GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoD in Nocardioides daejeonensis MJ31

Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate WP_110206713.1 DNK54_RS09440 3-oxoacid CoA-transferase subunit B

Query= reanno::psRCH2:GFF1044
         (209 letters)



>NCBI__GCF_003194585.1:WP_110206713.1
          Length = 236

 Score =  184 bits (468), Expect = 9e-52
 Identities = 93/206 (45%), Positives = 140/206 (67%), Gaps = 4/206 (1%)

Query: 4   TREQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEEEID 63
           T +++A+  A+++ +G ++NLGIG PT +A+++P  + V L +ENG+LG+GP    ++ID
Sbjct: 29  TMDELAEVIARDIPEGSFLNLGIGQPTKIADHLPAELGVILHTENGMLGMGPAADGDQID 88

Query: 64  PDLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPGK-- 121
           PDL NAGK  VT LPG+S+F +A SFAM+RGGH+++ +LGA QV+  GDLANW   GK  
Sbjct: 89  PDLTNAGKVPVTELPGASYFHHADSFAMMRGGHLDVCVLGAYQVAANGDLANWH-TGKPD 147

Query: 122 MVKGMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDVT 181
            +  +GGAMDL  G K V+V+M    K G  K++ +C  PLTG+G V R+ TD G+ +V 
Sbjct: 148 AIPAVGGAMDLAIGAKDVLVMMTLFGKDGTPKLVRSCSYPLTGVGCVSRVYTDHGIFEVG 207

Query: 182 EQGLKLVELAEGVSFDELQEATGSPI 207
            + + +V    G+S  +L+E  G P+
Sbjct: 208 GESV-VVRATWGISVADLEERLGMPL 232


Lambda     K      H
   0.318    0.138    0.404 

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: 182
Number of extensions: 12
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: 209
Length of database: 236
Length adjustment: 22
Effective length of query: 187
Effective length of database: 214
Effective search space:    40018
Effective search space used:    40018
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.

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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