GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Shewanella sp. ANA-3

Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate 7025397 Shewana3_2552 acyl-CoA dehydrogenase domain-containing protein (RefSeq)

Query= reanno::psRCH2:GFF2397
         (379 letters)



>FitnessBrowser__ANA3:7025397
          Length = 596

 Score =  119 bits (298), Expect = 2e-31
 Identities = 98/318 (30%), Positives = 142/318 (44%), Gaps = 45/318 (14%)

Query: 100 GNEQQKSDFLTPLARGEQIGAFALTEPQAGSDASSLRTRARRDGDHY-VLNGAKQFITSG 158
           G+E  K  +L  L  GE  G   LTE  AG+D + LRT+A    D Y  + G K FI+SG
Sbjct: 141 GSEALKQKYLAKLVSGEWTGTMNLTESHAGTDLALLRTKAVPTADGYFAITGEKIFISSG 200

Query: 159 KHAGT-----VIVFAVTDPDAGKGGISAFIVPT----------DSPGYQVVRVEDKLGQH 203
            H  T     +++  + D   G  GIS F VP           ++       +E K+G H
Sbjct: 201 DHQFTDNIVHLVLARLPDAPEGVKGISLFAVPKVLVNSDGSLGEANSLYASGLEHKMGIH 260

Query: 204 ASDTCQIAFEDLRVPVANRLGEEGEGYRIALANLEGGRIGIAAQAVGMARAAFEAARDYA 263
            + TC + FE     +   +GE  +G R     +   R+G+  Q +G++  A+++A  YA
Sbjct: 261 GNSTCVMVFEGA---LGELVGEPHQGLRAMFTMMNQARLGVGMQGLGVSEIAYQSALAYA 317

Query: 264 RDR------------ETFGKPIIEHQAVAFRLADMATQIAVARQMVHHAAA-LREVGR-- 308
           +DR            E    PI+ H  V   L         AR +V   A  L E  R  
Sbjct: 318 KDRLQSRAISGAKAPEKAADPILVHGDVRRMLLSQKAFNEGARALVGQQALWLDEAERHS 377

Query: 309 ---PALVEASMAKLFA-------SEMAEKVCSAAIQTLGGYGYLADFPVERIYRDVRVCQ 358
               A V A +A LF        +      C  A Q  GG+GY+ ++ +E+  RD R+  
Sbjct: 378 DPAKAKVAAQLAALFTPVVKGFITNRGFNACVDAQQVFGGHGYIHEWGMEQFVRDSRIAL 437

Query: 359 IYEGTSDIQRL-VISRNL 375
           IYEGT+ IQ L ++ R L
Sbjct: 438 IYEGTNGIQALDLVGRKL 455


Lambda     K      H
   0.320    0.135    0.391 

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: 517
Number of extensions: 28
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: 379
Length of database: 596
Length adjustment: 33
Effective length of query: 346
Effective length of database: 563
Effective search space:   194798
Effective search space used:   194798
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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