G+ARLVR + L L+  +F+ AA+ AGA   
Sbjct: 129 PSFFLILAVIAFLEPSLLNIMAVIGLTSWMGVARLVRAETLSLRERDFIAAARLAGAGPV 188

Query: 193 YIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGIGMMMA 252
            I+  H+LPN + P+LV+   GV GA++TES L+ +G+GV+PPMPSWGN++ EG  ++  
Sbjct: 189 RILCLHVLPNAVAPVLVSATLGVAGAILTESALSFLGLGVQPPMPSWGNMLLEGKDVLEI 248

Query: 253 FPHLLIFPAVTFAFTLISFTFLADGLRDAFNPR 285
            P L +FP      T++ +  L + LRD  +PR
Sbjct: 249 APWLSVFPGCAILLTVLGYNLLGESLRDLLDPR 281


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: 238
Number of extensions: 10
Number of successful extensions: 1
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: 284
Length adjustment: 26
Effective length of query: 263
Effective length of database: 258
Effective search space:    67854
Effective search space used:    67854
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: 47 (22.7 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 paper from 2022 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