GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaP in Klebsiella michiganensis M5al

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 BWI76_RS00280 BWI76_RS00280 ribose ABC transporter permease

Query= TCDB::Q7BSH3
         (333 letters)



>FitnessBrowser__Koxy:BWI76_RS00280
          Length = 321

 Score =  181 bits (458), Expect = 3e-50
 Identities = 103/300 (34%), Positives = 165/300 (55%), Gaps = 4/300 (1%)

Query: 14  LIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVAANLAFT 73
           + ++V+I + ST + +F T  NL  I   TS+  I+A+    VILT  IDLSV + LA T
Sbjct: 24  IALLVLIAIVSTMSPNFFTVNNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLALT 83

Query: 74  GMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTIYRGMA 133
           G   A +     ++  +V +  A+ +GA +GA+ G +V    +   + TL  + + RG+ 
Sbjct: 84  GAVAASIVGI--EVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVT 141

Query: 134 FVLSGGAWVNAH--QMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQFGRSAYA 191
            V + G+ VN        +F        LG+P   W+  I+ +  + +L +T+ GR  YA
Sbjct: 142 MVYTNGSPVNTGFTDNADLFGWFGIGRPLGIPTPVWIMAIVFLAAWYMLHHTRLGRYIYA 201

Query: 192 TGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFELDSVAAC 251
            GGN  A   +GI     K + + L G LA LA  + V+R + A      G+ELD++AA 
Sbjct: 202 LGGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEVARLSSAQPTAGTGYELDAIAAV 261

Query: 252 VIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAVAFNARRE 311
           V+GG S+AGG G + GT++GAL LG + N L ++G+S + QM +   VI+LAV  + +++
Sbjct: 262 VLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVDNKKQ 321


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: 260
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: 321
Length adjustment: 28
Effective length of query: 305
Effective length of database: 293
Effective search space:    89365
Effective search space used:    89365
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: 48 (23.1 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