GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapE in Klebsiella michiganensis M5al

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate BWI76_RS12865 BWI76_RS12865 acetylornithine deacetylase

Query= curated2:Q2W0E7
         (379 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS12865 BWI76_RS12865
           acetylornithine deacetylase
          Length = 389

 Score =  113 bits (282), Expect = 1e-29
 Identities = 104/325 (32%), Positives = 152/325 (46%), Gaps = 27/325 (8%)

Query: 55  NLYARLGTEAPN-LCFAGHTDVVP-PGKGWTVEPFAAGIDQGRLFGRGSADMKGAIACFV 112
           NLYARLG   P  +  +GHTDVVP  G+ WTV PFA     GR +GRGSADMKG IAC +
Sbjct: 53  NLYARLGPSGPGGVMLSGHTDVVPVDGQAWTVPPFALTERDGRYYGRGSADMKGFIACVL 112

Query: 113 AAVARLLEDGAP-KGSLSLLITGDEEGPAVDGTVKVLDWLAARGERIDCCIVGEPTNPRK 171
           A++   L   AP +  L L  + DEE   + G   ++D+L A  E+   CI+GEPT+ R 
Sbjct: 113 ASLEAFL--AAPLRMPLHLAFSYDEEVGCL-GVRSLVDFLRASAEKPALCIIGEPTDMRP 169

Query: 172 LGDMMKIGRRGSLNCRLTVFGTQGHSAYPHLADNPIPRLLDILRRLTEAPLDEGTPHFQ- 230
           +      G +G L  R  V G   HSAY     N I     ++ RL +A  +  + H   
Sbjct: 170 V-----YGHKGKLAVRCRVEGHACHSAYAPQGVNAISYAAKLIYRL-DALGESFSQHLDR 223

Query: 231 -----ASTLALTTVDVGNPATNVIPAEARAGFNIRF----NDLHSGASLERWIRDTVAQA 281
                + TL + T+  G  A N++P      F IR+           +L  + R+ +  A
Sbjct: 224 RFSPPSGTLQVGTIR-GGEALNIVPQSCWFDFEIRYLPGTRPQAVTDALGDYAREQLLPA 282

Query: 282 GGEVEIKVEVSGESFLTPPGALSD---ALAEAAFEVTGLRPELSTSGGTSDARFIKNHCP 338
             +V    ++  ++    PG LSD   A A    +  G     + + GT    F +    
Sbjct: 283 MRKVAQCSDIHFQTLSHYPGLLSDPQSAFARWLAQWCGSDDFTTVAYGTEGGLFDEAGVA 342

Query: 339 VVEFGLVGQTM-HKSDEHVSVADME 362
            +  G       H++DE++S+   E
Sbjct: 343 TLICGPGSMAQGHRADEYISIPQTE 367


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: 382
Number of extensions: 18
Number of successful extensions: 4
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: 389
Length adjustment: 30
Effective length of query: 349
Effective length of database: 359
Effective search space:   125291
Effective search space used:   125291
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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