GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Stenotrophomonas chelatiphaga DSM 21508

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate WP_057507594.1 ABB28_RS05080 isovaleryl-CoA dehydrogenase

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



>NCBI__GCF_001431535.1:WP_057507594.1
          Length = 387

 Score =  112 bits (279), Expect = 2e-29
 Identities = 79/254 (31%), Positives = 123/254 (48%), Gaps = 21/254 (8%)

Query: 13  RDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHWPKEYGGTGWSSV 72
           RD V QF    +       L      T +  +  +R L ++G       +EYGGTG   +
Sbjct: 18  RDSVAQFAAAEIAP-----LAAHADETNQFPLALWRKLGEQGLLGMTVEEEYGGTGMGYL 72

Query: 73  QHYIFNEELQAAPAPQPLAFGV--SMVGPVIYTFGSEEQKKRFLPRIANVDDWWCQGFSE 130
            H +  EE+  A     L++G   ++    +   G++ QK+RFLP + + +       SE
Sbjct: 73  AHVVAMEEVSRASGGIGLSYGAHSNLCVNQLRKNGTQAQKQRFLPGLCSGELVGALAMSE 132

Query: 131 PGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAKKQEGISFILV 190
           PG+GSD+ S+K +AEK+GD++++NG K W T    AD +    +TDP A   +GI+  LV
Sbjct: 133 PGAGSDVVSMKLRAEKRGDRYVLNGNKMWITNGPDADVLVVYAKTDPDA-GAKGITAFLV 191

Query: 191 DMKTKGITVRPIQTID----GGHEVNEVFFDDVEVPLENLVGQEN-------KGWDYAKF 239
           +   KG +    Q +D         +E+ F D EVP EN++GQE         G DY + 
Sbjct: 192 EKGMKGFST--AQKLDKLGMRSSPTSELVFQDCEVPAENVLGQEGSGVRVLMSGLDYERV 249

Query: 240 LLGNERTGIARVGM 253
           +L     G+    M
Sbjct: 250 VLSGGPLGLMAAAM 263


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: 338
Number of extensions: 16
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: 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