GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artM in Herbaspirillum seropedicae SmR1

Align Histidine transport system permease protein HisM (characterized)
to candidate HSERO_RS10770 HSERO_RS10770 amino acid ABC transporter permease

Query= SwissProt::P0AEU3
         (238 letters)



>FitnessBrowser__HerbieS:HSERO_RS10770
          Length = 221

 Score =  117 bits (294), Expect = 1e-31
 Identities = 73/206 (35%), Positives = 113/206 (54%), Gaps = 10/206 (4%)

Query: 22  GVAITLWLLILSVVIGGVLALFLAIGRVSSNKYIQFPIWLFTYIFRGTPLYVQLLVFYSG 81
           GV  TL   + S++ G VL   LA+ R+   + I +P  ++  + RGTPL VQ+ V Y G
Sbjct: 19  GVGYTLLFALASMLGGLVLGFVLAVARIVPWRPIHWPAAIYVSMMRGTPLLVQIFVVYYG 78

Query: 82  MYTLEIVKGTEFLNAFFRSGLNCTVLALTLNTCAYTTEIFAGAIRSVPHGEIEAARAYGF 141
           +  +    G EF      S L   VL L+LN  AY +E   GAI  V  G+  AA + G 
Sbjct: 79  LPGM----GIEF------SPLTAGVLTLSLNASAYLSESLRGAILGVTRGQWNAAFSVGL 128

Query: 142 STFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVPDLLKIARDINAATYQPFT 201
           + F+  R II+P A+RIA+P+ SN +I ++  T+L    TV +L+   +++ A T++P  
Sbjct: 129 TYFQTLRYIIVPQAVRIAVPSMSNTLISLIKDTSLVSVITVTELMLATKEVIAVTFRPLP 188

Query: 202 AFGIAAVLYLIISYVLISLFRRAEKR 227
            +  AA +Y ++S    +L  R EK+
Sbjct: 189 LYVAAAAIYWMLSLCFEALQHRLEKK 214


Lambda     K      H
   0.330    0.142    0.438 

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: 100
Number of extensions: 4
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: 238
Length of database: 221
Length adjustment: 23
Effective length of query: 215
Effective length of database: 198
Effective search space:    42570
Effective search space used:    42570
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 (21.9 bits)
S2: 46 (22.3 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