GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaS in Rhizobium leguminosarum bv. trifolii WSM1325

Align RhaS, 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_003553864.1 RLEG_RS27470 rhamnose ABC transporter substrate-binding protein

Query= TCDB::Q7BSH5
         (331 letters)



>NCBI__GCF_000023185.1:WP_003553864.1
          Length = 331

 Score =  622 bits (1604), Expect = 0.0
 Identities = 318/331 (96%), Positives = 323/331 (97%)

Query: 1   MKLAKTLALGVALAVAMMAGTASAKDIKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEV 60
           MKLAK LA+GVA AVAMMAGTASA DIKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEV
Sbjct: 1   MKLAKKLAIGVAFAVAMMAGTASAADIKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEV 60

Query: 61  IYTGPTSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVA 120
           IYTGPT+TTAEGQIEVINSLIAQGV AIAVSANDPDALVPALKKA QRGIKVISWDSGVA
Sbjct: 61  IYTGPTTTTAEGQIEVINSLIAQGVSAIAVSANDPDALVPALKKAAQRGIKVISWDSGVA 120

Query: 121 PEGRILQLNPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKKQLKD 180
           PEGRILQLNPSSNELIGKMCLTL KDHL+GGKGDFAILSATTTSTNQNIWIDQMKKQLKD
Sbjct: 121 PEGRILQLNPSSNELIGKMCLTLVKDHLDGGKGDFAILSATTTSTNQNIWIDQMKKQLKD 180

Query: 181 FPGLNLVTTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGLVGKV 240
           FPGLNLVTTVYGDDLSDKSYREAEGLLK+NPN+KVIVAPTTVGVLAASKVVEDKGLVGKV
Sbjct: 181 FPGLNLVTTVYGDDLSDKSYREAEGLLKANPNIKVIVAPTTVGVLAASKVVEDKGLVGKV 240

Query: 241 YVTGLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEINAGRM 300
           YVTGLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEI  GRM
Sbjct: 241 YVTGLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEIEVGRM 300

Query: 301 GKIKVGDNGEAAMADPFVYNASNIDQFSKVF 331
           GKIKVGDNGEAAMADPFVYNASNIDQFSKVF
Sbjct: 301 GKIKVGDNGEAAMADPFVYNASNIDQFSKVF 331


Lambda     K      H
   0.313    0.131    0.365 

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: 533
Number of extensions: 15
Number of successful extensions: 1
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: 331
Length of database: 331
Length adjustment: 28
Effective length of query: 303
Effective length of database: 303
Effective search space:    91809
Effective search space used:    91809
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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