GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galactonolactonase in Klebsiella michiganensis M5al

Align galactaro-1,5-lactonase (characterized)
to candidate BWI76_RS21470 BWI76_RS21470 gluconolaconase

Query= reanno::WCS417:GFF3393
         (291 letters)



>FitnessBrowser__Koxy:BWI76_RS21470
          Length = 290

 Score =  150 bits (379), Expect = 3e-41
 Identities = 100/289 (34%), Positives = 132/289 (45%), Gaps = 13/289 (4%)

Query: 6   IVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIARTDAGN 65
           + D    + ECP W   E ALYW DI +  + R+   TG       P+   C A    G 
Sbjct: 7   LFDYTGHLPECPTWSEAEQALYWADIMECEIHRYDVRTGEHQVLQFPEEPGCFALRAKGG 66

Query: 66  WVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNMGLN 125
           ++  + +G +    H  G L   +     +P Q  R NDG  DR GRF+AG+       N
Sbjct: 67  FIVALRSGIWLTDAH--GLLQRKVCDNPSNP-QLARFNDGGTDRDGRFYAGTFWGPGDFN 123

Query: 126 AAEGTLYRYTSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYDIDTGT 185
            A   L R  S  +P          NGLAFS D R MY SD+   V      D     G 
Sbjct: 124 GA--LLMRIDSDLSPQVIQCDIHGANGLAFSEDKRWMYTSDTPNAVIYRTPLD---KRGE 178

Query: 186 PSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTVPVKKPTM 245
              R VF   H   G PDGAA+DA+GCYW    D   I RFSP G       +PV+ PTM
Sbjct: 179 AGKREVFRRFHPGEGIPDGAAIDAEGCYWSAMFDGWRIARFSPTGEQLEEHRLPVRCPTM 238

Query: 246 CAFGGSRLDTLFVTSIRDDQSEQS-----LSGGVFALNPGVVGLPEPTF 289
             FGG+ + TL++T+ R++   +      LSG +F L   V G+ +  F
Sbjct: 239 VCFGGTDMKTLYITTTRENMDAEEVAKYPLSGAIFTLPVSVAGMKKLPF 287


Lambda     K      H
   0.321    0.137    0.443 

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: 338
Number of extensions: 19
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: 291
Length of database: 290
Length adjustment: 26
Effective length of query: 265
Effective length of database: 264
Effective search space:    69960
Effective search space used:    69960
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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