GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Paraburkholderia bryophila 376MFSha3.1

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate H281DRAFT_01346 H281DRAFT_01346 isovaleryl-CoA dehydrogenase

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



>FitnessBrowser__Burk376:H281DRAFT_01346
          Length = 393

 Score =  110 bits (274), Expect = 9e-29
 Identities = 67/200 (33%), Positives = 106/200 (53%), Gaps = 16/200 (8%)

Query: 62  KEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGV--SMVGPVIYTFGSEEQKKRFLPRIAN 119
           +EYGG       H +  EE+  A A   L++G   ++    I+  G+E QK+++LP++ +
Sbjct: 63  EEYGGANMGYTAHMVAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEAQKQKYLPKLVS 122

Query: 120 VDDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAA 179
            +       SEP +GSD+ S+K +A++KGD++++NG K W T     D +    +TD  A
Sbjct: 123 GEHVGALAMSEPNAGSDVVSMKLRADRKGDRYVLNGTKMWITNGPDCDTLVVYAKTDVEA 182

Query: 180 KKQEGISFILVDMKTKGITVRPIQTID----GGHEVNEVFFDDVEVPLENLVGQEN---- 231
             + GI+  +V+   KG +V   Q +D     G    E+ F DVEVP EN++GQ N    
Sbjct: 183 NSR-GITAFIVEKGMKGFSV--AQKLDKLGMRGSHTGELVFQDVEVPEENILGQLNGGVK 239

Query: 232 ---KGWDYAKFLLGNERTGI 248
               G DY + +L    TGI
Sbjct: 240 VLMSGLDYERAVLAGGPTGI 259


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: 314
Number of extensions: 17
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 396
Length of database: 393
Length adjustment: 31
Effective length of query: 365
Effective length of database: 362
Effective search space:   132130
Effective search space used:   132130
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