GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lhgD in Magnetospirillum magneticum AMB-1

Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate WP_011386171.1 AMB_RS19325 NAD(P)/FAD-dependent oxidoreductase

Query= SwissProt::Q9LES4
         (483 letters)



>lcl|NCBI__GCF_000009985.1:WP_011386171.1 AMB_RS19325
           NAD(P)/FAD-dependent oxidoreductase
          Length = 374

 Score =  327 bits (839), Expect = 3e-94
 Identities = 190/402 (47%), Positives = 240/402 (59%), Gaps = 43/402 (10%)

Query: 76  AKERVDTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPN 135
           A ERVD VVIGAGVVGLAVAR L+  G EV+IL+A  + G+  SSRNSEV+HAG+YYP  
Sbjct: 11  AAERVDCVVIGAGVVGLAVARSLAHAGAEVIILEAEGAIGSGISSRNSEVIHAGMYYPAG 70

Query: 136 SLKAKFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRM 195
           SL+A+ CV G  LL  Y +   + H   GKLIVAT  +E  +LD ++  G  N V GL  
Sbjct: 71  SLRARLCVEGNRLLRDYAASRGVAHAMTGKLIVATDEAEAAQLDAILAKGRANGVEGLTR 130

Query: 196 LEGFEAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQN 255
           +    A  MEP L CV AL SP +GI+DTH  MLSL+                  GEA+ 
Sbjct: 131 ISAAHAREMEPDLACVAALWSPATGIIDTHGLMLSLL------------------GEAEE 172

Query: 256 NHATFSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALA 315
             A  +  + V  GR  +  M L V           AE    L  N+V+ +AGL +  L 
Sbjct: 173 RGAALALKSPVTGGRATDDGMLLSVGG---------AEPTTLLARNVVL-AAGLSSPRLG 222

Query: 316 KRLHGLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFG 375
             L GL +  VP +H  +G YFTLSG    PF +LVYP+P   GLGVH T+DL G  +FG
Sbjct: 223 AAL-GLKN--VPPAHLCKGNYFTLSG--RTPFTRLVYPVPVAAGLGVHFTLDLGGRGRFG 277

Query: 376 PDVEWIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSG 435
           PDVEW+E            DY+V+P+R + FY  IR+Y+PDL DG+LEP Y+GIRPK++ 
Sbjct: 278 PDVEWVEAE----------DYQVDPRRGDSFYAAIRRYWPDLADGALEPAYAGIRPKITA 327

Query: 436 PKQSPADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHI 477
             +  ADF+I G    GVPG+  L+GIESPGLTSSLAIA H+
Sbjct: 328 EGEPAADFLIHGPRETGVPGVAALYGIESPGLTSSLAIAGHV 369


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: 454
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: 483
Length of database: 374
Length adjustment: 32
Effective length of query: 451
Effective length of database: 342
Effective search space:   154242
Effective search space used:   154242
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: 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 preprint 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