GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Pseudomonas stutzeri RCH2

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate GFF2310 Psest_2358 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>FitnessBrowser__psRCH2:GFF2310
          Length = 252

 Score =  132 bits (333), Expect = 6e-36
 Identities = 90/254 (35%), Positives = 135/254 (53%), Gaps = 15/254 (5%)

Query: 17  ERLKNKVVLLTGAAQGIGEAIVAAFASQQARLVIS-----DIQAEKVETVAAHWRERGAD 71
           +R   +  L+TGAA GIG A   A A++ AR+ I+     D+  + VE + A+    G D
Sbjct: 4   KRFAGQTALITGAATGIGRATALALAAEGARVWINHRDQHDLANQLVEQITAN----GGD 59

Query: 72  VHALKADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLD 131
             A++ADVS+   + AM    +E  G +D+LVN AGV + +  LE +E DW     +DL 
Sbjct: 60  AWAIEADVSDPAAVAAMFE-TIEAQGSLDLLVNNAGVILEKPFLETSEADWAMVLGVDLG 118

Query: 132 GAWYGCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPK 191
           G +  C+  L QM  +  G+I+N+AS            Y  AK G++GLTR+L  E+A  
Sbjct: 119 GVYRCCRHALAQMQPRRSGAIVNVASDLGFLGREQYVAYCTAKAGVIGLTRSLAREFAAD 178

Query: 192 GVRVNAIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDE 251
           G+RVN +APG I T +        +D +  ++ A+   P  R+G P EVA   VFL S +
Sbjct: 179 GIRVNGVAPGPIATAMVSP--EHMSDEWMAKELAI---PMARLGTPEEVAAAIVFLLSPQ 233

Query: 252 APFINASCITIDGG 265
           A +     +  +GG
Sbjct: 234 ASYFTGQLLGPNGG 247


Lambda     K      H
   0.321    0.137    0.419 

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: 157
Number of extensions: 10
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: 272
Length of database: 252
Length adjustment: 25
Effective length of query: 247
Effective length of database: 227
Effective search space:    56069
Effective search space used:    56069
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: 47 (22.7 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