GapMind for catabolism of small carbon sources

 

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

Align galactonate dehydratase [EC: 4.2.1.6] (characterized)
to candidate Pf6N2E2_1104 Gluconate dehydratase (EC 4.2.1.39)

Query= reanno::BFirm:BPHYT_RS16405
         (382 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1104
          Length = 399

 Score =  107 bits (268), Expect = 4e-28
 Identities = 86/272 (31%), Positives = 138/272 (50%), Gaps = 18/272 (6%)

Query: 18  LKIETDEGIVGWGEPVVEGRAHTVAAAVEELSDYLIGKDPLLIEDHWQVMYRSGFYRGGP 77
           ++IE  +G VG+   V  G         + L+ ++ G     IE  W  MY+S  Y G  
Sbjct: 61  VEIEASDGTVGFA--VTTGGEPAAYIVEKHLARFVEGARVTDIEKIWDQMYQSTLYYGRK 118

Query: 78  -ITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIKVYSWIGGDRPSDVANNARAVV 136
            + ++ I+GVD ALWD+ GK    P+H LLGG VRD+++ Y+   G RP D+A     + 
Sbjct: 119 GLVINTISGVDLALWDLLGKIRQEPVHQLLGGAVRDELQFYA--TGARP-DLAQKMGFI- 174

Query: 137 ERGFKAVKMNGSEELQIIDTFDKVQGVINNVAAVREAVGPNIGIGVDFHGRVHKPMAKVL 196
             G K    +G  E +     + ++  +  +A +RE VGP+  + +D    +    A  L
Sbjct: 175 --GGKMPLHHGPAEGE-----EGLRKNLEALATMRERVGPDFWLMLDCWMSLDLNYATKL 227

Query: 197 AKELDPYKLLFIEEPVLSEN---AEALRDIVNQTNTPIALGERLYSRWDFKHILSGGYVD 253
           A     + L +IEE +  ++     ALR+ V +    +  GE   +RW F+ +L  G  D
Sbjct: 228 AVGAHEHGLKWIEEALPPDDYWGYAALRNNVPK-GMLVTTGEHEATRWGFRMLLEMGCCD 286

Query: 254 IIQPDASHAGGITECRKIASMAEAYDVALALH 285
           IIQPD    GG+TE  KI+++A+A++  +  H
Sbjct: 287 IIQPDVGWCGGLTELVKISALADAHNALVIPH 318


Lambda     K      H
   0.319    0.139    0.428 

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: 434
Number of extensions: 21
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: 382
Length of database: 399
Length adjustment: 31
Effective length of query: 351
Effective length of database: 368
Effective search space:   129168
Effective search space used:   129168
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