GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Dyadobacter tibetensis Y620-1

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_025764976.1 X939_RS0119550 acyl-CoA dehydrogenase

Query= BRENDA::B0EVL5
         (395 letters)



>NCBI__GCF_000566685.1:WP_025764976.1
          Length = 387

 Score =  192 bits (487), Expect = 2e-53
 Identities = 118/368 (32%), Positives = 194/368 (52%), Gaps = 5/368 (1%)

Query: 25  RMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYGGSGMNYVCY 84
           R+++++ R ++ + + P + E    +     +F+ +GELGL+G  +PEQYGG+G+ Y  Y
Sbjct: 18  RLIQETVRDFALKNIQPHIMEWDESQHFPTEVFHSLGELGLMGMLVPEQYGGAGLGYQEY 77

Query: 85  GLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWVGCFGLTEPN 144
                 + +VD      M+  +SL    I  FG+E+ K KYLPKLA+GEW+G +GLTEPN
Sbjct: 78  ITAIIALSKVDPSIGLSMAAHNSLCTNHILMFGNEDQKNKYLPKLASGEWIGAWGLTEPN 137

Query: 145 HGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAK-DDAGDIRG---FVLEKG 200
            GSD G+M T A +    + L+GAK +ITN     V VV  +  + GD  G   F++E G
Sbjct: 138 TGSDAGNMKTTAVRDGEDWILNGAKNFITNGQSGRVAVVITRTGEPGDKHGATAFIVEHG 197

Query: 201 WKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTV-RGLKGPFTCLNSARYGIAWG 259
             G ++     K+G+RAS T E++ ++    +      +  G       L+  R  IA  
Sbjct: 198 THGFTSGRKENKLGMRASETVELLFEDCRISDSQRLGQIGEGFIQSLKILDGGRISIAAL 257

Query: 260 ALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQGCLRLGRLKDEG 319
            +G A   YE A  Y+ +R QFG+ +++ Q I  KLADM T+I        + G+ KD G
Sbjct: 258 GVGTALGAYEAALAYSKERHQFGKAISSFQGIAFKLADMYTDIQASTLLTFQAGKEKDLG 317

Query: 320 NAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLEVVNTYEGTHDIH 379
                  ++ K +S   ++ +A  A  + GG G + ++   +   + ++    EGT +I 
Sbjct: 318 QKVSLSGAVAKYHSSETAVRVATEAVQIYGGYGFTKDYPAEKFYRDSKLCTIGEGTSEIQ 377

Query: 380 ALILGRAI 387
            +++ + I
Sbjct: 378 KMVISKEI 385


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: 333
Number of extensions: 14
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: 395
Length of database: 387
Length adjustment: 31
Effective length of query: 364
Effective length of database: 356
Effective search space:   129584
Effective search space used:   129584
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