GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF2987
          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:

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