GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Geotalea uraniireducens Rf4

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_011938637.1 GURA_RS08815 phosphoglycerate dehydrogenase

Query= SwissProt::Q9C4M5
         (331 letters)



>NCBI__GCF_000016745.1:WP_011938637.1
          Length = 541

 Score =  203 bits (517), Expect = 7e-57
 Identities = 114/323 (35%), Positives = 190/323 (58%), Gaps = 13/323 (4%)

Query: 4   KVFITRQIPENGIKMIEKFYEIELWKDPKAP-PRGVLLEKVREVDALVTLVTDKVDKELL 62
           KV +T ++ + G++++++   +EL  D +    +  LL  + + + ++T     VDK+LL
Sbjct: 2   KVIVTDEVAQEGLELLKQDPRVEL--DIRLGLKKEELLAIIGDYEVIITRSGTTVDKDLL 59

Query: 63  ENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVEA 122
           +   KLK++A+  VG DN+DI+ A+ +G+ V N P   T++ A+ A ALLL+  R I +A
Sbjct: 60  DAGKKLKMVARAGVGIDNVDIDYASSKGVIVVNAPFGNTNSAAEHAMALLLSFCRNITKA 119

Query: 123 DAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSRT 182
           +A ++SGEWK++        F G  LKGKT G++G G++G  +A R K F   ++     
Sbjct: 120 NASLKSGEWKRAP-------FTGVELKGKTAGVIGLGKVGGRVATRLKAFECDVLGCDPY 172

Query: 183 RKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSRG 242
              +   ++G + V  E + K  D I+ H PL +ET +M+GEKE+ +MK   ILIN +RG
Sbjct: 173 IAVKRAHDLGVKLVSHEEIYKNCDIITFHTPLNEETRNMVGEKEIAMMKDGVILINAARG 232

Query: 243 AVVDTNALIKALKEGWIAGAGLDVFEEEPYYNE---ELFKLKNVVLAPHIGSATHEAREG 299
            +++  AL+ ALK G + GA +DV+ EEP  +E   EL     +V+ PH+G+ T EA+  
Sbjct: 233 GIINEQALLNALKGGKVFGAAMDVWSEEPPKSETLKELISQDKLVVTPHLGANTFEAQIN 292

Query: 300 MAELVAKNLIAFAKGEIPPNLVN 322
           +A  V+K ++ +   +   N VN
Sbjct: 293 VAVDVSKEILNYLDEQPLENAVN 315


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: 403
Number of extensions: 11
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: 541
Length adjustment: 32
Effective length of query: 299
Effective length of database: 509
Effective search space:   152191
Effective search space used:   152191
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 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