GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Halococcus hamelinensis 100A6

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; EC 1.1.1.401 (characterized)
to candidate WP_007693551.1 C447_RS10170 zinc-dependent alcohol dehydrogenase family protein

Query= SwissProt::P0DOW0
         (331 letters)



>NCBI__GCF_000336675.1:WP_007693551.1
          Length = 358

 Score =  140 bits (353), Expect = 5e-38
 Identities = 105/340 (30%), Positives = 157/340 (46%), Gaps = 13/340 (3%)

Query: 1   MKTLTWTAKETMSILSAPAPVPEPGWIALRVAGVGICGSELSGYLGHNELRKPPLVMGHE 60
           M+    TA   + +   P P      + +RV   G+C ++   Y G  E    PLV+GHE
Sbjct: 16  MRASVLTAVGEVEVQDRPRPTVADDDVLIRVGACGVCMTDYHMYHGSFEA-PTPLVLGHE 74

Query: 61  FSGVVEEVGHGVTNVKIGDLVTANPLVTCGRCIHCLRGERQRCESRRIIG----IDFPGA 116
            +G V EVG  VTNV +GD VT NP V C  C  C RGE   C     IG        G+
Sbjct: 75  TAGEVVEVGENVTNVTVGDRVTLNPTVPCNACPACKRGETNLCADNTSIGGAGNTIRDGS 134

Query: 117 YAERVLVPSNQCYAVKD--AIDGALVEPLACAVRAVGLARIKVGDTAVVIGAGIIGLMTV 174
           +AE V  P++      D      AL EPLAC V AV  A +  GDT  VIGAG IGL+ V
Sbjct: 135 FAEYVAAPASVVVDCGDLPVRTAALAEPLACCVHAVDRADVTTGDTVAVIGAGPIGLLMV 194

Query: 175 RLLGLSGAKRIAVVDPNDERLKISQLWG---ATEMAPNLGALLTDNHPQSFDCVIDAVGL 231
           +   ++GA  + V + + +R +++   G   A + A               D   + VG 
Sbjct: 195 QSFRVAGAGEVIVSELDADRRELALELGADHAVDPADGDAVEQVTAVDGPVDVAAEVVGQ 254

Query: 232 STTRRDSLNALIRGGRAVWIGL--HEALTHLDGNQIVRDELEVRGSFCYTDDEFIRAVSL 289
           + T   +     +GGR +  G+   +A        +  DE+ + G+F  T + F RAV+L
Sbjct: 255 TATIEQARAMTGKGGRTLVAGVPPQDATMEFSPFDLYFDEVSMVGTFALTQESFERAVTL 314

Query: 290 INSQKFLPVDRQWLDVRSLEEGPAAFKELVNGSPFSKIIL 329
           + + + + VD    +   L+    AF+ + N     K+++
Sbjct: 315 LRNDR-IDVDPLVTEEIGLDGLEGAFERMGNTEGLKKLVV 353


Lambda     K      H
   0.322    0.139    0.424 

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: 331
Number of extensions: 23
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: 358
Length adjustment: 29
Effective length of query: 302
Effective length of database: 329
Effective search space:    99358
Effective search space used:    99358
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 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