GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoA in Nocardiopsis gilva YIM 90087

Align 2-dehydro-3-deoxy-D-gluconate-6-phosphate aldolase (EC 4.1.2.55) (characterized)
to candidate WP_017619057.1 CDO52_RS15330 bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase

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



>NCBI__GCF_002263495.1:WP_017619057.1
          Length = 212

 Score =  216 bits (551), Expect = 2e-61
 Identities = 108/203 (53%), Positives = 143/203 (70%)

Query: 7   SAEQILTAGPVVPVIVINKLEHAVPMAKALVAGGVRVLELTLRTECAVEAIRLIAQEVPD 66
           S++ I    PV+PV+V+  +E AVP+A+ALVAGG+  +E+TLRTE A+ AI  IA EVPD
Sbjct: 5   SSDDIFALAPVIPVVVLEDVETAVPLARALVAGGLPTIEVTLRTEAALPAIERIAAEVPD 64

Query: 67  AIVGAGTVTNPQQLAEVTAAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMD 126
           A VGAGTVT P+Q      AG+ F +SPG T+ L  A  +  +P +PG++T SE M  ++
Sbjct: 65  AAVGAGTVTTPEQAQAAANAGSAFLVSPGCTDRLQGALHDTGLPYLPGVATASEAMAMLE 124

Query: 127 YGLREFKFFPAEANGGVKALQAIAGPFGKIRFCPTGGISLKNYRDYLALKSVLCVGGSWL 186
            G+R  KFFPAEA GG   L++++GP  + RFCPTGGI+L    DYLAL +V CVGG+WL
Sbjct: 125 RGVRALKFFPAEAAGGRTYLKSLSGPLPQARFCPTGGITLATAPDYLALPNVGCVGGTWL 184

Query: 187 VPADALESGDYDRITALAREAVA 209
            PADA+ +GD+ RI  LAREA A
Sbjct: 185 TPADAIATGDWGRIKTLAREAAA 207


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: 175
Number of extensions: 6
Number of successful extensions: 1
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: 212
Length adjustment: 21
Effective length of query: 192
Effective length of database: 191
Effective search space:    36672
Effective search space used:    36672
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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