GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Magnetospirillum magneticum AMB-1

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate WP_011383120.1 AMB_RS03480 isovaleryl-CoA dehydrogenase

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



>NCBI__GCF_000009985.1:WP_011383120.1
          Length = 389

 Score =  108 bits (270), Expect = 3e-28
 Identities = 85/261 (32%), Positives = 126/261 (48%), Gaps = 23/261 (8%)

Query: 3   LNFSKEEIA--FRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60
           LNF   E A   RD V  F    +  +  +  I+  +    E+  W R L   G      
Sbjct: 8   LNFDLGETADMMRDSVAAFAATEIAPRAAE--IDRSNEFPNEL--WPR-LGAMGLLGITV 62

Query: 61  PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGV--SMVGPVIYTFGSEEQKKRFLPRIA 118
            ++YGG G   ++H +  EE+  A A   L++G   ++    I   G+E QK ++LP++ 
Sbjct: 63  DEKYGGAGMGYLEHVVAMEEISRASASVGLSYGAHSNLCVNQIKRNGTEAQKMKYLPKLI 122

Query: 119 NVDDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPA 178
           + +       SEP +GSD+ S+K KAEKKGD++++NG K W T    AD I    +TD  
Sbjct: 123 SGEYIGALAMSEPNAGSDVVSMKLKAEKKGDRYVLNGTKMWITNGPDADVIVVYAKTDVT 182

Query: 179 AKKQEGISFILVDMKTKGITVRPIQTID----GGHEVNEVFFDDVEVPLENLVGQENK-- 232
           A  + GI+  LV+   KG +V   Q +D     G    E+ F D EVP EN++G   K  
Sbjct: 183 AGPR-GITAFLVEKTFKGFSV--AQKLDKLGMRGSNTGELVFQDCEVPEENVLGAVGKGV 239

Query: 233 -----GWDYAKFLLGNERTGI 248
                G DY + +L     GI
Sbjct: 240 NVLMSGLDYERVVLTGGPLGI 260


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: 317
Number of extensions: 18
Number of successful extensions: 3
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: 389
Length adjustment: 31
Effective length of query: 365
Effective length of database: 358
Effective search space:   130670
Effective search space used:   130670
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 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 (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