GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA4 in Desulfovibrio vulgaris Hildenborough

Align 2-keto-3-deoxy-L-rhamnonate aldolase; KDR aldolase; EC 4.1.2.53; 2-dehydro-3-deoxyrhamnonate aldolase (uncharacterized)
to candidate 209277 DVU0343 HPCH/HPAI aldolase family protein

Query= curated2:B5R262
         (267 letters)



>MicrobesOnline__882:209277
          Length = 260

 Score =  122 bits (305), Expect = 1e-32
 Identities = 79/243 (32%), Positives = 120/243 (49%), Gaps = 9/243 (3%)

Query: 6   SNPFKEGLRKGDTQIGLWLSSTTSYMAEIAATSGYDWLLIDGEHAPNTVQDLYHQLQAIA 65
           ++  +  +++G+  IG W+   ++ +AEI   +GYDW+ +D EHA  T   L    +AI 
Sbjct: 4   AHDIRSKMQRGEATIGTWMQLPSTDVAEILGRAGYDWVAVDLEHAAFTRAMLPDLFRAIE 63

Query: 66  PYASQPVIRPIEGSKALIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYP----PLGQRG 121
              + P  R  E +   IK  LD GA  ++ PM++T EQ    +    YP    P G RG
Sbjct: 64  LGGTAPFARVAEATLTDIKAALDSGAHGIIFPMIETREQLDAAIGWALYPRTDGPSGIRG 123

Query: 122 VGASVARAARWGR-IDNYMAQANESLCLLVQVESKVALENLDAILEVEGIDGVFIGPADL 180
           VG    R   +GR  D Y       L  + Q+E   A+ENLDAIL    +D + +GP DL
Sbjct: 124 VG--YCRGNLFGREFDAYRNTTARDLVFVAQIEHIRAVENLDAILAHPRLDAIMVGPYDL 181

Query: 181 SASLGYPDNAGHPEVQRIIESCIYRIRAAGKAAGFLAVDP--AMAQKCLAWGANFVAVGV 238
           S S+G      HP+ +  ++    +  A G   G   V P  A+ +  +A G  F+A G+
Sbjct: 182 SGSMGLTAQFDHPDFKAALDRIRDKAVAHGVPMGLHIVQPDEALVRAKVAEGYRFIAYGI 241

Query: 239 DTM 241
           D +
Sbjct: 242 DAV 244


Lambda     K      H
   0.318    0.132    0.384 

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: 146
Number of extensions: 6
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: 267
Length of database: 260
Length adjustment: 25
Effective length of query: 242
Effective length of database: 235
Effective search space:    56870
Effective search space used:    56870
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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