GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treF in Escherichia coli BW25113

Align trehalase (TreF;b3519) (EC 3.2.1.28) (characterized)
to candidate 17580 b3519 cytoplasmic trehalase (NCBI)

Query= CAZy::AAC76544.1
         (549 letters)



>FitnessBrowser__Keio:17580
          Length = 549

 Score = 1145 bits (2962), Expect = 0.0
 Identities = 549/549 (100%), Positives = 549/549 (100%)

Query: 1   MLNQKIQNPNPDELMIEVDLCYELDPYELKLDEMIEAEPEPEMIEGLPASDALTPADRYL 60
           MLNQKIQNPNPDELMIEVDLCYELDPYELKLDEMIEAEPEPEMIEGLPASDALTPADRYL
Sbjct: 1   MLNQKIQNPNPDELMIEVDLCYELDPYELKLDEMIEAEPEPEMIEGLPASDALTPADRYL 60

Query: 61  ELFEHVQSAKIFPDSKTFPDCAPKMDPLDILIRYRKVRRHRDFDLRKFVENHFWLPEVYS 120
           ELFEHVQSAKIFPDSKTFPDCAPKMDPLDILIRYRKVRRHRDFDLRKFVENHFWLPEVYS
Sbjct: 61  ELFEHVQSAKIFPDSKTFPDCAPKMDPLDILIRYRKVRRHRDFDLRKFVENHFWLPEVYS 120

Query: 121 SEYVSDPQNSLKEHIDQLWPVLTREPQDHIPWSSLLALPQSYIVPGGRFSETYYWDSYFT 180
           SEYVSDPQNSLKEHIDQLWPVLTREPQDHIPWSSLLALPQSYIVPGGRFSETYYWDSYFT
Sbjct: 121 SEYVSDPQNSLKEHIDQLWPVLTREPQDHIPWSSLLALPQSYIVPGGRFSETYYWDSYFT 180

Query: 181 MLGLAESGREDLLKCMADNFAWMIENYGHIPNGNRTYYLSRSQPPVFALMVELFEEDGVR 240
           MLGLAESGREDLLKCMADNFAWMIENYGHIPNGNRTYYLSRSQPPVFALMVELFEEDGVR
Sbjct: 181 MLGLAESGREDLLKCMADNFAWMIENYGHIPNGNRTYYLSRSQPPVFALMVELFEEDGVR 240

Query: 241 GARRYLDHLKMEYAFWMDGAESLIPNQAYRHVVRMPDGSLLNRYWDDRDTPRDESWLEDV 300
           GARRYLDHLKMEYAFWMDGAESLIPNQAYRHVVRMPDGSLLNRYWDDRDTPRDESWLEDV
Sbjct: 241 GARRYLDHLKMEYAFWMDGAESLIPNQAYRHVVRMPDGSLLNRYWDDRDTPRDESWLEDV 300

Query: 301 ETAKHSGRPPNEVYRDLRAGAASGWDYSSRWLRDTGRLASIRTTQFIPIDLNAFLFKLES 360
           ETAKHSGRPPNEVYRDLRAGAASGWDYSSRWLRDTGRLASIRTTQFIPIDLNAFLFKLES
Sbjct: 301 ETAKHSGRPPNEVYRDLRAGAASGWDYSSRWLRDTGRLASIRTTQFIPIDLNAFLFKLES 360

Query: 361 AIANISALKGEKETEALFRQKASARRDAVNRYLWDDENGIYRDYDWRREQLALFSAAAIV 420
           AIANISALKGEKETEALFRQKASARRDAVNRYLWDDENGIYRDYDWRREQLALFSAAAIV
Sbjct: 361 AIANISALKGEKETEALFRQKASARRDAVNRYLWDDENGIYRDYDWRREQLALFSAAAIV 420

Query: 421 PLYVGMANHEQADRLANAVRSRLLTPGGILASEYETGEQWDKPNGWAPLQWMAIQGFKMY 480
           PLYVGMANHEQADRLANAVRSRLLTPGGILASEYETGEQWDKPNGWAPLQWMAIQGFKMY
Sbjct: 421 PLYVGMANHEQADRLANAVRSRLLTPGGILASEYETGEQWDKPNGWAPLQWMAIQGFKMY 480

Query: 481 GDDLLGDEIARSWLKTVNQFYLEQHKLIEKYHIADGVPREGGGGEYPLQDGFGWTNGVVR 540
           GDDLLGDEIARSWLKTVNQFYLEQHKLIEKYHIADGVPREGGGGEYPLQDGFGWTNGVVR
Sbjct: 481 GDDLLGDEIARSWLKTVNQFYLEQHKLIEKYHIADGVPREGGGGEYPLQDGFGWTNGVVR 540

Query: 541 RLIGLYGEP 549
           RLIGLYGEP
Sbjct: 541 RLIGLYGEP 549


Lambda     K      H
   0.319    0.138    0.434 

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: 1460
Number of extensions: 74
Number of successful extensions: 1
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: 549
Length of database: 549
Length adjustment: 36
Effective length of query: 513
Effective length of database: 513
Effective search space:   263169
Effective search space used:   263169
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 (21.7 bits)
S2: 53 (25.0 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