GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Thiothrix lacustris DSM 21227

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_211248857.1 Q394_RS0118475 glucose 1-dehydrogenase

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



>NCBI__GCF_000621325.1:WP_211248857.1
          Length = 255

 Score =  124 bits (310), Expect = 3e-33
 Identities = 81/251 (32%), Positives = 127/251 (50%), Gaps = 8/251 (3%)

Query: 17  ERLKNKVVLLTGAAQGIGEAIVATFASQQARLIISDIQGEKVEKVAAHWRDQGADVVAIK 76
           + L  KVV++TGA+ GIGEA    F  +  +L++   + E+ E VAA  R  G + V + 
Sbjct: 7   QNLAGKVVVITGASSGIGEAAAHAFGREGCKLVLGARRAEEGEAVAAAIRATGGEAVFVC 66

Query: 77  ADVSRQQDLHAMARLAIDLHGRIDVLVNCAGV-NVFRDPLEMTEEDWRRCFAIDLDGAWY 135
            DV ++ D+  + + A+D  G +DVL N AG   V     E +  ++      ++    +
Sbjct: 67  TDVLQEADIARLVQTALDTFGGLDVLFNNAGTEGVSSAFTEQSTAEYDFTMNTNVRSVLW 126

Query: 136 GCKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRV 195
           G +  +  M   G G+IIN AS  +         Y  +K  ++G+TR   +EY  +G+R+
Sbjct: 127 GMQHAIRAMQSAG-GAIINNASIVAHVGFANTALYSASKAAVVGMTRVAAVEYFKQGIRI 185

Query: 196 NAIAPGYIETQLNVDYWNGFADPHAERQRAF-DLHPPRRIGQPIEVAMTAVFLASDEAPF 254
           NA+ PG   T ++     G      + Q AF    P  R GQP E+A   VFLAS  A +
Sbjct: 186 NAVCPGITYTPMSQRLLGG-----EDEQNAFMATTPAGRTGQPEEIAAAVVFLASGNASY 240

Query: 255 INASCITIDGG 265
           I+  C+ +DGG
Sbjct: 241 ISGQCLNVDGG 251


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: 139
Number of extensions: 6
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: 255
Length adjustment: 25
Effective length of query: 247
Effective length of database: 230
Effective search space:    56810
Effective search space used:    56810
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 Apr 09 2024. 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