GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Alkalihalobacterium alkalinitrilicum DSM 22532

Align 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) (characterized)
to candidate WP_078429241.1 BK574_RS15640 bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase

Query= BRENDA::D4GV57
         (219 letters)



>NCBI__GCF_002019605.1:WP_078429241.1
          Length = 214

 Score =  176 bits (447), Expect = 2e-49
 Identities = 90/201 (44%), Positives = 130/201 (64%), Gaps = 1/201 (0%)

Query: 13  LADSGVVAVMRGADADTIIDVADALHEGGVTAYEITADNPDAMDLIREVSASFSDNEAIV 72
           L +  +VA++RG +  + + VADA+H GGV   E+T +  DA  +I ++  S S+ +  +
Sbjct: 7   LKEYRLVAIIRGIETSSAVPVADAIHAGGVHLIEVTMNTDDAPQMISKLVDS-SNGKMYI 65

Query: 73  GAGTALDAPTANAAIQAGAEFVVGPNFDEGVVETCNRYGTLVAPGIMTPTEATDAYSAGA 132
           GAGT L+   A  AI AGA++++ PN DE V++     G  V PG+MTPTE   AY+AGA
Sbjct: 66  GAGTVLNKEMAKEAIAAGAQYLITPNVDEDVIKFGLERGIDVLPGVMTPTEIVKAYNAGA 125

Query: 133 DLVKVFPASSLGPGHLKSMKGPLPQIPMMPTGGVGLDNAADYIEAGAVVVGAGGALMDDE 192
            +VKVFP+SSLG  HLK ++GPL  IPM+  GGV +DN   + +AGAV VG G +L+  E
Sbjct: 126 KMVKVFPSSSLGVSHLKELQGPLGHIPMVAVGGVNIDNVKSFFKAGAVAVGVGSSLIKKE 185

Query: 193 AIENGDFEAITETAREFSNII 213
           AI  G+F+ +T++A  F   I
Sbjct: 186 AITQGNFDLLTQSANAFMQTI 206


Lambda     K      H
   0.314    0.133    0.374 

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: 147
Number of extensions: 8
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: 219
Length of database: 214
Length adjustment: 22
Effective length of query: 197
Effective length of database: 192
Effective search space:    37824
Effective search space used:    37824
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Apr 09 2024. 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