GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Sinorhizobium meliloti 1021

Align 2-dehydro-3-deoxy-D-gluconate-6-phosphate aldolase (EC 4.1.2.55) (characterized)
to candidate SMc02043 SMc02043 KHG/KDPG aldolase

Query= metacyc::MONOMER-15645
         (213 letters)



>FitnessBrowser__Smeli:SMc02043
          Length = 217

 Score =  158 bits (399), Expect = 8e-44
 Identities = 89/205 (43%), Positives = 123/205 (60%), Gaps = 3/205 (1%)

Query: 9   EQILTAGPVVPVIVINKLEHAVPMAKALVAGGVRVLELTLRTECAVEAIRLIAQEVPDAI 68
           +Q  T G VVPVI I +   AV +A AL+ GG+ + E+T RTE A E I ++A++ P+ +
Sbjct: 6   DQAATLG-VVPVIAIERSSDAVALADALLEGGLPLAEITFRTEAAAEVIAIMAEKRPELL 64

Query: 69  VGAGTVTNPQQLAEVTAAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYG 128
           VGAGT+  P  L    +AGA+F ++PG    ++ AA     P  PGI T S+L      G
Sbjct: 65  VGAGTILTPDALRAAISAGARFGLAPGFDAEIVAAAKAKDFPFAPGIMTPSDLTAVSRNG 124

Query: 129 LREFKFFPAEANGGVKALQAIAGPFGKI--RFCPTGGISLKNYRDYLALKSVLCVGGSWL 186
           L+  KFFPA+A GG   L+AI+ PF  +  RF PTGG+SL N  ++L L +V  VGG+W+
Sbjct: 125 LKLAKFFPAKAAGGPSMLEAISAPFAHLGTRFVPTGGVSLDNMHEWLKLGAVAAVGGTWI 184

Query: 187 VPADALESGDYDRITALAREAVAGA 211
                +  G +  ITA AR AVA A
Sbjct: 185 ATKADIGEGRWADITAKARAAVARA 209


Lambda     K      H
   0.318    0.135    0.390 

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: 168
Number of extensions: 7
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: 213
Length of database: 217
Length adjustment: 22
Effective length of query: 191
Effective length of database: 195
Effective search space:    37245
Effective search space used:    37245
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: 45 (21.9 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