GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Paraburkholderia bryophila 376MFSha3.1

Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate H281DRAFT_01117 H281DRAFT_01117 aldehyde dehydrogenase (NAD+)

Query= reanno::Burk376:H281DRAFT_01117
         (795 letters)



>FitnessBrowser__Burk376:H281DRAFT_01117
          Length = 795

 Score = 1593 bits (4126), Expect = 0.0
 Identities = 795/795 (100%), Positives = 795/795 (100%)

Query: 1   MSVAEYFSSMDYGPAPEDDQPARQWLAQHEARFGHFIGGAWHAPASGAQFVSHAPASGER 60
           MSVAEYFSSMDYGPAPEDDQPARQWLAQHEARFGHFIGGAWHAPASGAQFVSHAPASGER
Sbjct: 1   MSVAEYFSSMDYGPAPEDDQPARQWLAQHEARFGHFIGGAWHAPASGAQFVSHAPASGER 60

Query: 61  LADIAQGDAADIDAALAAARAAQPGWLALGGKGRARHLYALARMVQRHSRLFAVLEALDN 120
           LADIAQGDAADIDAALAAARAAQPGWLALGGKGRARHLYALARMVQRHSRLFAVLEALDN
Sbjct: 61  LADIAQGDAADIDAALAAARAAQPGWLALGGKGRARHLYALARMVQRHSRLFAVLEALDN 120

Query: 121 GKPIRETRDLDVPLVARHFLHHAGWAQLQDSEFADHAPLGVIGQIVPWNFPLLMLAWKIA 180
           GKPIRETRDLDVPLVARHFLHHAGWAQLQDSEFADHAPLGVIGQIVPWNFPLLMLAWKIA
Sbjct: 121 GKPIRETRDLDVPLVARHFLHHAGWAQLQDSEFADHAPLGVIGQIVPWNFPLLMLAWKIA 180

Query: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHQAGLPAGVLNVVTGDGSTGAALVEHPQVDKI 240
           PAIATGNCVVLKPAEYTPLTALLFAELAHQAGLPAGVLNVVTGDGSTGAALVEHPQVDKI
Sbjct: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHQAGLPAGVLNVVTGDGSTGAALVEHPQVDKI 240

Query: 241 AFTGSTEVGKLIRSVTAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300
           AFTGSTEVGKLIRSVTAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC
Sbjct: 241 AFTGSTEVGKLIRSVTAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300

Query: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGPSLDKSIDMGAIVDPVQLERIHSLVETGRR 360
           CAGSRLLVQEGIEARFIAKLKRRMETLRVGPSLDKSIDMGAIVDPVQLERIHSLVETGRR
Sbjct: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGPSLDKSIDMGAIVDPVQLERIHSLVETGRR 360

Query: 361 EGCAIWQAADTPLPANGCFYPPTLVTNVAPASTLAQEEIFGPVLVTMSFRTPDEAIALAN 420
           EGCAIWQAADTPLPANGCFYPPTLVTNVAPASTLAQEEIFGPVLVTMSFRTPDEAIALAN
Sbjct: 361 EGCAIWQAADTPLPANGCFYPPTLVTNVAPASTLAQEEIFGPVLVTMSFRTPDEAIALAN 420

Query: 421 NSRYGLAASVWSETIGRALDVAPRLAAGVVWVNATNLFDAAVGFGGYRESGYGREGGREG 480
           NSRYGLAASVWSETIGRALDVAPRLAAGVVWVNATNLFDAAVGFGGYRESGYGREGGREG
Sbjct: 421 NSRYGLAASVWSETIGRALDVAPRLAAGVVWVNATNLFDAAVGFGGYRESGYGREGGREG 480

Query: 481 IHEYLKPRAWLNLPKRQPVSAATNASDDRQVSNLALVDRTAKLFIGGKQVRPDSGYSLPV 540
           IHEYLKPRAWLNLPKRQPVSAATNASDDRQVSNLALVDRTAKLFIGGKQVRPDSGYSLPV
Sbjct: 481 IHEYLKPRAWLNLPKRQPVSAATNASDDRQVSNLALVDRTAKLFIGGKQVRPDSGYSLPV 540

Query: 541 HAPDGTRVGEVGEGNRKDIRNAVQAARAAQKWSQASTHNRAQVLFYLAENLAVRADEFAH 600
           HAPDGTRVGEVGEGNRKDIRNAVQAARAAQKWSQASTHNRAQVLFYLAENLAVRADEFAH
Sbjct: 541 HAPDGTRVGEVGEGNRKDIRNAVQAARAAQKWSQASTHNRAQVLFYLAENLAVRADEFAH 600

Query: 601 QLTVRNGATDAAAHAEVEASVTRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVIGIA 660
           QLTVRNGATDAAAHAEVEASVTRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVIGIA
Sbjct: 601 QLTVRNGATDAAAHAEVEASVTRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVIGIA 660

Query: 661 CPDEAPLLAFVSLAAPALAMGNRVVVLPGEACPLAVTDFYQVVETSDVPGGVVNIVTGKR 720
           CPDEAPLLAFVSLAAPALAMGNRVVVLPGEACPLAVTDFYQVVETSDVPGGVVNIVTGKR
Sbjct: 661 CPDEAPLLAFVSLAAPALAMGNRVVVLPGEACPLAVTDFYQVVETSDVPGGVVNIVTGKR 720

Query: 721 EALLPALARHDDVDAVWCFGSAADATLIERESVGNLKRTFTDYGRQFDWFDRASEGLPFL 780
           EALLPALARHDDVDAVWCFGSAADATLIERESVGNLKRTFTDYGRQFDWFDRASEGLPFL
Sbjct: 721 EALLPALARHDDVDAVWCFGSAADATLIERESVGNLKRTFTDYGRQFDWFDRASEGLPFL 780

Query: 781 RQAVQVKNIWIPYGD 795
           RQAVQVKNIWIPYGD
Sbjct: 781 RQAVQVKNIWIPYGD 795


Lambda     K      H
   0.320    0.135    0.411 

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: 2207
Number of extensions: 98
Number of successful extensions: 8
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: 795
Length of database: 795
Length adjustment: 41
Effective length of query: 754
Effective length of database: 754
Effective search space:   568516
Effective search space used:   568516
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: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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