GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Rhodococcus qingshengii djl-6-2

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_102999338.1 C1M55_RS10010 glucose 1-dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2119
         (272 letters)



>NCBI__GCF_002893965.1:WP_102999338.1
          Length = 256

 Score =  144 bits (363), Expect = 2e-39
 Identities = 86/250 (34%), Positives = 133/250 (53%), Gaps = 7/250 (2%)

Query: 19  LKNKVVLLTGAAQGIGEAIVATFASQQARLIISDIQGEKVEKVAAHWRDQGADVVAIKAD 78
           L NKV ++TGA  GIG AI   F ++ AR+++SDI G   + VA    D     +A+  D
Sbjct: 5   LANKVAIVTGAGAGIGAAIARAFGAEGARVVVSDINGGAAQAVA----DSIDGAIAVTTD 60

Query: 79  VSRQQDLHAMARLAIDLHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCK 138
           V+ +Q +  +   A++  G ++V+V  AG+      +E + EDWR+  +++L+G +   +
Sbjct: 61  VTDEQQVKDLVARAVEEFGGLNVVVPNAGIATTTPLIETSFEDWRKVMSVNLNGVFLTVR 120

Query: 139 AVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAI 198
             LP ++  G GSI+NI+S  ST   P    Y  AK  +  LT  L  E    G+R NA+
Sbjct: 121 HSLPALVASGGGSIVNISSISSTTGSPLIGSYAAAKAAVRNLTETLSAELRFHGIRANAL 180

Query: 199 APGYIETQLNVDYWNGFADPHAERQRAFD---LHPPRRIGQPIEVAMTAVFLASDEAPFI 255
            PG+I+T L   +   F +        FD   +    R G+  EVA  AVF ASD++ + 
Sbjct: 181 LPGFIDTDLVKSHQQDFENALGLESGGFDDLMVTKQTRYGRTEEVAAAAVFFASDQSSWC 240

Query: 256 NASCITIDGG 265
           N S + +DGG
Sbjct: 241 NGSSLVLDGG 250


Lambda     K      H
   0.322    0.138    0.426 

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: 7
Number of successful extensions: 3
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: 256
Length adjustment: 25
Effective length of query: 247
Effective length of database: 231
Effective search space:    57057
Effective search space used:    57057
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 (21.9 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