GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Nocardiopsis baichengensis YIM 90130

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_017559746.1 C892_RS0126925 phosphoglycerate dehydrogenase

Query= SwissProt::Q9C4M5
         (331 letters)



>NCBI__GCF_000341205.1:WP_017559746.1
          Length = 529

 Score =  233 bits (594), Expect = 8e-66
 Identities = 124/321 (38%), Positives = 194/321 (60%), Gaps = 10/321 (3%)

Query: 2   KPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKEL 61
           KP V +  ++   G+ ++E  +E+   +      R  LL  + +VDAL+     +VD E 
Sbjct: 3   KPSVLVAEELSPAGLALLEGDFEV---RHTTGADRSQLLPALADVDALIVRSATQVDAEA 59

Query: 62  LENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVE 121
           L  APKLK++A+  VG DN+D++ ATK G+ V N P     + A+ A  LLLA AR    
Sbjct: 60  LAAAPKLKVVARAGVGLDNVDVDAATKAGVLVVNAPTSNIISAAEQAVNLLLASARNTAP 119

Query: 122 ADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSR 181
           A   + +GEWK+S+       + G  +  KT+G+VG GRIG  +A+R   FG K+I Y  
Sbjct: 120 AHNALVNGEWKRSK-------YTGVEVYDKTVGVVGLGRIGALVAQRLAAFGTKLIAYDP 172

Query: 182 TRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSR 241
             +P    ++G E V  + LL+ SDFI++H+P +K+T  +IG++ L  +KP+  +IN +R
Sbjct: 173 FVQPARAAQMGVEMVSLDELLQRSDFITVHLPKSKDTLGLIGDEALHKVKPSVRVINAAR 232

Query: 242 GAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREGMA 301
           G ++D +AL +A+KEG +AGAG+DV+  EP  +  LF+ +NVV+APH+G++THEA+E   
Sbjct: 233 GGILDEDALYRAIKEGRVAGAGIDVWASEPCTDSPLFEFENVVVAPHLGASTHEAQEKAG 292

Query: 302 ELVAKNLIAFAKGEIPPNLVN 322
             V +++     GE  P+ VN
Sbjct: 293 TQVVRSVKLALAGEFVPDAVN 313


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: 374
Number of extensions: 15
Number of successful extensions: 3
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: 529
Length adjustment: 32
Effective length of query: 299
Effective length of database: 497
Effective search space:   148603
Effective search space used:   148603
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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