GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA3 in Pseudomonas fluorescens FW300-N1B4

Align Putative L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate Pf1N1B4_398 Galactonate dehydratase (EC 4.2.1.6)

Query= curated2:A8MA91
         (398 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_398
          Length = 382

 Score =  118 bits (296), Expect = 3e-31
 Identities = 90/274 (32%), Positives = 141/274 (51%), Gaps = 23/274 (8%)

Query: 68  VEVESSDGEVGFG---ISTGGYPAAWIIENHLSRFVVGKYVGEVEKTWDQMFKATIYYGR 124
           ++VE+ +G  G+G   +    +  A  +E  LS +++GK    +E  W  +++   Y G 
Sbjct: 18  LKVETDEGVTGWGEPVVEGRAHTVAAAVEE-LSDYLIGKDPRNIEDIWTVLYRGGFYRGG 76

Query: 125 RGIVMNAISAVDLALWDLMGKVRGLPVYDLLGGPVRDELTFYA--TGPRP-DVAK----- 176
             I M+A++ +D ALWD+ GK  G+ V DLLGG VRD++  Y+   G RP D A+     
Sbjct: 77  -AIHMSALAGIDQALWDIKGKALGVSVSDLLGGQVRDKIRVYSWIGGDRPADTARAAKEA 135

Query: 177 -SLGFIGGKLPLIHGP-----ADGIEGLRENVRIFKEAREKVGDDFLLMYDCWMSLDLPY 230
            S GF   K+   +G       D  E +   +      R+ VG +  +  D    +  P 
Sbjct: 136 VSRGFTAVKM---NGTEELQFLDSFEKVDLALANVAAVRDAVGPNVGIGVDFHGRVHKPM 192

Query: 231 AQRLLSELKPYGLFWIEEPFIPDDYWSFGALANIAPPTLVASGEHESTVHGFRLLLELGK 290
           A+ L+ EL PY L +IEEP + ++Y +   LA +   T +A GE   +   F+ +L  G 
Sbjct: 193 AKVLMKELDPYKLMFIEEPVLSENYEALKELAPLT-STPIALGERLFSRWDFKRVLSEGY 251

Query: 291 VNVIQPDVTWVGGVTPMIKIAALAEAYGAWVIPH 324
           V++IQPD +  GG+T   KIA +AEAY   +  H
Sbjct: 252 VDIIQPDASHAGGITETRKIANMAEAYDVALALH 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: 414
Number of extensions: 23
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: 1
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