GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xad in Pseudomonas fluorescens FW300-N2E2

Align D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) (characterized)
to candidate Pf6N2E2_5977 Galactonate dehydratase (EC 4.2.1.6)

Query= metacyc::MONOMER-18070
         (393 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5977
          Length = 382

 Score =  204 bits (520), Expect = 3e-57
 Identities = 134/358 (37%), Positives = 193/358 (53%), Gaps = 11/358 (3%)

Query: 28  VRVTTNDGRVGWGETVSALRAEAVANFVKKINTVLKGNDVFNVEKNRLEWYKHDFNMTIS 87
           ++V T++G  GWGE V   RA  VA  V++++  L G D  N+E      Y+  F    +
Sbjct: 18  LKVETDEGVTGWGEPVVEGRAHTVAAAVEELSDYLIGKDPRNIEDIWTVLYRGGFYRGGA 77

Query: 88  LESTTAYSAVDIASWDIIGKELGAPLYKLLGGKTRDKVLVYANGWYQNCVKPEDFAEKAK 147
           +  + A + +D A WDI GK LG  +  LLGG+ RDK+ VY+  W     +P D A  AK
Sbjct: 78  IHMS-ALAGIDQALWDIKGKALGVSVSDLLGGQVRDKIRVYS--WIGGD-RPADTARAAK 133

Query: 148 EIVKMGYKALKFDPFGPY-FNDISKKGLDIAEERVKAVREAVGDNVDILIEHHGRFNANS 206
           E V  G+ A+K +      F D  +K +D+A   V AVR+AVG NV I ++ HGR +   
Sbjct: 134 EAVARGFTAVKMNGTEELQFLDTFEK-VDLALANVAAVRDAVGPNVGIGVDFHGRVHKPM 192

Query: 207 AIMIAKRLEKYNPLFMEEPIHPEDVEGLRKYRNNTSLRIALGERIINKQQALYFMKEGLV 266
           A ++ K L+ Y  +F+EEP+  E+ E L++    TS  IALGER+ ++      + EG V
Sbjct: 193 AKVLMKELDPYKLMFIEEPVLSENYEALKELAPLTSTPIALGERLFSRWDFKRVLSEGYV 252

Query: 267 DFLQADLYRIGGVTETKKVVGIAETFDVQMAFHNAQGPILNAVTLQFDAFIPNFLIQESF 326
           D +Q D    GG+TET+K+  +AE +DV +A H   GPI  A  LQ DA   N  IQE  
Sbjct: 253 DIIQPDASHAGGITETRKIANMAEAYDVALALHCPLGPIALAACLQLDAVCYNAFIQEQS 312

Query: 327 YDWFPSWKRELI-YNGTP----IDNGYAIIPERPGLGVEVNEKMLDSLKVKGEEYFNP 379
                +   +L+ Y   P     D G+  IP  PGLG+E+NE+ +      G  + NP
Sbjct: 313 LGIHYNESNDLLDYIKDPQVFDYDKGFVKIPNGPGLGIEINEEYVIERAAIGHRWRNP 370


Lambda     K      H
   0.319    0.137    0.409 

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: 391
Number of extensions: 21
Number of successful extensions: 5
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: 393
Length of database: 382
Length adjustment: 30
Effective length of query: 363
Effective length of database: 352
Effective search space:   127776
Effective search space used:   127776
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 (21.7 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