GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lhgD in Marinobacter adhaerens HP15

Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate GFF2544 HP15_2488 FAD dependent oxidoreductase

Query= SwissProt::Q9LES4
         (483 letters)



>FitnessBrowser__Marino:GFF2544
          Length = 369

 Score =  308 bits (788), Expect = 3e-88
 Identities = 180/396 (45%), Positives = 228/396 (57%), Gaps = 41/396 (10%)

Query: 82  TVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSLKAKF 141
           TVVIGAGV+GLA+AR L+  G EV++L+++  FG   SSRNSEVVHAGIYYP  SLKA+ 
Sbjct: 10  TVVIGAGVIGLAIARALARAGHEVIVLESSDRFGEGISSRNSEVVHAGIYYPQGSLKAEL 69

Query: 142 CVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLEGFEA 201
           CV GR+ LY YC  +++ H+K GK IVA   ++  KL  +      N V  L   +G   
Sbjct: 70  CVEGRQQLYDYCLTHKVGHRKCGKWIVAVDEAQNDKLCDIKAAAASNGVE-LEFYDGERV 128

Query: 202 MRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNHATFS 261
            +  P +     L SPE+GI+D+H  MLSL+                  GE  +     +
Sbjct: 129 AQGVPGICASSGLWSPETGIVDSHGLMLSLL------------------GELHDAGGQLA 170

Query: 262 YNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKRLHGL 321
             + V     + ++  L VA           E  L L    V+N+AGLGA  LAK   GL
Sbjct: 171 LRSPVAAAESDSQRHRLNVA----------GETPLILEAKNVINAAGLGAVPLAKNWAGL 220

Query: 322 DHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPDVEWI 381
               +P   +ARG YF+ SG    PF  L+YP+PE GGLG+H+T+DL G  +FGPDVEWI
Sbjct: 221 PDDCIPRQWFARGVYFSYSG--RTPFRTLIYPVPEPGGLGIHLTLDLAGQARFGPDVEWI 278

Query: 382 ECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPKQSPA 441
           E          K DY V P R E F   IR+++P L    L+P Y+GIRPKL GP    A
Sbjct: 279 E----------KEDYTVEPSRQEGFARGIRQWWPGLDPTRLQPAYAGIRPKLIGPDGGFA 328

Query: 442 DFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHI 477
           DF I G ETHG+PGLVNLFGIESPGLTS LAIAE +
Sbjct: 329 DFRIDGPETHGLPGLVNLFGIESPGLTSCLAIAERV 364


Lambda     K      H
   0.318    0.136    0.401 

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: 473
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: 483
Length of database: 369
Length adjustment: 32
Effective length of query: 451
Effective length of database: 337
Effective search space:   151987
Effective search space used:   151987
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 (21.7 bits)
S2: 50 (23.9 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:

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