GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Brevibacterium jeotgali SJ5-8

Align Glutaryl-CoA dehydrogenase, mitochondrial; GCD; EC 1.3.8.6 (characterized)
to candidate WP_101588067.1 BJEO58_RS04410 acyl-CoA dehydrogenase

Query= SwissProt::P81140
         (408 letters)



>NCBI__GCF_900169175.1:WP_101588067.1
          Length = 405

 Score =  325 bits (834), Expect = 1e-93
 Identities = 177/351 (50%), Positives = 233/351 (66%), Gaps = 12/351 (3%)

Query: 63  REIISEMGELGVLGPTIKGYGCAGVSSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIY 122
           RE+   +GELGVLG  ++GY CAG ++  YGL  RELE VDSG RS +SVQ SL M  I+
Sbjct: 56  RELAEGLGELGVLGMHLEGYECAGSTATQYGLACRELEAVDSGLRSLVSVQGSLAMFSIH 115

Query: 123 AYGSEEQQQQKYLPRLAKGELLGCFGLTEPNHGSDPGSMETRALHNPSNRSYTLNGAKTW 182
            +GSEEQ+Q+ +LP++A G  +GCFGLTEP+ GSDP  M+TRA  + S+  + LNGAK W
Sbjct: 116 HWGSEEQKQE-WLPQMAAGRAIGCFGLTEPDVGSDPAGMKTRATKDGSD--WILNGAKMW 172

Query: 183 ITNSPVADLFVVWARCED--------NCIRGFLLEKGMRGLSAPKIEGKFSLRASATGMI 234
           ITNSPV+D+ VVWA+ ++          +RGF++     G+  P+++ K SLRAS TG I
Sbjct: 173 ITNSPVSDVMVVWAKTDEVDEKTGEKGVVRGFVVPTDTPGVETPEVQRKLSLRASITGEI 232

Query: 235 IMDDVEVPEENVLPKASSLAVPFGCLNNARYGISWGVLGAAEFCLHTARQYTLDRIQFGV 294
           ++D+V +PE  +LPKAS L  P   L+ ARYGI +GV GAA   L  A +YT  RIQF  
Sbjct: 233 VLDNVRLPESAMLPKASGLKGPLSALSEARYGIVFGVTGAARDSLEEALRYTDTRIQFDR 292

Query: 295 PLAKNQLIQRKLADMLTEITLGLHACLQLGRLKDQDK-VTPEMVSLLKRNNCGKALDIAR 353
           PL+  Q+ Q+KLA    E +        +GRLKD    V PE +SL K  N   A++IAR
Sbjct: 293 PLSSFQISQQKLAKAFGEYSAITLTAAHIGRLKDSAAGVRPEQISLGKMVNVDTAMNIAR 352

Query: 354 QARDMLGGNGISDEYHVIRHAMNLEAVNTYEGTHDIHALILGRAITGIQAF 404
             R + GG+GI+ EY  +RHA+NLE V TYEGTH++H L LGRA+TGI AF
Sbjct: 353 DLRALFGGSGITSEYSPLRHAINLETVLTYEGTHEVHQLTLGRAMTGINAF 403


Lambda     K      H
   0.319    0.136    0.404 

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: 435
Number of extensions: 17
Number of successful extensions: 5
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: 408
Length of database: 405
Length adjustment: 31
Effective length of query: 377
Effective length of database: 374
Effective search space:   140998
Effective search space used:   140998
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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