GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1748 in Geobacter daltonii FRC-32

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 WP_012648104.1 GEOB_RS15070 ABC transporter permease

Query= TCDB::Q9X270
         (289 letters)



>NCBI__GCF_000022265.1:WP_012648104.1
          Length = 284

 Score =  231 bits (589), Expect = 1e-65
 Identities = 114/274 (41%), Positives = 171/274 (62%), Gaps = 6/274 (2%)

Query: 17  WLRFKKNKMAVIGGVFVLILIALAILAPYIAPYPYDEPHYIRAFE---GPSKDFIFGTDA 73
           W RF+ N +A+ G + V I+  ++ LAP I PY   +P+ + A+     PS    FGTD 
Sbjct: 13  WRRFRGNPLALSGALVVCIMFLISFLAPAITPY---QPNTLDAYHVLLPPSTSHWFGTDD 69

Query: 74  LGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVDIMFAFP 133
           LGRD+FSR+++  R +  +GF +  +  +IG ++G +AG+ GGW+D  +M  VDIM  FP
Sbjct: 70  LGRDVFSRMVFGARVSLKVGFVAIGIATVIGTVVGLIAGYYGGWVDSLLMRFVDIMLCFP 129

Query: 134 TFLFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAAGASTFY 193
           TF   + +VT     +  I L IG TGW G++RLVR +VL L+  +FV AA+A G S   
Sbjct: 130 TFFLILAIVTIREPSILNIMLIIGFTGWMGVSRLVRAEVLSLRERDFVLAARAIGCSDLR 189

Query: 194 IIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGIGMMMAF 253
           II +HILPN IGP+LV    G+  A++TES L+ +G+GV+PP PSWGN++  G   +   
Sbjct: 190 IIFRHILPNAIGPVLVYATLGIAAAILTESSLSFLGIGVQPPEPSWGNILASGKEFLEFA 249

Query: 254 PHLLIFPAVTFAFTLISFTFLADGLRDAFNPRSE 287
             L +FP +    T +S+  + +G+RDA +PR++
Sbjct: 250 WWLFLFPGLAITITTLSYYLVGEGIRDALDPRNK 283


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: 272
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: 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 24 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