GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Algoriphagus aquaeductus T4

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_111394018.1 CLV31_RS16420 glucose 1-dehydrogenase

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



>NCBI__GCF_003253485.1:WP_111394018.1
          Length = 264

 Score =  147 bits (370), Expect = 3e-40
 Identities = 88/248 (35%), Positives = 137/248 (55%), Gaps = 5/248 (2%)

Query: 19  LKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRER-GADVHALKA 77
           LK K  ++TG  +G+G A+ A  AS  A +++   +A   +  AA   E+ G       A
Sbjct: 17  LKGKSAIITGGTKGLGLAMAAGLASAGANVLLVSRKASDGDQAAAEIAEKFGVKALTFSA 76

Query: 78  DVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137
           DV++Q  + AMA+ A E  G ID+L+N AG+N+     E+T ED+ +   ++++G W  C
Sbjct: 77  DVADQAGMEAMAKFAHEAFGSIDILINSAGINIRGAIDELTHEDFTKVMEVNVNGTWLAC 136

Query: 138 KAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNA 197
           +AV P M EQ  G+IIN+AST     +    PY  +K  ++ +TRAL +E AP  + VNA
Sbjct: 137 RAVTPFMKEQKKGAIINLASTLGLVGLANRTPYTASKGAVVQMTRALALELAPWNINVNA 196

Query: 198 IAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINA 257
           I PG   T++N+      AD    ++  +      R G+  E+   A+FLAS  A ++  
Sbjct: 197 ICPGPFLTEMNLP----IADTEEGKKFVVGATALGRWGELKEIQGAAIFLASYAATYMVG 252

Query: 258 SCITIDGG 265
           S +T+DGG
Sbjct: 253 SMVTVDGG 260


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: 151
Number of extensions: 9
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: 264
Length adjustment: 25
Effective length of query: 247
Effective length of database: 239
Effective search space:    59033
Effective search space used:    59033
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 24 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