GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Klebsiella michiganensis M5al

Align glyoxylate reductase (EC 1.1.1.26); glycerate dehydrogenase (EC 1.1.1.29); hydroxypyruvate reductase (EC 1.1.1.81) (characterized)
to candidate BWI76_RS12790 BWI76_RS12790 lactate dehydrogenase

Query= BRENDA::Q9C9W5
         (386 letters)



>FitnessBrowser__Koxy:BWI76_RS12790
          Length = 329

 Score =  112 bits (281), Expect = 1e-29
 Identities = 77/242 (31%), Positives = 114/242 (47%), Gaps = 25/242 (10%)

Query: 63  CDGVIGQLTEDWGETLFSALSKAGGKAFSNMAVGYNNVDVEAANKYGIAVGNTPGVLTET 122
           C+ V   + +D    +   L   G K  +    G+NNVD++AA + G+ V   P    E 
Sbjct: 45  CEAVCIFVNDDGSRPVLEELKAHGVKYIALRCAGFNNVDLDAAKELGLRVVRVPAYSPEA 104

Query: 123 TAELAASLSLAAARRIVEADEFMRGGLY--EGWLPHLFVGNLLKGQTVGVIGAGRIGSAY 180
            AE A  + ++  RRI  A +  R   +  EG       G  + G+T GVIG G+IG A 
Sbjct: 105 VAEHAIGMMMSLNRRIHRAYQRTRDANFSLEG-----LTGFTMHGKTAGVIGTGKIGVAA 159

Query: 181 ARMMVEGFKMNLIYFDLYQSTRLEKFVTAYGQFLKANGEQPVTWKRASSMEEVLREADLI 240
            R++ +GF M L+ FD Y S         Y                   +E + RE+D+I
Sbjct: 160 LRIL-KGFGMRLLAFDPYPSAAALDMGVEY-----------------VDLETLYRESDVI 201

Query: 241 SLHPVLDKTTYHLVNKERLAMMKKEAILVNCSRGPVIDEAALVEHLKENPMFRVGLDVFE 300
           SLH  L    YHL+N      MK   +++N SRG +ID  A ++ LK   +  +G+DV+E
Sbjct: 202 SLHCPLTDENYHLLNHAAFERMKDGVMIINTSRGALIDSQAAIDALKHQKIGALGMDVYE 261

Query: 301 EE 302
            E
Sbjct: 262 NE 263


Lambda     K      H
   0.318    0.135    0.399 

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: 257
Number of extensions: 12
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: 386
Length of database: 329
Length adjustment: 29
Effective length of query: 357
Effective length of database: 300
Effective search space:   107100
Effective search space used:   107100
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: 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