GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lhgD in Methylocystis bryophila S285

Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate WP_085771178.1 B1812_RS08345 NAD(P)/FAD-dependent oxidoreductase

Query= SwissProt::Q9LES4
         (483 letters)



>NCBI__GCF_002117405.1:WP_085771178.1
          Length = 367

 Score =  345 bits (884), Expect = 2e-99
 Identities = 184/398 (46%), Positives = 246/398 (61%), Gaps = 40/398 (10%)

Query: 80  VDTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSLKA 139
           VD VV+GAGV+GLAV R L+L GR V++L+     G+VTSSRNSEV+H+GIYYP  SLKA
Sbjct: 4   VDAVVVGAGVIGLAVVRALALTGRSVIVLETERLIGSVTSSRNSEVIHSGIYYPQGSLKA 63

Query: 140 KFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLEGF 199
           + CV GR  LY++C  + + +++ GKLIVAT   E P ++ L   G  N V  L  L   
Sbjct: 64  RLCVEGRRRLYEFCDAHGVGYQRCGKLIVATNEKERPAVEALFQKGLANGVEDLVWLSAA 123

Query: 200 EAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNHAT 259
           EA  MEP L CV AL +P +GILD+H FML+                  ++G+A+++ A 
Sbjct: 124 EATAMEPALHCVGALFAPSTGILDSHGFMLA------------------MRGDAEDHGAA 165

Query: 260 FSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKRLH 319
            ++NT  L+ ++E+  + +       +  +  A          ++N AGL A  +A+ + 
Sbjct: 166 IAFNTPFLSAKIEDDGIVISAGGAEPTTLKTAA----------LINCAGLQASKVARAIV 215

Query: 320 GLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPDVE 379
           GL+H  VP + YA+G YF L+G    PF +L+YP P   GLGVH+T DL G V+FGPDVE
Sbjct: 216 GLEHALVPETRYAKGNYFALTG--RSPFRRLIYPAPHSHGLGVHLTFDLAGQVRFGPDVE 273

Query: 380 WIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPKQS 439
           WIE          + DY V+P+R E F   IR Y+P L+D +L   Y+GIRPK+SGP  S
Sbjct: 274 WIE----------EIDYAVDPRRCEGFSEAIRSYWPGLRDDALVAAYAGIRPKISGPADS 323

Query: 440 PADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHI 477
            ADF + G E HGV GLVNLFGIESPGLTSSLAIAE +
Sbjct: 324 AADFRLDGPERHGVRGLVNLFGIESPGLTSSLAIAEQV 361


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: 468
Number of extensions: 16
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: 367
Length adjustment: 32
Effective length of query: 451
Effective length of database: 335
Effective search space:   151085
Effective search space used:   151085
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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