GapMind for Amino acid biosynthesis

 

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

Align Acetylornithine deacetylase (EC:3.5.1.16) (characterized)
to candidate 7023614 Shewana3_0843 hypothetical protein (RefSeq)

Query= reanno::MR1:202842
         (275 letters)



>FitnessBrowser__ANA3:7023614
          Length = 275

 Score =  542 bits (1397), Expect = e-159
 Identities = 265/275 (96%), Positives = 268/275 (97%)

Query: 1   MVSRSPFESFQWKSDIFNCESTDIDNFYLQLEQEMSRLGMVEKKLGEVGKYSVSLYQSPA 60
           MVSRSPFESFQWKSDIFNCESTDIDNFYLQLEQEMSRLGMVEKKLGEVGKYSVSLYQSPA
Sbjct: 1   MVSRSPFESFQWKSDIFNCESTDIDNFYLQLEQEMSRLGMVEKKLGEVGKYSVSLYQSPA 60

Query: 61  AKSGLPSLLICAGFHGEESAGPWGLLHFLSEASVELFERVNLSILPLVNPTGFKRGHRFN 120
           AKSGLPSLLI AGFHGEESAGPWGLLHFLSEAS +LFERVNLSILPLVNPTGFKRGHRFN
Sbjct: 61  AKSGLPSLLISAGFHGEESAGPWGLLHFLSEASADLFERVNLSILPLVNPTGFKRGHRFN 120

Query: 121 KFGENPNRGFEFENGKPKANEGTSVEGKLLLEHAQLLIAASRDGILTCHEDVLSHDAYVY 180
           KFGENPNRGF FENGKPKANE TSVEGKLLL+HAQLLIAASRDGILTCHEDVLS DAYVY
Sbjct: 121 KFGENPNRGFVFENGKPKANESTSVEGKLLLDHAQLLIAASRDGILTCHEDVLSRDAYVY 180

Query: 181 SFEPSQVPGRFSLDLRDTLAGYFPIAVDGEIDGCPVKDGLIFNHFDTSFEACLVRSGARV 240
           SFEPSQVPGRFS+DLRDTL GYFPIA DGEIDGCPVKDGLIFNHFDTSFEACLVRSGARV
Sbjct: 181 SFEPSQVPGRFSIDLRDTLGGYFPIAEDGEIDGCPVKDGLIFNHFDTSFEACLVRSGARV 240

Query: 241 GACTETPALQNFDQRVLANSAAMTHFLALCAPLCD 275
           GACTETPALQNFDQRVLANSAAMTHFLALCAPLCD
Sbjct: 241 GACTETPALQNFDQRVLANSAAMTHFLALCAPLCD 275


Lambda     K      H
   0.320    0.137    0.418 

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: 411
Number of extensions: 7
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: 275
Length of database: 275
Length adjustment: 25
Effective length of query: 250
Effective length of database: 250
Effective search space:    62500
Effective search space used:    62500
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: 47 (22.7 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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