GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaP in Dinoroseobacter shibae DFL-12

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 3609042 Dshi_2431 Monosaccharide-transporting ATPase (RefSeq)

Query= TCDB::Q7BSH3
         (333 letters)



>FitnessBrowser__Dino:3609042
          Length = 328

 Score =  145 bits (365), Expect = 2e-39
 Identities = 94/313 (30%), Positives = 163/313 (52%), Gaps = 19/313 (6%)

Query: 1   MARLIRKRETLLFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTK 60
           M + ++  ETLL L+ + + V  S  +  F    NL+    + +   ++A A   +I++ 
Sbjct: 16  MEQRLKSWETLLLLVAIGIFVANSFASPYFLNAWNLSDATFNFTEKAMIAFAMALLIISG 75

Query: 61  SIDLSVAANLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIV 120
            IDLSVA+ +A    + AM  A    +    L+L+ + +G   GA NG LV  + +P IV
Sbjct: 76  EIDLSVASIIALA--STAMGAAVQMGVGTPGLVLIGLGVGLLCGAFNGVLVTRMGLPSIV 133

Query: 121 VTLGTLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRT-PVLGLPVLSWV-------GIII 172
           VT+GT++++RG+++++ G            F   P +    G   + WV         II
Sbjct: 134 VTIGTMSLFRGISYIVLGDQ---------AFRGYPESFSWFGQGYVWWVISFELVLFAII 184

Query: 173 VILMYVLLRYTQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRY 232
            ++  +LL  T FGR+ YA G N T A+++GI     KF+ F+L+G ++G+A+    +R 
Sbjct: 185 AVIYAMLLHKTNFGRAVYAIGNNATGAMFSGIRVQRVKFILFLLTGLMSGVAAICLTARL 244

Query: 233 AVAYVDIANGFELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQ 292
                 IA G+EL+ V   V+GG+SI GG G++ G V+ A  +G++   L ++ +     
Sbjct: 245 GSTRPSIAMGWELEVVTMVVLGGVSILGGSGTILGVVIAAFVMGLVTFGLGLLNVPGIVM 304

Query: 293 MAISGTVIILAVA 305
             + G ++I  +A
Sbjct: 305 SIVIGALLIGVIA 317


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: 266
Number of extensions: 17
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: 328
Length adjustment: 28
Effective length of query: 305
Effective length of database: 300
Effective search space:    91500
Effective search space used:    91500
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 17 2021. 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