GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA3 in Amantichitinum ursilacus IGB-41

Align Putative L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate WP_053939463.1 WG78_RS19245 galactonate dehydratase

Query= curated2:A8MA91
         (398 letters)



>NCBI__GCF_001294205.1:WP_053939463.1
          Length = 382

 Score =  128 bits (322), Expect = 2e-34
 Identities = 101/352 (28%), Positives = 173/352 (49%), Gaps = 28/352 (7%)

Query: 68  VEVESSDGEVGFG--ISTGGYPAAWIIENHLSRFVVGKYVGEVEKTWDQMFKATIYYGRR 125
           +++E+ +G VG+G  +  G         + +S +++G+    +   W  +++A  Y G  
Sbjct: 18  LKIETDEGIVGWGEPVLEGRAKTVEAAVHEMSEYLIGQDPARINDLWQVLYRAGFYRGG- 76

Query: 126 GIVMNAISAVDLALWDLMGKVRGLPVYDLLGGPVRDELTFYA--TGPRP-DVAKSL---- 178
           GI+M+AI+ +D ALWD+ GK  G+PVY LLGG VRD +  Y+   G RP D+ + +    
Sbjct: 77  GILMSAIAGIDQALWDIKGKALGVPVYQLLGGLVRDRVKTYSWVGGDRPADIIRDIQARV 136

Query: 179 --GFIGGKLPLIHGPA--DGIEGLRENVRIFKEAREKVGDDFLLMYDCWMSLDLPYAQRL 234
             GF   K+      A  D    +   VR   E RE  G+      D    +  P A+ L
Sbjct: 137 DVGFDTFKMNGCEELAVIDNSRAIDAAVRKVAEIREAFGNKIEFGLDFHGRVTAPMARVL 196

Query: 235 LSELKPYGLFWIEEPFIPD--DYWSFGALANIAPPTLVASGEHESTVHGFRLLLELGKVN 292
           + EL+PY   +IEEP + +  +Y+   A     P   +A+GE   +   F+ +L  G ++
Sbjct: 197 IKELEPYRPLFIEEPVLAEQAEYYPKLAAQTHIP---LAAGERMYSRFEFKNVLAAGGLS 253

Query: 293 VIQPDVTWVGGVTPMIKIAALAEAYGAWVIPHGSSVYGYHFIITRVNSPFAEYLVVSPDA 352
           ++QPD++  GG+T  +KIA++AEAY   + PH     G   +   +   F  +     + 
Sbjct: 254 ILQPDLSHAGGITECMKIASMAEAYDVALAPH--CPLGPIALAACLQVDFVSWNAFIQEQ 311

Query: 353 TKIVPQ-------FHPLLRDEPIPQNGKVRLSRKPGFGVELNRDLLVRPFKS 397
           +  +          + L + +   +NG ++   KPG GVEL+  L++   K+
Sbjct: 312 SMGIHYNKGGEVLDYVLNKADFALENGHIKPFTKPGLGVELDEALIIERSKN 363


Lambda     K      H
   0.321    0.141    0.440 

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: 412
Number of extensions: 25
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 398
Length of database: 382
Length adjustment: 30
Effective length of query: 368
Effective length of database: 352
Effective search space:   129536
Effective search space used:   129536
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 (21.8 bits)
S2: 50 (23.9 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