GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Gracilibacillus halophilus YIM-C55.5

Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_003462994.1 J416_RS00905 3-oxoacyl-[acyl-carrier-protein] reductase

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



>NCBI__GCF_000359605.1:WP_003462994.1
          Length = 247

 Score =  133 bits (335), Expect = 3e-36
 Identities = 91/265 (34%), Positives = 137/265 (51%), Gaps = 31/265 (11%)

Query: 7   LKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQS--------SGNYNFWPT 58
           L++K+  VTG + GIG AI  ++   GA+V +      DK Q+         G       
Sbjct: 2   LQDKVALVTGASRGIGRAIALQMAKNGASVAVNYAGSADKAQAVVDEIEEIGGTAIKIQA 61

Query: 59  DISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNI 118
           ++S+  EV   V   I  FGR+D LVNNAG+    LL+          ++E  F+ +++ 
Sbjct: 62  NVSNEKEVKAMVKQTIDTFGRLDVLVNNAGITKDNLLM---------RMSEEDFDDVIDT 112

Query: 119 NQKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKEL 178
           N KGVF+ ++AV RQM+KQ+SG I+NVSS  G+ G+ GQ+ Y + KA +   T+S ++EL
Sbjct: 113 NLKGVFVCTKAVTRQMMKQKSGRIINVSSVVGISGNPGQANYVSAKAGVIGLTKSAAQEL 172

Query: 179 GKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEV 238
               I V  VAPG +            A   T  +T +Q  +  S   IPL   G   +V
Sbjct: 173 AAKNILVNAVAPGFI------------ATDMTDELTEDQKEQILS--LIPLKTLGEAEDV 218

Query: 239 ADFVCYLLSERASYMTGVTTNIAGG 263
           A+   +L S ++ Y+TG T  + GG
Sbjct: 219 ANTAVFLASNQSKYITGQTIQVDGG 243


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: 151
Number of extensions: 8
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: 247
Length adjustment: 24
Effective length of query: 243
Effective length of database: 223
Effective search space:    54189
Effective search space used:    54189
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 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