GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA3 in Acidovorax sp. GW101-3H11

Align Putative L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate Ac3H11_600 Galactonate dehydratase (EC 4.2.1.6)

Query= curated2:A8MA91
         (398 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_600
          Length = 382

 Score =  115 bits (287), Expect = 3e-30
 Identities = 84/273 (30%), Positives = 139/273 (50%), Gaps = 21/273 (7%)

Query: 68  VEVESSDGEVGFG--ISTGGYPAAWIIENHLSRFVVGKYVGEVEKTWDQMFKATIYYGRR 125
           +++E+ +G  G+G  +  G         + L+ +++GK    +E  W  +++   Y G  
Sbjct: 18  LKIETDEGITGWGEPVLEGRAHTVAAAVDELADYLIGKDPRHIEDHWTVLYRGGFYRGG- 76

Query: 126 GIVMNAISAVDLALWDLMGKVRGLPVYDLLGGPVRDELTFYA--TGPRP-------DVAK 176
           G+ M+A++ +D ALWD+ GK  G+PV +LLGG VR  +  Y+   G RP         A 
Sbjct: 77  GVHMSALAGIDQALWDIKGKALGVPVSELLGGNVRSHIKVYSWIGGDRPSETAAAAQAAV 136

Query: 177 SLGFIGGKLPLIH-----GPADGIEGLRENVRIFKEAREKVGDDFLLMYDCWMSLDLPYA 231
           + GF   K+            D +E   +NV   +EA   VG +  +  D    +  P A
Sbjct: 137 ARGFTAVKMNGTEEVQYVDSYDKVERCLQNVAAVREA---VGPNVGIGVDFHGRVHRPMA 193

Query: 232 QRLLSELKPYGLFWIEEPFIPDDYWSFGALANIAPPTLVASGEHESTVHGFRLLLELGKV 291
           + L+ EL+PY L +IEEP + +   +   +A I+  T +A GE   +   F+ +L+ G  
Sbjct: 194 KVLVKELEPYKLMFIEEPVLSEHEEALKEIARIS-STPIALGERLYSRWDFKRVLQGGYA 252

Query: 292 NVIQPDVTWVGGVTPMIKIAALAEAYGAWVIPH 324
           ++IQPD +  GG+T   KIA++AEAY   +  H
Sbjct: 253 DIIQPDPSHAGGITETRKIASMAEAYDVALALH 285


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: 402
Number of extensions: 25
Number of successful extensions: 5
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 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