GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoD in Burkholderia phytofirmans PsJN

Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate BPHYT_RS21420 BPHYT_RS21420 3-oxoadipate CoA-transferase subunit B

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



>lcl|FitnessBrowser__BFirm:BPHYT_RS21420 BPHYT_RS21420 3-oxoadipate
           CoA-transferase subunit B
          Length = 219

 Score =  219 bits (558), Expect = 3e-62
 Identities = 108/205 (52%), Positives = 144/205 (70%), Gaps = 1/205 (0%)

Query: 4   TREQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEEEID 63
           TR++MA+R A ++ +G YVNLGIG+PTLVAN++    +++L SENGLLG+GP P + E D
Sbjct: 5   TRDEMAKRVALDIPEGAYVNLGIGVPTLVANHLDADKEIFLHSENGLLGMGPAPAKGEED 64

Query: 64  PDLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPG-KM 122
            +LINAGKQ VT L G  +F +A SFAM+RGGH++  +LGA QVS KGDLANW       
Sbjct: 65  DELINAGKQHVTLLTGGCYFHHADSFAMMRGGHLDFCVLGAFQVSAKGDLANWHTGAPDA 124

Query: 123 VKGMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDVTE 182
           +  +GGAMDL  G K+V V+MEH  K G  KI   C  P+TG+G VDRI TDL ++DVT+
Sbjct: 125 IPAVGGAMDLAIGAKQVYVMMEHLTKQGESKIAAECSYPVTGVGCVDRIYTDLAMIDVTD 184

Query: 183 QGLKLVELAEGVSFDELQEATGSPI 207
           +GL + E+   + FD L + TG P+
Sbjct: 185 RGLVVREIFSDIDFDALHKLTGVPL 209


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: 181
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: 209
Length of database: 219
Length adjustment: 22
Effective length of query: 187
Effective length of database: 197
Effective search space:    36839
Effective search space used:    36839
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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