GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_3581
          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:

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