GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaS in Herbaspirillum seropedicae SmR1

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 HSERO_RS05095 HSERO_RS05095 LacI family transcription regulator

Query= TCDB::Q7BSH5
         (331 letters)



>FitnessBrowser__HerbieS:HSERO_RS05095
          Length = 335

 Score =  125 bits (314), Expect = 1e-33
 Identities = 96/295 (32%), Positives = 144/295 (48%), Gaps = 12/295 (4%)

Query: 2   KLAKTLALGVALAVAMMAGTASAKDIKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEVI 61
           K A  L   +A      A  A  K I I  VVK  G  +F+    G +E A    GV   
Sbjct: 5   KSACVLVSALAAVGFASALQAQNKPIDIVTVVKITGISWFNRMEVGVKEFAAANPGVTTR 64

Query: 62  YTGPTSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVAP 121
             GP  + A  Q  ++  L+A+ VDAIAV + DP  L P LK+A  RGIKV++ ++    
Sbjct: 65  QIGPAQSDAAQQQRLVEDLVAKKVDAIAVVSMDPPTLEPVLKRALDRGIKVVTHEAD-NQ 123

Query: 122 EGRILQLNPSSNELIGKMCLTLAKDHLE---GGKGDFAILSATTTSTNQNIWIDQ-MKKQ 177
           +  ++ +    N   G        D L    G  G ++ L  +  S +Q  W D      
Sbjct: 124 KNTLVDIEAFDNTAYGARL----NDRLAACMGQAGKWSSLVGSLGSQSQVQWADGGAANA 179

Query: 178 LKDFPGLNLVTTVYGD-DLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGL 236
            K +P + LV       + ++K+Y +A+ +L+ +P++K     +++ VL   + VE+ GL
Sbjct: 180 AKKYPKMTLVDAKNESANDAEKAYAKAKEILRKHPDIKGFQGSSSLDVLGIGRAVEEAGL 239

Query: 237 VGKVYVTGLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGE--TDG 289
            GKV V G GLPSE A  ++SGA    A W+P D G +  + A  LV+G+  TDG
Sbjct: 240 QGKVCVYGTGLPSEAAKFLESGAVGGIAFWDPKDAGLAMNKAAMMLVQGKKITDG 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: 258
Number of extensions: 14
Number of successful extensions: 2
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: 335
Length adjustment: 28
Effective length of query: 303
Effective length of database: 307
Effective search space:    93021
Effective search space used:    93021
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