GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Desulfoscipio geothermicus DSM 3669

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_092482325.1 BM299_RS04760 hydroxyacid dehydrogenase

Query= curated2:B1L765
         (332 letters)



>NCBI__GCF_900115975.1:WP_092482325.1
          Length = 330

 Score =  219 bits (557), Expect = 1e-61
 Identities = 129/334 (38%), Positives = 205/334 (61%), Gaps = 12/334 (3%)

Query: 1   MKPRVFVTREIPERGLSKIEEHFELDLWKDEAPPSKKVIIERVKDCDALVSLLTDPIDAE 60
           M  +V +T  I E G++ I E  EL++  D   P ++ +I+ + D DAL+ + +  + + 
Sbjct: 1   MTKKVLLTEAIHEEGMNIIREAAELEIAAD---PGEETVIKAIADADALI-VRSSKVTSA 56

Query: 61  VFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAARRVV 120
           + EA  KL+++ ++ +G DNID+K A + G+ V NTP     + A+   A ++   +R+ 
Sbjct: 57  IIEAGKKLKVIGRHGMGLDNIDLKAADQYGVAVVNTPDANVLSVAEHVLATMLYLCKRLK 116

Query: 121 EADRYVREGKW-KVAWHPMMM--LGY---DVYGRTLGIVGMGRIGAAVARRA-KGFGMRI 173
           E D  +R G++ +    P ++  LGY   ++YG+TLG+VG+G+I   +A    KGF M++
Sbjct: 117 EVDNALRTGEFDRPGSLPGLVTKLGYTTQELYGKTLGLVGVGKIARRIAEICTKGFDMQV 176

Query: 174 LYYDSIRREDFEKELGVEYV-PLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAI 232
             YD+    D  ++ GVE    LE++ E++DF+S+HVPLT  T  +IG++QL  MK TA 
Sbjct: 177 CGYDAYLAPDVIQQAGVEPCGSLEEVFEKADFISVHVPLTPGTRGLIGKKQLDLMKPTAF 236

Query: 233 LVNTSRGKVVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDPLLKLENVVLAPHAASASH 292
           L+N++RG VV++  LY+ALKE  IAGA +DVF QEP   + PL  L+NVV+ PH A+ + 
Sbjct: 237 LINSARGGVVNEDDLYQALKEKSIAGAAVDVFAQEPPGKNHPLFTLDNVVVTPHIAAMTD 296

Query: 293 ETRSRMAEMVAENLIAFKRGEIPPNLVNQEVVKV 326
               RMA  VAE +++  RGE P  LVN  + K+
Sbjct: 297 GALVRMARDVAEGVVSVLRGERPKYLVNPRIWKI 330


Lambda     K      H
   0.319    0.137    0.398 

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: 291
Number of extensions: 11
Number of successful extensions: 6
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: 332
Length of database: 330
Length adjustment: 28
Effective length of query: 304
Effective length of database: 302
Effective search space:    91808
Effective search space used:    91808
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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