GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Pseudomonas fluorescens FW300-N2E2

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate Pf6N2E2_1339 Acetylornithine deacetylase (EC 3.5.1.16)

Query= curated2:Q2W0E7
         (379 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339
          Length = 394

 Score =  118 bits (295), Expect = 3e-31
 Identities = 108/341 (31%), Positives = 153/341 (44%), Gaps = 23/341 (6%)

Query: 55  NLYARLGTEAPN-LCFAGHTDVVP-PGKGWTVEPFAAGIDQGRLFGRGSADMKGAIACFV 112
           NL A +G   P  +  +GHTDVVP  G+ WTV+PF      G+ FGRG+ADMKG +A  +
Sbjct: 59  NLLASIGPAVPGGVVLSGHTDVVPVDGQAWTVDPFCLTEMDGKWFGRGTADMKGYLASVL 118

Query: 113 AAVARLLEDGAPKGSLSLLITGDEEGPAVDGTVKVLDWLAARGERIDCCIVGEPTNPRKL 172
           AAV   L     +  + L  + DEE   + G   +L+ L  R  +   C++GEPT  R +
Sbjct: 119 AAVPVFLSSPL-RRPVHLAFSYDEEVGCL-GVHSLLEVLVRRIAQPALCLIGEPTQLRPV 176

Query: 173 GDMMKIGRRGSLNCRLTVFGTQGHSAYPHLADNPIPRLLDILRRLTE--APLDEGTPHFQ 230
                +G +G L  R  V G   HSAY     N I +   ++ RL E  A L E + H  
Sbjct: 177 -----LGHKGKLAMRCHVRGAACHSAYAPYGVNAIEQAARLIGRLGEIGAQLAEPSRHDP 231

Query: 231 ASTLALTTVDV----GNPATNVIPAEARAGFNIR----FNDLHSGASLERWIRDTVAQAG 282
               A +TV V    G  A N++PA+ R  F +R    F+ L     L+ +   T+  A 
Sbjct: 232 RFDPACSTVQVGVVHGGTALNIVPADCRFDFEVRALPDFDPLVVVEQLQGYAEQTLLPAM 291

Query: 283 GEVEIKVEVSGESFLTPPGALS---DALAEAAFEVTGLRPELSTSGGTSDARFIKNHCPV 339
             V     +  E     PG  +    A A    ++ G     + + GT    F +   P 
Sbjct: 292 QAVAGDTAIRFEPLSAYPGLATSPDSAAARLIAQLCGSDAFGTVAFGTEGGLFHQAGVPT 351

Query: 340 VEFGLVGQTM-HKSDEHVSVADMEALTEIYRRVLVRLAAPS 379
           V  G       HK DE+VSV  M A   +  R+   L  P+
Sbjct: 352 VVCGPGSMDQGHKPDEYVSVEQMAACDRLMDRLASYLCEPN 392


Lambda     K      H
   0.319    0.137    0.412 

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: 363
Number of extensions: 19
Number of successful extensions: 5
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: 379
Length of database: 394
Length adjustment: 30
Effective length of query: 349
Effective length of database: 364
Effective search space:   127036
Effective search space used:   127036
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: 50 (23.9 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