GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Methylocystis bryophila S285

Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_085771999.1 B1812_RS13135 glucose 1-dehydrogenase

Query= reanno::Koxy:BWI76_RS01745
         (267 letters)



>NCBI__GCF_002117405.1:WP_085771999.1
          Length = 249

 Score =  102 bits (253), Expect = 1e-26
 Identities = 83/263 (31%), Positives = 128/263 (48%), Gaps = 27/263 (10%)

Query: 7   LKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQSSGNYNFWPT----DISS 62
           L  K+  VTGG SGIGL+      A+GA++ +      +   +             D+S 
Sbjct: 4   LSGKVAVVTGGNSGIGLSTAQLFAAEGAHLVVTGRRKAELDTAVAEIGHGAVGVQGDVSK 63

Query: 63  ASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQKG 122
            +++      +  +FGRID L  NAGV        E AP     ++E  F+K+ +IN KG
Sbjct: 64  LADLDALYAEVKSKFGRIDILFANAGVC-------ELAPL--VGVSEEHFDKVFDINVKG 114

Query: 123 VFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKHG 182
           +    Q  A  +      +I+N SS +   G      Y+ATKAA+ SF R+W+ EL    
Sbjct: 115 LLFTVQK-ALPLFADGGSIILN-SSVANTTGIPAFGVYSATKAAVRSFARTWTSELKDRN 172

Query: 183 IRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNS--IPLGRSGRLTEVAD 240
           IRV  ++PG +E     TP + +       ++ EQL+E  ++ S  +PLGR G+  E+A 
Sbjct: 173 IRVNVISPGPIE-----TPIFGKV-----GLSAEQLQEFDAQISAKVPLGRFGKPEEIAK 222

Query: 241 FVCYLLSERASYMTGVTTNIAGG 263
              +L S+ ASY+ G    + GG
Sbjct: 223 AALFLASDDASYVAGADLYVDGG 245


Lambda     K      H
   0.315    0.132    0.378 

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: 156
Number of extensions: 7
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: 267
Length of database: 249
Length adjustment: 24
Effective length of query: 243
Effective length of database: 225
Effective search space:    54675
Effective search space used:    54675
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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