GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araD in Dethiosulfovibrio salsuginis USBA 82

Align L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4) (characterized)
to candidate WP_085544742.1 B9Y55_RS07460 L-fuculose-phosphate aldolase

Query= BRENDA::C4B4W3
         (240 letters)



>NCBI__GCF_900177735.1:WP_085544742.1
          Length = 217

 Score =  107 bits (267), Expect = 2e-28
 Identities = 74/219 (33%), Positives = 111/219 (50%), Gaps = 13/219 (5%)

Query: 23  REIVSNLHAELPRWQLVVWTAGNVSQRVVVDKEAGPGPEDLFVIKPSGVSYDELTPEAMV 82
           RE V     +L    L   T GNVS   V ++E G        + PSG+ Y ++ PE +V
Sbjct: 7   REQVVEYGRKLMEANLTTGTGGNVS---VFNREEG-----YIALSPSGMDYFDVKPEDVV 58

Query: 83  VCNTEGDLIEGTRS-PSSDTAAHAYVYKHMDTVGGIVHTHSTYACAWAALGEEVPCVLTM 141
           +   +G  +E     P+++   H  +YK       IVH HS YA A + LG ++P V  M
Sbjct: 59  IMTLDGGFVEEDHLVPTTEWGLHLGLYKVRPDASAIVHCHSDYATAVSCLGIDLPAVNYM 118

Query: 142 MADEFGGPVPIGPFAIIGDDSIGRGIVDTLKTSRSPAVLMKNHGPFTIGKDGRDAVKAAV 201
           +A   G  VPI PFA+ G   + + + D +      AVLM NHG   +G+  + A   A+
Sbjct: 119 VAVA-GDRVPITPFAVYGTPELAKNVADNIGDYN--AVLMANHGQIALGRSMKAAFTVAL 175

Query: 202 MVEEVSKAAHLARTIGTPQIVPDEAIDALYDRYQNVYGQ 240
            VE V++   LA++ G P I+P EAI+    ++ + YGQ
Sbjct: 176 NVEYVARLYILAKSAGEPVILPKEAIEGTQRQFAS-YGQ 213


Lambda     K      H
   0.316    0.132    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: 141
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: 240
Length of database: 217
Length adjustment: 23
Effective length of query: 217
Effective length of database: 194
Effective search space:    42098
Effective search space used:    42098
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. 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