GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaS in Sinorhizobium meliloti 1021

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 SM_b20484 SM_b20484 sugar ABC transporter substrate-binding protein

Query= TCDB::Q7BSH5
         (331 letters)



>FitnessBrowser__Smeli:SM_b20484
          Length = 330

 Score =  129 bits (325), Expect = 8e-35
 Identities = 102/297 (34%), Positives = 156/297 (52%), Gaps = 12/297 (4%)

Query: 3   LAKTLALGVALAVAMMAGTASAKDI-KIGLVVKSLGNGFFDAANKGAQEAAKELGGVEVI 61
           LA  LA  ++LA A    TA+A+D  K+G+VVK  G  +F+A   G +E  ++LG V+  
Sbjct: 6   LAAALAASLSLAGAY---TAAAQDTGKVGVVVKIGGIPWFNAMEAGIKERGEKLG-VDAF 61

Query: 62  YTGPTSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVAP 121
             GPTS     Q+  I  LIAQ V  I V  ND   L P L KA ++GI VI+ +S  + 
Sbjct: 62  MVGPTSADPALQVRAIEDLIAQNVKVIGVVPNDAKVLEPVLTKAREKGIIVITHESP-SQ 120

Query: 122 EGRILQLNPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKKQLK-D 180
           +G       +S    G+    L  + + GGKG++A+   + T    N W D   + +K +
Sbjct: 121 KGADWDFELASATGFGEAHAKLLAEKM-GGKGEYAVFVGSLTVPLHNAWADAAIEYIKKN 179

Query: 181 FPGLNLVTTVYG--DDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGLVG 238
            P + LV   YG  +D+ DKS   A  L+ ++P++K  +A  + G + A + +E++  VG
Sbjct: 180 HPEMTLVGDRYGVAEDV-DKSRSTALDLISAHPDLKGFLAFGSQGPIGAGRAIEERRKVG 238

Query: 239 KVYVTGLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEI 295
           +++V G   P +    IKS A     +WNP   G     +A +L+KGE + K G EI
Sbjct: 239 EIFVLGPFSPGQGQKLIKSDAISGGFMWNPKQAGEVFVTLAAKLMKGE-EIKDGEEI 294


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: 287
Number of extensions: 19
Number of successful extensions: 4
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: 330
Length adjustment: 28
Effective length of query: 303
Effective length of database: 302
Effective search space:    91506
Effective search space used:    91506
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 Sep 17 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