GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Pantoea rwandensis LMG 26275

Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_084935308.1 HA51_RS14510 3-oxoacyl-ACP reductase FabG

Query= uniprot:Q8EGC1
         (252 letters)



>NCBI__GCF_002095475.1:WP_084935308.1
          Length = 244

 Score =  144 bits (364), Expect = 1e-39
 Identities = 85/252 (33%), Positives = 133/252 (52%), Gaps = 13/252 (5%)

Query: 1   MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYAL 60
           M  + KV ++TG + G+G A+A      GAK+      +   E   A LG + +  G  L
Sbjct: 1   MSFEGKVALVTGASRGIGRAIAETLVARGAKVVGTATSESGAEAISAYLGDNGK--GLLL 58

Query: 61  DITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINV 120
           ++TD   + +    +  +FG++++LVNNAGI RD +L++ KD         D++  +++ 
Sbjct: 59  NVTDAASIESVLEKVRAEFGEVDILVNNAGITRDNLLMRMKD---------DEWADILDT 109

Query: 121 NLTGTFLCGREAAAAMIESGQAGVIVNISSLAKAGNVGQSNYAASKAGVAAMSVGWAKEL 180
           NLT  F   +    AM++     +I   S +   GN GQ+NYAA+KAG+   S   A+E+
Sbjct: 110 NLTSVFRLSKAVLRAMMKKRVGRIITIGSVVGTMGNAGQANYAAAKAGLIGFSKSLAREI 169

Query: 181 ARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFII--ENDY 238
           A   I    VAPG I T+MT A+  +    +   VP GRLG  +EIA+ V F+   E  Y
Sbjct: 170 ASRGITVNVVAPGFIETDMTRALNEDQRSGILAEVPAGRLGDPQEIANAVAFLASDEASY 229

Query: 239 VNGRVFEVDGGI 250
           + G    V+GG+
Sbjct: 230 ITGETLHVNGGM 241


Lambda     K      H
   0.317    0.134    0.369 

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: 164
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: 252
Length of database: 244
Length adjustment: 24
Effective length of query: 228
Effective length of database: 220
Effective search space:    50160
Effective search space used:    50160
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: 46 (22.3 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