GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS12865
          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:

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