GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Sinorhizobium meliloti 1021

Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate SM_b20679 SM_b20679 tartronate semialdehyde reductase

Query= reanno::psRCH2:GFF2390
         (296 letters)



>FitnessBrowser__Smeli:SM_b20679
          Length = 294

 Score =  158 bits (399), Expect = 2e-43
 Identities = 106/287 (36%), Positives = 145/287 (50%), Gaps = 8/287 (2%)

Query: 3   IGFIGLGNMGAPMAHNLLKAGHQLSVFDLNAAAVENLVGAGALPVDSPTAIAQGNAELII 62
           IGFIGLG MG PMA +L  AGH++          + LV  G   V++P A+A+   + II
Sbjct: 4   IGFIGLGIMGTPMARHLQDAGHEIITSKFVIPPRQELVENGLEIVETPKALAE-TVDTII 62

Query: 63  TMLPAAAHVKGVYLGVNGLIAHSRAGVMLIDCSTIDPHSAREVAKAAAEHGNPMLDAPVS 122
            MLP    VK V  G NG+      G ++ID S+I P   +E AK   E G   +DAPVS
Sbjct: 63  LMLPDTPEVKDVLFGENGVYYGLGEGKLVIDMSSISPIETKEFAKKVRETGAEYIDAPVS 122

Query: 123 GGTGGAAAGTLTFMVGGSDPDFDHAQPILAAMGKNIVHCGAAGNGQVAKVANNMLLGISM 182
           GG  GA   +L+ M GG    F+ A P+   MGKNI   G  G+GQV KVAN +++ +++
Sbjct: 123 GGEVGAKNASLSIMAGGKPSSFERALPLFKLMGKNITLVGDCGDGQVTKVANQIIVALTI 182

Query: 183 IGVAEAMALGVALGMDAKTLAGVINTSSGRCWSSDTYNPFPGVLDNVPSSRGYSGGFGSD 242
             V+EA+      G D    A V     G   SS        V  +    R +  GF   
Sbjct: 183 EAVSEALVFASKAGADP---ARVREALMGGFASSRILE----VHGDRMIKRTFEPGFRIS 235

Query: 243 LMLKDLGLATEAAKQVRQPVILGALAQQLYQSFSAQGHGGLDFSAII 289
           L  KDL LA + AK +   +   A  Q+L+ + +A G  GLD S ++
Sbjct: 236 LHQKDLNLALQGAKSLGISLPNTAATQELFNNCAANGDSGLDHSGLV 282


Lambda     K      H
   0.318    0.134    0.392 

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: 211
Number of extensions: 9
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: 296
Length of database: 294
Length adjustment: 26
Effective length of query: 270
Effective length of database: 268
Effective search space:    72360
Effective search space used:    72360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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