GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaP in Tistlia consotensis USBA 355

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_085121058.1 B9O00_RS01465 ABC transporter permease

Query= TCDB::Q7BSH3
         (333 letters)



>NCBI__GCF_900177295.1:WP_085121058.1
          Length = 335

 Score =  165 bits (417), Expect = 2e-45
 Identities = 110/318 (34%), Positives = 173/318 (54%), Gaps = 13/318 (4%)

Query: 3   RLIRKRETLLFL----IIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVIL 58
           RL+++  T L L    + +V+  V S  +  F T  N+  I + + ++ IL++    VIL
Sbjct: 23  RLLKQLATSLELRMLGLALVIGAVLSLLSPYFLTESNIFNILDQSVVIGILSIGMTFVIL 82

Query: 59  TKSIDLSVAANLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPP 118
           T  IDLSV +    +G+ + +   A  D P+ V IL+ V+ GA +G ++G L+    +  
Sbjct: 83  TGGIDLSVGSVAGLSGIVLGL---ALKDYPIPVAILLGVLTGAGVGLVSGILIGYFRLAA 139

Query: 119 IVVTLGTLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYV 178
            VVTLG + I R +A++ SG   ++         S+  T V G+P          +L + 
Sbjct: 140 FVVTLGMMAIGRSLAYIFSGQTAISGFPSD--LSSIVYTDVFGIPTNVLFLGFAYLLAWG 197

Query: 179 LLRYTQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVD 238
            L YT+ GR+ YA G N  AA  AG+   +   L +V+SGALA +A    V++       
Sbjct: 198 YLTYTKGGRTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVDPL 257

Query: 239 IANGFELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGT 298
             NG ELD++AA VIGG S+ GG GS+ GT++G L + +I+N L ++G+SPF Q +  G+
Sbjct: 258 TGNGMELDAIAAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQGSAIGS 317

Query: 299 VIILAV----AFNARRER 312
           +II+A+       AR ER
Sbjct: 318 IIIMALLVERLVRARSER 335


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: 290
Number of extensions: 25
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 333
Length of database: 335
Length adjustment: 28
Effective length of query: 305
Effective length of database: 307
Effective search space:    93635
Effective search space used:    93635
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 Apr 09 2024. 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