GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gyaR in Marinobacter adhaerens HP15

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate GFF2987 HP15_2931 glycerate dehydrogenase

Query= SwissProt::Q9C4M5
         (331 letters)



>lcl|FitnessBrowser__Marino:GFF2987 HP15_2931 glycerate
           dehydrogenase
          Length = 320

 Score =  174 bits (441), Expect = 3e-48
 Identities = 109/278 (39%), Positives = 162/278 (58%), Gaps = 16/278 (5%)

Query: 39  LLEKVREVDALVTLVTDKV--DKELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNT 96
           +LE++R  D   T++ +KV   +E  +  P+LK IA  A G +NID   A   GI V N 
Sbjct: 47  ILERIRGFD---TVLVNKVVLTREHFDACPELKTIAVVATGLNNIDQAAAKDHGIKVMNV 103

Query: 97  PGVLTDATADLAFALLLAVARRIVEADAFVRSGEWKKSEVGW---HPLMFLGYGLKGKTL 153
                   A    AL+LA+A R+++    V++G W KS++     HP+M     L+G+TL
Sbjct: 104 TNYGRSTVAQHTMALMLALATRLLDYTRDVQAGHWGKSDMFCLMDHPIM----ELEGRTL 159

Query: 154 GIVGFGRIGQALAKRAKGFGMKIIYYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVP 213
           GIVG+G +GQ +A+RA  FGMK++  +R  +     + G   +  + LL ++D +SLH  
Sbjct: 160 GIVGYGDLGQGVAERAAAFGMKVLLGARPGQEPGVVD-GYSRIPLDELLPQADVVSLHCL 218

Query: 214 LTKETYHMIGEKELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYY 273
           LT ET  +IG +ELK+MKP+++LINTSRG +V+  AL  AL+ G I GAG DV  EEP  
Sbjct: 219 LTDETRDLIGARELKMMKPDSLLINTSRGGLVNEQALADALRAGEIGGAGFDVLTEEPPR 278

Query: 274 NEELF---KLKNVVLAPHIGSATHEAREGMAELVAKNL 308
           N        + N+++ PH   A+ EAR+ +  + A NL
Sbjct: 279 NGNPLLADDIPNLIVTPHSAWASREARQRIVGITAVNL 316


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: 238
Number of extensions: 11
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: 320
Length adjustment: 28
Effective length of query: 303
Effective length of database: 292
Effective search space:    88476
Effective search space used:    88476
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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