GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Tatumella morbirosei LMG 23360

Align sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_038017555.1 HA49_RS11675 L-idonate 5-dehydrogenase

Query= metacyc::MONOMER-17164
         (369 letters)



>NCBI__GCF_000757425.2:WP_038017555.1
          Length = 343

 Score =  169 bits (428), Expect = 1e-46
 Identities = 101/314 (32%), Positives = 158/314 (50%), Gaps = 15/314 (4%)

Query: 40  IVQVIVTGLCGSDIHYWQHGRIGRYVVEAPIVLGHESAGIVVECGSKSGFAIGDRVALEP 99
           +V++   G+CGSD+HY+QHG++G + V+ P++LGHE  G VV+  +        +VA+ P
Sbjct: 31  LVRITRGGICGSDLHYYQHGKVGSFAVKMPMILGHEVIGYVVKSDNPE-LQENQKVAVNP 89

Query: 100 GIACNTCHHCRAGRYNLCSAMRFAATPPY----DGTLATYYRLPAECCYKLPAHVSLQHG 155
              C  C +C AG+ N C+ MRF  +  Y    DG  + Y  +    C         +  
Sbjct: 90  SKPCGHCKYCEAGQENQCTTMRFFGSAMYFPHVDGGFSQYKIVDTAQCIPFNHQADDRVM 149

Query: 156 ALVEPLSVAVHSCRLAGDMQQKSVVVFGAGPVGLLCASVSRAFGASTVVVVDINSDRLSV 215
              EPL+V +H+   AGD+Q K V + G GP+G L A+ ++A GA+ VV  DI+   LS+
Sbjct: 150 VFAEPLAVCIHATHQAGDLQDKKVFISGVGPIGCLIAAAAKARGAAEVVCADISPRSLSM 209

Query: 216 AQKYGATHTYKMSNESPEHNAARILEEMELDNG-AHIVLDATGAEPCMNCGISVLASGGT 274
           A+  GAT T   +N                D G   +  +A+G    +   + V  + GT
Sbjct: 210 AEAMGATQTIDAANGD--------FTPFLADKGYFDVSFEASGHPASLTRCLEVTRAKGT 261

Query: 275 FVQVGLGKPNPSLPVGQICDKEAIFRGSFRYGPGDYRTAIGLLSSGRVVLEGLVTHEFPF 334
            VQVG+G   P  P+  +  KE    GSFR+   ++ TA+  L  G +    L + EF +
Sbjct: 262 LVQVGMGGDVPGFPIMMLIAKEINLVGSFRF-THEFATAVEWLEKGTINPLPLYSGEFDY 320

Query: 335 TQAEEAFKNVGNRQ 348
            + + A    G++Q
Sbjct: 321 HEIDAALNFAGDKQ 334


Lambda     K      H
   0.321    0.137    0.420 

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: 330
Number of extensions: 15
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: 369
Length of database: 343
Length adjustment: 29
Effective length of query: 340
Effective length of database: 314
Effective search space:   106760
Effective search space used:   106760
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: 49 (23.5 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