GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Dechlorosoma suillum PS

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate Dsui_0124 Dsui_0124 lactate dehydrogenase-like oxidoreductase

Query= SwissProt::Q9C4M5
         (331 letters)



>FitnessBrowser__PS:Dsui_0124
          Length = 322

 Score =  192 bits (487), Expect = 1e-53
 Identities = 106/272 (38%), Positives = 160/272 (58%), Gaps = 17/272 (6%)

Query: 61  LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120
           L+   P+LK++A  A G +N+D+E A ++GI V+N  G       +  F+LLLA++R ++
Sbjct: 57  LMARLPQLKMVAVAATGTNNVDLEAARRQGIVVSNIQGYAVHTVPEHVFSLLLALSRNLL 116

Query: 121 EADAFVRSGEWKKSEVGW---HPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKII 177
                V  G W+++E      HP+      L G TLG+VG G +GQ + + A+ FGMK++
Sbjct: 117 AYRQSVAEGRWQRAEQFCFFDHPIR----DLHGATLGVVGGGSLGQGVVRLAQAFGMKVL 172

Query: 178 YYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILI 237
              R    +    +   Y  F T+L E+D +SLH PLT ET H+IG  EL+ MKP+A+LI
Sbjct: 173 QAER----KGAAVVRPGYTAFATVLAEADALSLHCPLTAETRHLIGAAELQAMKPSALLI 228

Query: 238 NTSRGAVVDTNALIKALKEGWIAGAGLDVF------EEEPYYNEELFKLKNVVLAPHIGS 291
           NT+RG +VD  AL +AL+EGWIAGAG DV       ++ P  + +L    N +L PH+  
Sbjct: 229 NTARGGLVDEAALARALREGWIAGAGFDVLTAEPPTDDHPLLSPDLLAAPNFLLTPHVAW 288

Query: 292 ATHEAREGMAELVAKNLIAFAKGEIPPNLVNK 323
           A+  A + +A+ +  NL AFA+G + P   N+
Sbjct: 289 ASAPAMQALADQLIDNLEAFARGAMTPGAANR 320


Lambda     K      H
   0.317    0.137    0.392 

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: 227
Number of extensions: 8
Number of successful extensions: 4
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: 331
Length of database: 322
Length adjustment: 28
Effective length of query: 303
Effective length of database: 294
Effective search space:    89082
Effective search space used:    89082
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. 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