GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Haloglycomyces albus DSM 45210

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate WP_025272362.1 HALAL_RS0101795 3-oxoacyl-ACP reductase FabG

Query= SwissProt::Q1NEI6
         (249 letters)



>NCBI__GCF_000527155.1:WP_025272362.1
          Length = 236

 Score =  127 bits (319), Expect = 2e-34
 Identities = 80/232 (34%), Positives = 123/232 (53%), Gaps = 5/232 (2%)

Query: 14  IVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATHVVALDVSDHAAVAAA 73
           ++TGG  G+G+  A R+  +G  VA+      ++   +  +D  H   +DVSD  A    
Sbjct: 7   LITGGTRGIGRAAAQRLKDDGFTVAV---ASRSIPDAENRLDVHHY-QVDVSDGNACKDL 62

Query: 74  AKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREVVPFMLEN 133
                  +G +D+LI SAGI   + P+     D +  VI  NL+G +   R +   M++ 
Sbjct: 63  ITTVEDEVGDIDVLINSAGIVRDS-PLLTMTGDDWNDVIRTNLDGTYNMCRSMAFSMMKR 121

Query: 134 GYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTPATFESPI 193
             G I+NL+SVAG +GNP  S YSASKAG+IGF+K+L KEL    +  N + P   E+ +
Sbjct: 122 KNGSIINLSSVAGIQGNPTQSNYSASKAGIIGFSKALSKELGRFNIRVNVVAPGFIETDM 181

Query: 194 LDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGG 245
              L +S        IP+GR+G V++ A +V F+AS   ++ T +     GG
Sbjct: 182 TADLAESVKKKAVENIPLGRMGSVDDVAHLVGFLASPRATYMTGAVVPVDGG 233


Lambda     K      H
   0.318    0.132    0.381 

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: 149
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: 249
Length of database: 236
Length adjustment: 23
Effective length of query: 226
Effective length of database: 213
Effective search space:    48138
Effective search space used:    48138
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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