GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaP in Rhodococcus qingshengii djl-6-2

Align RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate WP_007730024.1 C1M55_RS26585 ABC transporter permease

Query= TCDB::Q7BSH3
         (333 letters)



>NCBI__GCF_002893965.1:WP_007730024.1
          Length = 347

 Score =  169 bits (427), Expect = 1e-46
 Identities = 101/305 (33%), Positives = 160/305 (52%), Gaps = 3/305 (0%)

Query: 5   IRKRETLLFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDL 64
           + K    +  + V +  VFS   + F T  NL+ +    + ++I+A+A   VI    IDL
Sbjct: 25  VNKPTLAMLAVTVAVAAVFSATTSSFLTFTNLSNLATQIAPVLIIAVAMTFVITAGQIDL 84

Query: 65  SVAANLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLG 124
           SV A +AF     A +  A  D  LV   + A V+GA  G +NG+L     IPP +VTL 
Sbjct: 85  SVGAIVAFVAAMSAELIQAGVDSSLV--FVAAPVMGAAWGLVNGWLAAYQGIPPFIVTLA 142

Query: 125 TLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQ 184
           T+++ RG+A   + G  V     T  F  +  +  LG    +W+ +++V++  + L   +
Sbjct: 143 TMSVIRGIALYRTEGFSVPVPADT-YFAKLGTSEFLGFSASAWIALVVVVIGAIALNRMR 201

Query: 185 FGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFE 244
           FGR     G N  +   +G++T     +  V +G  AG+A  L  +R      + A GFE
Sbjct: 202 FGRYVTGIGSNVESVRRSGVNTRRVLMMTLVFTGLAAGIAGLLIAARLGSGSANSATGFE 261

Query: 245 LDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAV 304
           L  + A V+GG ++ GG G+V GTV+GA+  G+I N L ++G+SPF    I+G V++LA+
Sbjct: 262 LTVITAVVLGGTNLFGGRGTVIGTVIGAVLTGIIANGLTLLGVSPFLTPIITGVVLLLAI 321

Query: 305 AFNAR 309
             N R
Sbjct: 322 WINMR 326


Lambda     K      H
   0.328    0.141    0.413 

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: 294
Number of extensions: 15
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: 333
Length of database: 347
Length adjustment: 28
Effective length of query: 305
Effective length of database: 319
Effective search space:    97295
Effective search space used:    97295
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: 49 (23.5 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