GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagX in Shewanella sp. ANA-3

Align DUF5009 domain-containing protein (characterized, see rationale)
to candidate 7025963 Shewana3_3111 hypothetical protein (RefSeq)

Query= uniprot:A0KZW6
         (395 letters)



>FitnessBrowser__ANA3:7025963
          Length = 395

 Score =  800 bits (2065), Expect = 0.0
 Identities = 395/395 (100%), Positives = 395/395 (100%)

Query: 1   MSTTAPESITNTGVNAQEAAAKKRQSKPRLMSLDALRGFDMFWILGGEALFGALLMLTGW 60
           MSTTAPESITNTGVNAQEAAAKKRQSKPRLMSLDALRGFDMFWILGGEALFGALLMLTGW
Sbjct: 1   MSTTAPESITNTGVNAQEAAAKKRQSKPRLMSLDALRGFDMFWILGGEALFGALLMLTGW 60

Query: 61  AGWQWGDTQMHHSEWNGFRFYDLIFPLFIFLSGVALGLSPKRLDKLPMQERMPVYRHGIK 120
           AGWQWGDTQMHHSEWNGFRFYDLIFPLFIFLSGVALGLSPKRLDKLPMQERMPVYRHGIK
Sbjct: 61  AGWQWGDTQMHHSEWNGFRFYDLIFPLFIFLSGVALGLSPKRLDKLPMQERMPVYRHGIK 120

Query: 121 RLFLLLLLGILYNHGWGTGAPADPEKVRYASVLGRIAFAWFFAALLVWHTSLRTQVLVAL 180
           RLFLLLLLGILYNHGWGTGAPADPEKVRYASVLGRIAFAWFFAALLVWHTSLRTQVLVAL
Sbjct: 121 RLFLLLLLGILYNHGWGTGAPADPEKVRYASVLGRIAFAWFFAALLVWHTSLRTQVLVAL 180

Query: 181 GILVAYGAVQLWLPFPGGQAGVLSPTESINAYVDSLLLPGVSYQGRTPDPEGVLSTLPAV 240
           GILVAYGAVQLWLPFPGGQAGVLSPTESINAYVDSLLLPGVSYQGRTPDPEGVLSTLPAV
Sbjct: 181 GILVAYGAVQLWLPFPGGQAGVLSPTESINAYVDSLLLPGVSYQGRTPDPEGVLSTLPAV 240

Query: 241 VNALAGVFVGHFIVKSHPKGEWAKVGLLSVAGGVCLALGWLLGGVIPVNKELWTSSFVLV 300
           VNALAGVFVGHFIVKSHPKGEWAKVGLLSVAGGVCLALGWLLGGVIPVNKELWTSSFVLV
Sbjct: 241 VNALAGVFVGHFIVKSHPKGEWAKVGLLSVAGGVCLALGWLLGGVIPVNKELWTSSFVLV 300

Query: 301 TSGWSMLLLALFYALVDVLKWQKLAFIFVVIGTNAIIIYLASSLVDWKYIAQSVFGGVIA 360
           TSGWSMLLLALFYALVDVLKWQKLAFIFVVIGTNAIIIYLASSLVDWKYIAQSVFGGVIA
Sbjct: 301 TSGWSMLLLALFYALVDVLKWQKLAFIFVVIGTNAIIIYLASSLVDWKYIAQSVFGGVIA 360

Query: 361 VLPENAQPLGAVIGLLTVQWLVLYWMYRRNIFVRI 395
           VLPENAQPLGAVIGLLTVQWLVLYWMYRRNIFVRI
Sbjct: 361 VLPENAQPLGAVIGLLTVQWLVLYWMYRRNIFVRI 395


Lambda     K      H
   0.326    0.141    0.457 

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: 856
Number of extensions: 24
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: 395
Length of database: 395
Length adjustment: 31
Effective length of query: 364
Effective length of database: 364
Effective search space:   132496
Effective search space used:   132496
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 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