GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glcD in Acidovorax sp. GW101-3H11

Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate Ac3H11_2934 D-2-hydroxyglutarate dehydrogenase

Query= reanno::Smeli:SMc00832
         (479 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2934
           D-2-hydroxyglutarate dehydrogenase
          Length = 474

 Score =  181 bits (460), Expect = 4e-50
 Identities = 145/459 (31%), Positives = 225/459 (49%), Gaps = 35/459 (7%)

Query: 38  ERGLKPFETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLSGGAIP 97
           E  L  +E D     R   LAVV P  T+ VAAV+K C+  G  IVP+G  T L+ G+ P
Sbjct: 20  EGDLTAWEQDWRRRVRGKALAVVRPANTQEVAAVVKACAAVGTAIVPQGGNTGLAVGSTP 79

Query: 98  QEDA--IVVGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSSQLACT 155
            +    IV+ L++M+    +D  N T TV+AG    N+ D     G  +    +++ +CT
Sbjct: 80  DDSGTQIVLSLTRMNAVRSVDTDNLTMTVEAGCILQNLQDVAQNAGVLFPLSLAAEGSCT 139

Query: 156 IGGNIGMNSGGAHCLKYGVTTNNLLGVKMVLFDGTVIE-LGGKALDAPGYDLLGLVCGSE 214
           IGGN+G N+GG   ++YG   +  LG+++V   G V + L G   D  GYDL  L  GSE
Sbjct: 140 IGGNLGTNAGGTQVVRYGNARDLCLGLEVVTAQGEVWDGLKGLRKDNTGYDLRDLFIGSE 199

Query: 215 GQLGIVTEATVRLIAKPEGARPVLFGFASSESAGSCVADI------IGSGIIPVAIEFMD 268
           G LGI+T AT++L  +P      L  +A++ S    VA +      +G+G+     E M 
Sbjct: 200 GTLGIITAATMKLYPQPAAN---LTAWAAAPSMEHAVALLGLAHKQLGAGL--TGFEVMG 254

Query: 269 RPAIEIC-EAFAQAGYPL--DVEALLIVEVEGSEAEMD----ATLAGIIEIARRHGVMT- 320
           + A+ +  +   Q   P   D  A   V +E S++E +    A    ++E A   G +T 
Sbjct: 255 QFALSLVGKHMPQLRVPFLGDDNAPWCVLLENSDSESEEHARARFESLLETAFEMGCVTD 314

Query: 321 IRESQSALEAALIWKGRKSAFGATGRIADYICMDGTVPLSQLSHVLRRTGEIVAGY--GL 378
              +++  +A  +W  R+S   A       I  D ++ +S++   +  T  ++     G+
Sbjct: 315 AVVAENLTQAHQLWHIRESIPLAQAEEGLNIKHDISIQISRIPAFVAHTDAVLQREIPGV 374

Query: 379 RVANVFHAGDGNMHPLILYNI-----NDPEEAARAEAA--GNDILKLCVEAGGCLTGEHG 431
           R+ N  H GDGN+H    YN+      DP+   R + A   + + +   E GG  + EHG
Sbjct: 375 RLVNFGHLGDGNLH----YNVQAPAAGDPKAFLREQEARVNHLVYEAVAEFGGSFSAEHG 430

Query: 432 VGIEKRDLMLHQYSRADLGQQMAARAAFDPQWLMNPSKV 470
           +G  K D +    S   LG   A + A DPQ +MNP +V
Sbjct: 431 IGELKADKLAKYQSPVALGMMRAIKQALDPQGVMNPGRV 469


Lambda     K      H
   0.320    0.138    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: 517
Number of extensions: 20
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: 479
Length of database: 474
Length adjustment: 33
Effective length of query: 446
Effective length of database: 441
Effective search space:   196686
Effective search space used:   196686
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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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