GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Arenimonas metalli CF5-1

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate WP_034211337.1 N787_RS05630 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-20676
         (396 letters)



>NCBI__GCF_000747155.1:WP_034211337.1
          Length = 387

 Score = 86.7 bits (213), Expect = 1e-21
 Identities = 68/221 (30%), Positives = 105/221 (47%), Gaps = 15/221 (6%)

Query: 6   SKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHWPKEYG 65
           S+EE   +D V +F  + V         +GR  +  E+V     +   G ++   P++YG
Sbjct: 16  SEEERMIQDSVARFTDERVLPIIGDCFDQGRFPS--ELVPEIAAMGLFGSSL---PEKYG 70

Query: 66  GTGWSSVQHYIFNEELQAAPAPQPLAFGV--SMVGPVIYTFGSEEQKKRFLPRIANVDDW 123
             G ++V + +  +EL+   +       V  S+    IY +GSEEQ++++LP +A  +  
Sbjct: 71  CAGLNAVSYGLICQELERGDSGIRSFVSVQSSLCMYPIYAYGSEEQRQQYLPGMARGEII 130

Query: 124 WCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAKKQE 183
            C G +EP  GSD A++KT A++ G  WIING K W T    AD       TD      E
Sbjct: 131 GCFGLTEPHGGSDPANMKTTAKRDGGDWIINGAKMWITNGSIADIAIVWAMTD------E 184

Query: 184 GISFILVDMKTKGITVRPIQTIDG--GHEVNEVFFDDVEVP 222
           GI   +V   TKG   + +           + +FFD V VP
Sbjct: 185 GIQGFIVPKGTKGFDTQVVHKKMSLRASVTSALFFDGVRVP 225


Lambda     K      H
   0.317    0.135    0.411 

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: 316
Number of extensions: 23
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: 396
Length of database: 387
Length adjustment: 31
Effective length of query: 365
Effective length of database: 356
Effective search space:   129940
Effective search space used:   129940
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 (21.6 bits)
S2: 50 (23.9 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