GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Dyadobacter tibetensis Y620-1

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_025763370.1 X939_RS0111250 glucose 1-dehydrogenase

Query= reanno::pseudo1_N1B4:Pf1N1B4_412
         (272 letters)



>NCBI__GCF_000566685.1:WP_025763370.1
          Length = 257

 Score =  143 bits (360), Expect = 4e-39
 Identities = 91/258 (35%), Positives = 136/258 (52%), Gaps = 11/258 (4%)

Query: 18  RLKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKA 77
           RLKNKV L+TG + GIG      FA + A++V+SD+  E  ++ A    EQG +   I +
Sbjct: 2   RLKNKVALITGGSGGIGRETALLFAREGAQIVVSDVNQEMGQQTADMIVEQGGEAYFIYS 61

Query: 78  DVSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQMTEED--WHRCFAIDLDGAWY 135
           DVS+  D  AM     E  G++++L N AG+    D   MT E+  W     I+  G + 
Sbjct: 62  DVSKDADCKAMVAFTEEKFGKLNILFNNAGIMHSDDDNAMTTEESVWDLTMNINAKGVFL 121

Query: 136 GCKAVLPQMIEQGIGSIINIASTHSTHIIPGCFP---YPVAKHGLLGLTRALGIEYAPKG 192
           GCK  +P +   G GS+IN AS     I+    P   Y  +K  +L LTR L + +A + 
Sbjct: 122 GCKYGIPALQRAGGGSVINTAS--FVAILGAATPQIAYTASKGAVLALTRELAVIHAREN 179

Query: 193 IRVNAIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEA 252
           IRVNA+ PG + T+L + + N       ++QR     P  R G+  E+A   +FLASDE+
Sbjct: 180 IRVNALCPGPLRTELLMKFLN----TEEKKQRRLVHVPMGRFGEAKEMASAVLFLASDES 235

Query: 253 PFINASCITIDGGRSVMY 270
            ++  +   +DGG +  Y
Sbjct: 236 TYVTGTDFLVDGGITAAY 253


Lambda     K      H
   0.321    0.138    0.424 

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: 140
Number of extensions: 5
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: 257
Length adjustment: 25
Effective length of query: 247
Effective length of database: 232
Effective search space:    57304
Effective search space used:    57304
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