GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Sulfuricurvum kujiense DSM 16994

Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate WP_013460983.1 SULKU_RS10705 SDR family oxidoreductase

Query= BRENDA::Q9WYX9
         (309 letters)



>NCBI__GCF_000183725.1:WP_013460983.1
          Length = 312

 Score =  141 bits (356), Expect = 2e-38
 Identities = 99/311 (31%), Positives = 162/311 (52%), Gaps = 15/311 (4%)

Query: 3   ILVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENLNRNALFYEQSIEDEEMMERIF 62
           ILVTGGAGF+GSH+  +L+  G  VI +DN  +G  EN+          +   ++ E I 
Sbjct: 5   ILVTGGAGFVGSHLCRRLLNEGNDVICLDNFFTGSKENIIDLLPHPYFELIRHDVQEPI- 63

Query: 63  SLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKKFIFSSTGGAIY 122
            L   + +++LA  AS      +P    +T+++G++ +L+ + K   K  I  ++   +Y
Sbjct: 64  -LLEVDEIYNLACPASPPHYQFDPVATTRTSVLGAINMLDIARKCKAK--ILQASTSEVY 120

Query: 123 GENVKVFPTPETEIPHPISPYGI------AKYSTEMYLEFFAREYGLKYTVLRYANVYGP 176
           G+  +V P PE+     +S  GI       K   E     + R++G+K  V+R  N YGP
Sbjct: 121 GDP-EVHPQPES-YRGSVSTTGIRACYDEGKRCAETLFFDYYRQHGVKIKVIRIFNTYGP 178

Query: 177 RQDPYGEAGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAMEKGDNEV--F 234
             +P  +  VV+ F  + LR +++ I+G G   R + YVDD+V   +  M   D+     
Sbjct: 179 YMNP-DDGRVVSNFIMQALRNQDITIYGAGTQTRSFQYVDDLVEGMIRLMNSDDSFTGPV 237

Query: 235 NIGTGRGTTVNQLFKLLKEITGYDKEPVYKPPRKGDVRKSILDYTKAKEKLGWEPKVSLE 294
           NIG     T+ +L + +  +TG   +  YKP  + D  +   D + AK++L WEP ++LE
Sbjct: 238 NIGNPGEFTMLELAQKIITLTGSSSKLTYKPLPQDDPLQRQPDISLAKKELDWEPTIALE 297

Query: 295 EGLKLTVEYFR 305
           EGLK T+ YF+
Sbjct: 298 EGLKKTIAYFK 308


Lambda     K      H
   0.318    0.139    0.396 

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: 255
Number of extensions: 15
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: 309
Length of database: 312
Length adjustment: 27
Effective length of query: 282
Effective length of database: 285
Effective search space:    80370
Effective search space used:    80370
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 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