GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_142248010.1 BK574_RS21120 D-glycerate dehydrogenase

Query= SwissProt::Q9C4M5
         (331 letters)



>NCBI__GCF_002019605.1:WP_142248010.1
          Length = 326

 Score =  286 bits (731), Expect = 6e-82
 Identities = 151/324 (46%), Positives = 216/324 (66%), Gaps = 6/324 (1%)

Query: 1   MKPKVFITRQIPENGIKMIEKFYEIELWKDPKAP-PRGVLLEKVREVDALVTLVTDKVDK 59
           MKP VF+TR++PE+ +  + +  E+ +W+    P P  VL +++   DAL +LV+D +  
Sbjct: 1   MKPYVFVTRKMPEHLLSDLYEIAEVGMWEHEDIPVPSEVLQKELERADALFSLVSDPLRS 60

Query: 60  ELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRI 119
           + L   PKLK+IA  AVGYDNID+E AT +GI V +TP VLTD TADL FALLLA AR+I
Sbjct: 61  QQLAKCPKLKVIANMAVGYDNIDVEHATNKGIVVCHTPDVLTDTTADLTFALLLATARKI 120

Query: 120 VEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYY 179
            EA  ++++ +W++    W P +  G  +  KT+GIVG GRIG+A+AKRAKGF M+I+Y+
Sbjct: 121 PEATDYIKNDQWQQ----WSPYLLAGTDVHHKTIGIVGMGRIGEAVAKRAKGFDMEILYH 176

Query: 180 SRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINT 239
           +R+RK E E+++GA+Y  FE LL++SD++    P T  T  +  ++  + MK +AI IN 
Sbjct: 177 NRSRKMETEQQLGAKYCSFEELLQQSDYVVCLAPFTPVTKELFDQQAFQQMKNSAIFINA 236

Query: 240 SRGAVVDTNALIKALKEGWIAGAGLDVFEEEPY-YNEELFKLKNVVLAPHIGSATHEARE 298
           SRG +V+  AL +AL++G I  AGLDVF EEP   N  L +L NVV  PHIGSAT E R+
Sbjct: 237 SRGGLVNEAALQEALEKGVIQAAGLDVFAEEPVRANHPLVQLPNVVAIPHIGSATVETRD 296

Query: 299 GMAELVAKNLIAFAKGEIPPNLVN 322
            M ++  +N+    +G+ P   VN
Sbjct: 297 AMVKMTVENIKKVLEGKPPLAAVN 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: 257
Number of extensions: 9
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: 326
Length adjustment: 28
Effective length of query: 303
Effective length of database: 298
Effective search space:    90294
Effective search space used:    90294
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: 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