GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gyaR in Dyella japonica UNC79MFTsu3.2

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate N515DRAFT_3581 N515DRAFT_3581 D-3-phosphoglycerate dehydrogenase

Query= SwissProt::Q9C4M5
         (331 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3581 N515DRAFT_3581
           D-3-phosphoglycerate dehydrogenase
          Length = 410

 Score =  159 bits (402), Expect = 1e-43
 Identities = 101/324 (31%), Positives = 166/324 (51%), Gaps = 14/324 (4%)

Query: 4   KVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKELLE 63
           KV +   + ++ +++  +    ++    K+ P   L  ++ E   +       +  ++LE
Sbjct: 11  KVLLLEGVSQSAVEVFRRAGYSQIEFHEKSLPEAELKARIAEAHIVGIRSRSHLTADVLE 70

Query: 64  NAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVEAD 123
            A +L  +  + +G + +D+E A ++G+ V N P   T + A+L  A  + + R I + +
Sbjct: 71  QARRLIAVGCFCIGTNQVDLETARQQGVPVFNAPYSNTRSVAELVIAEAIMLLRGIPQKN 130

Query: 124 AFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSRTR 183
           A    G W KS  G        + ++ K LGIVG+G IG  +   A+  GM++I++    
Sbjct: 131 ALCHRGGWTKSAAG-------SFEVRDKVLGIVGYGHIGTQVGVLAESLGMRVIFHDIET 183

Query: 184 KPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSRGA 243
           K        A  +D   LL+ +D ++LHVP T  T  MIG  EL  M+  A LIN SRG 
Sbjct: 184 KLSLGNARAAGSLD--DLLERADVVTLHVPETPATKLMIGATELAKMRKGAALINASRGT 241

Query: 244 VVDTNALIKALKEGWIAGAGLDVFEEEPYYNEE-----LFKLKNVVLAPHIGSATHEARE 298
           VVD +AL  AL+ G +AGA +DVF  EP  N++     L  + NV+L PHIG +T EA++
Sbjct: 242 VVDIDALAAALRTGHVAGAAVDVFPLEPKGNDDPFVSPLVGMDNVILTPHIGGSTLEAQD 301

Query: 299 GMAELVAKNLIAFAKGEIPPNLVN 322
            +   VA  L+ ++      + VN
Sbjct: 302 NIGIEVASKLVRYSDNGSTLSAVN 325


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: 276
Number of extensions: 19
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: 410
Length adjustment: 30
Effective length of query: 301
Effective length of database: 380
Effective search space:   114380
Effective search space used:   114380
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 Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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