GapMind for catabolism of small carbon sources

 

Alignments for a candidate for klh in Stenotrophomonas chelatiphaga DSM 21508

Align predicted periplasmic 3-ketoglycoside hydrolase (DUF1080) (characterized)
to candidate WP_057509066.1 ABB28_RS13230 DUF1080 domain-containing protein

Query= reanno::Pedo557:CA265_RS22975
         (260 letters)



>NCBI__GCF_001431535.1:WP_057509066.1
          Length = 247

 Score =  248 bits (634), Expect = 7e-71
 Identities = 130/257 (50%), Positives = 163/257 (63%), Gaps = 16/257 (6%)

Query: 6   LLFIPALFAGQAMAQDKKPDPAKDPKTTEVWEPVP-KVVTPGKLPQDAPSDATILFGGRN 64
           LL    L A   +      DPA+DP  TEVW+PVP  V TP      APSDAT+LF G++
Sbjct: 5   LLVTAGLLAAIPVFAQAGGDPARDPARTEVWKPVPASVATPAG---GAPSDATVLFDGKD 61

Query: 65  LDAWHSVKDPSKPAEWTIDDGFFTVKKGTGNIETNKKFTDYQLHMEWKIPENISG-EGQA 123
           + AW S  +   P  W + DG  TV  G+  I T ++F D QLH+EW+ P   +G +GQ 
Sbjct: 62  VSAWES--EQGGPVPWRLADGALTVVPGSKGIRTRQRFCDIQLHVEWRTPAATAGFDGQN 119

Query: 124 RGNSGVFLASTGGGDNGYEIQIMDAYNNKTYVNGQTGSVYKQAIPLANANKKPGEWQYYD 183
           RGNSGVFL         YE+Q++D+YNN TY NGQ GS+YKQA+PL NA++ PG+WQ YD
Sbjct: 120 RGNSGVFLQDL------YELQVLDSYNNPTYANGQAGSIYKQAMPLVNASRAPGQWQAYD 173

Query: 184 IIWNAPRFNEDGTVQKPASVTVFLNGVLLQNGFVLKGETRYIGAPEYKKHGPSSIKLQDH 243
           IIW APRF+  G +  PA +TV  NGVL+Q+  VL G T YIGAP Y  H  + I LQ+H
Sbjct: 174 IIWKAPRFSPGGGLVSPARITVLHNGVLVQDDTVLAGRTEYIGAPSYAPHDCAPISLQEH 233

Query: 244 GDPSPAISYRNIWVREL 260
                A+SYRNIWVREL
Sbjct: 234 ---DSAVSYRNIWVREL 247


Lambda     K      H
   0.314    0.134    0.416 

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: 304
Number of extensions: 20
Number of successful extensions: 6
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: 260
Length of database: 247
Length adjustment: 24
Effective length of query: 236
Effective length of database: 223
Effective search space:    52628
Effective search space used:    52628
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 46 (22.3 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