GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malP in Pedobacter sp. GW460-11-11-14-LB5

Align Maltose phosphorylase (EC 2.4.1.8); Trehalose phosphorylase (EC 2.4.1.64) (characterized)
to candidate CA265_RS24655 CA265_RS24655 family 65 glycosyl hydrolase

Query= reanno::Pedo557:CA265_RS24655
         (772 letters)



>FitnessBrowser__Pedo557:CA265_RS24655
          Length = 772

 Score = 1573 bits (4072), Expect = 0.0
 Identities = 772/772 (100%), Positives = 772/772 (100%)

Query: 1   MKNYIKADEWNIIEEGFDPHLNKISESIFSLGNGRMGQRANFEETYTGETLPGNYVAGVY 60
           MKNYIKADEWNIIEEGFDPHLNKISESIFSLGNGRMGQRANFEETYTGETLPGNYVAGVY
Sbjct: 1   MKNYIKADEWNIIEEGFDPHLNKISESIFSLGNGRMGQRANFEETYTGETLPGNYVAGVY 60

Query: 61  YPDKTRVGWWKNGYPEYFAKVLNAANWIGIEVKLDGEILDLATAEVSDFKRVLNMHAGYL 120
           YPDKTRVGWWKNGYPEYFAKVLNAANWIGIEVKLDGEILDLATAEVSDFKRVLNMHAGYL
Sbjct: 61  YPDKTRVGWWKNGYPEYFAKVLNAANWIGIEVKLDGEILDLATAEVSDFKRVLNMHAGYL 120

Query: 121 ERTFTAKLKSGKTLKVKSTRFCSIADDEVGAIRYSITPLNFDGRLTLMPFIDGDVKNQDS 180
           ERTFTAKLKSGKTLKVKSTRFCSIADDEVGAIRYSITPLNFDGRLTLMPFIDGDVKNQDS
Sbjct: 121 ERTFTAKLKSGKTLKVKSTRFCSIADDEVGAIRYSITPLNFDGRLTLMPFIDGDVKNQDS 180

Query: 181 NYDEKFWDKVADEISGTEAYIKLRTKKTEFEVCTGSNIELYKNAEKLAINPEAVRKEKFV 240
           NYDEKFWDKVADEISGTEAYIKLRTKKTEFEVCTGSNIELYKNAEKLAINPEAVRKEKFV
Sbjct: 181 NYDEKFWDKVADEISGTEAYIKLRTKKTEFEVCTGSNIELYKNAEKLAINPEAVRKEKFV 240

Query: 241 GQTFSLEVKANEEISLVKIAANLSSENYPKESLLKETKSIIAKASAKGFDTLLKEQTEAW 300
           GQTFSLEVKANEEISLVKIAANLSSENYPKESLLKETKSIIAKASAKGFDTLLKEQTEAW
Sbjct: 241 GQTFSLEVKANEEISLVKIAANLSSENYPKESLLKETKSIIAKASAKGFDTLLKEQTEAW 300

Query: 301 ASKWEESDIIIEGDVSAQQAIRFNIFQLFQTYTGKDDRLNIGPKGFTGEKYGGSTYWDTE 360
           ASKWEESDIIIEGDVSAQQAIRFNIFQLFQTYTGKDDRLNIGPKGFTGEKYGGSTYWDTE
Sbjct: 301 ASKWEESDIIIEGDVSAQQAIRFNIFQLFQTYTGKDDRLNIGPKGFTGEKYGGSTYWDTE 360

Query: 361 AYCVPFYLATAPQEVSKNLLVYRHKQLGKAIENAAKLGFKDGAALYPMVTMNGEECHNEW 420
           AYCVPFYLATAPQEVSKNLLVYRHKQLGKAIENAAKLGFKDGAALYPMVTMNGEECHNEW
Sbjct: 361 AYCVPFYLATAPQEVSKNLLVYRHKQLGKAIENAAKLGFKDGAALYPMVTMNGEECHNEW 420

Query: 421 EITFEEIHRNGAIAFAIFNYIRYTGDESYLSDFGLEVLIGIARFWKQRVNWSNDKQQYVM 480
           EITFEEIHRNGAIAFAIFNYIRYTGDESYLSDFGLEVLIGIARFWKQRVNWSNDKQQYVM
Sbjct: 421 EITFEEIHRNGAIAFAIFNYIRYTGDESYLSDFGLEVLIGIARFWKQRVNWSNDKQQYVM 480

Query: 481 LGVTGPNEYENNVNNNWYTNILATWCMKYATEAAEIVKTQQPEKYNSLLKSLNFDQKEFA 540
           LGVTGPNEYENNVNNNWYTNILATWCMKYATEAAEIVKTQQPEKYNSLLKSLNFDQKEFA
Sbjct: 481 LGVTGPNEYENNVNNNWYTNILATWCMKYATEAAEIVKTQQPEKYNSLLKSLNFDQKEFA 540

Query: 541 DWADIIEKMYYPQDEKLGIFLQQDGYLDKEQTLVKDLPASERPINQKWSWDRILRSCFIK 600
           DWADIIEKMYYPQDEKLGIFLQQDGYLDKEQTLVKDLPASERPINQKWSWDRILRSCFIK
Sbjct: 541 DWADIIEKMYYPQDEKLGIFLQQDGYLDKEQTLVKDLPASERPINQKWSWDRILRSCFIK 600

Query: 601 QADVLQGLYFFEEDYDLDTLKRNFDFYEPRTVHESSLSPCVHSILAAKLNDEARAYEFYL 660
           QADVLQGLYFFEEDYDLDTLKRNFDFYEPRTVHESSLSPCVHSILAAKLNDEARAYEFYL
Sbjct: 601 QADVLQGLYFFEEDYDLDTLKRNFDFYEPRTVHESSLSPCVHSILAAKLNDEARAYEFYL 660

Query: 661 RTARLDLDDYNNDTEDGLHITSMAGTWMSVVEGFAGMRVREGKLQFNPFLPGKWKSFSFT 720
           RTARLDLDDYNNDTEDGLHITSMAGTWMSVVEGFAGMRVREGKLQFNPFLPGKWKSFSFT
Sbjct: 661 RTARLDLDDYNNDTEDGLHITSMAGTWMSVVEGFAGMRVREGKLQFNPFLPGKWKSFSFT 720

Query: 721 IGFRGATLKINITESGISIKNNAAVDLEIGIRNQLYKLAGNTEIEVNNAELV 772
           IGFRGATLKINITESGISIKNNAAVDLEIGIRNQLYKLAGNTEIEVNNAELV
Sbjct: 721 IGFRGATLKINITESGISIKNNAAVDLEIGIRNQLYKLAGNTEIEVNNAELV 772


Lambda     K      H
   0.317    0.134    0.401 

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: 2202
Number of extensions: 78
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: 772
Length of database: 772
Length adjustment: 41
Effective length of query: 731
Effective length of database: 731
Effective search space:   534361
Effective search space used:   534361
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: 41 (21.6 bits)
S2: 55 (25.8 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