GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011386171.1
          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:

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