GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapL in Burkholderia phytofirmans PsJN

Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (characterized)
to candidate BPHYT_RS17305 BPHYT_RS17305 amidohydrolase

Query= SwissProt::D5E0A1
         (375 letters)



>FitnessBrowser__BFirm:BPHYT_RS17305
          Length = 398

 Score =  208 bits (530), Expect = 2e-58
 Identities = 118/343 (34%), Positives = 182/343 (53%), Gaps = 8/343 (2%)

Query: 2   AENEFVKIRRELHKIPELGFQEVKTQRFLLDYINTLPQERLEVKTW--KTGLFVKVHGTN 59
           A  E   +RR +H  PEL ++E  T   +     TL    +E      KTG+   +   N
Sbjct: 10  AHGEIQTLRRTIHAHPELRYEETATADLVA---RTLESWGIETHRGLGKTGVVGVLKRGN 66

Query: 60  PTKTIGYRADIDGLPITEETNYSFQSQHEGLMHACGHDMHMAIGLGVLTYFAQH-EIKDN 118
            +++IG RAD+D LPI E  ++  +S+++G MHACGHD H A+ LG   +  +H E    
Sbjct: 67  GSRSIGLRADMDALPIQELNSFDHRSKNDGKMHACGHDGHTAMLLGAARHLVKHGEFDGT 126

Query: 119 VLFIFQPAEEGPGGAQPMLQSDIMKEWLPDFIFALHVAPEYPVGSIALKEGLLFANTSEL 178
           ++FIFQPAEEG  GAQ M+   +  ++  D +F +H  P  P G   + EG + A+++E 
Sbjct: 127 IVFIFQPAEEGGAGAQAMIDDGLFVKFPVDAVFGIHNWPGMPAGQFGVTEGPIMASSNEF 186

Query: 179 FIDLKGKGGHAAYPHTTNDMVVAACQLVSQLQTIVARNVDPLDSAVITVGKIQGGTVQNI 238
            I++KG G HAA PH  +D V  A Q+ + LQ+I+ RN  PLD+AV+++ +I  G   N+
Sbjct: 187 HIEIKGVGSHAALPHNGHDPVFTAVQIANGLQSIITRNKKPLDTAVLSITQIHAGDAVNV 246

Query: 239 IAERARIEGTIRTLSPESMTRVKERIEAIVKGVEVGYQCETAIDYGCMYHQVYNHHEVTR 298
           +   A I GT+RT + +++  ++ R+  I +     Y C   I +   Y    N  E  R
Sbjct: 247 VPNNAWIAGTVRTFTTDTLDLIEARMRKIAESTAEAYDCSVDIQFHRNYPPTINSSEEAR 306

Query: 299 EFMEFAKEQTDVDVIE--CKEAMTGEDFGYMLKDIPGFMFWLG 339
                 KE    + ++   +  M  EDF +ML   PG   +LG
Sbjct: 307 FAATVMKEIVGAENVDDAVEPTMGAEDFSFMLLAKPGCYAFLG 349


Lambda     K      H
   0.320    0.137    0.410 

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: 375
Number of extensions: 22
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: 375
Length of database: 398
Length adjustment: 30
Effective length of query: 345
Effective length of database: 368
Effective search space:   126960
Effective search space used:   126960
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: 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