GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Lacinutrix algicola AKS293

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_055435174.1 ASC41_RS03050 acyl-CoA dehydrogenase

Query= BRENDA::B0EVL5
         (395 letters)



>NCBI__GCF_001418085.1:WP_055435174.1
          Length = 390

 Score =  154 bits (390), Expect = 3e-42
 Identities = 116/380 (30%), Positives = 189/380 (49%), Gaps = 10/380 (2%)

Query: 16  LDSQ-LTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQY 74
           +DS+  T+   + R S   + Q+ ++P + +  +    +R I+ + GE+G  G   PE Y
Sbjct: 1   MDSRYFTEEHNLFRQSLADFLQKEVVPHIDKWEKTGHIERFIWEKFGEMGFFGIAYPEAY 60

Query: 75  GGSGMNYVCYGLIAREVERVDSG-YRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGE 133
           GG  ++     +   E+++V+SG + + M   + L M  +N  GSEE KQKYL K  TGE
Sbjct: 61  GGMDLDLFYTVIFLEELQKVNSGGFAAAMWAHAYLAMTHVNAEGSEEIKQKYLTKSITGE 120

Query: 134 WVGCFGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAK--DDAGD 191
           ++G   +TEP  GSD   M T A K    Y L+G+K +ITN   +D  VV AK   + G+
Sbjct: 121 FIGAMAVTEPFGGSDVAGMRTTAVKEGNTYVLNGSKTFITNGVYSDYIVVAAKTSPELGN 180

Query: 192 --IRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTVRGLKGPFTCL 249
             I  F++++  KG+SA  +  K+G RAS TGEI  D V  P  +      G   P+   
Sbjct: 181 KGISMFIVDRDTKGVSATKL-DKLGWRASDTGEIAFDNVVIPASHLMGE-EGKGFPYIMQ 238

Query: 250 NSARYGIAWG--ALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQ 307
           + A   +  G  A   AE   E A +Y  +R+ FG+ +   Q ++  +AD   ++ +  +
Sbjct: 239 HFAFERLIMGVNAHARAEFALEYAVKYMGERQAFGKSIDKFQALRHTMADCYADMEVCKE 298

Query: 308 GCLRLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLE 367
               +    D+    V+  +I K  S   + D+      MLGG G  +E+ +AR L +  
Sbjct: 299 FNYTVAARLDKNEYVVKEATISKLRSTKMADDVIYQCLQMLGGYGYMEEYPMARLLRDSR 358

Query: 368 VVNTYEGTHDIHALILGRAI 387
           +     GT +I   I+ + +
Sbjct: 359 LGPIGGGTSEILREIIAKMV 378


Lambda     K      H
   0.319    0.136    0.409 

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: 355
Number of extensions: 17
Number of successful extensions: 4
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: 395
Length of database: 390
Length adjustment: 31
Effective length of query: 364
Effective length of database: 359
Effective search space:   130676
Effective search space used:   130676
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