GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapL in Klebsiella michiganensis M5al

Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate BWI76_RS13530 BWI76_RS13530 amidohydrolase family protein

Query= curated2:B7HMV1
         (376 letters)



>FitnessBrowser__Koxy:BWI76_RS13530
          Length = 373

 Score =  230 bits (586), Expect = 5e-65
 Identities = 142/364 (39%), Positives = 199/364 (54%), Gaps = 12/364 (3%)

Query: 2   VVSKFVQIRRDLHKIPEIGFKEWKTQRYILDYI--GTLSNEHVEVKVWRTGVIVKVKGKN 59
           +  + ++ RR+LH+ PE+  +E  T   I D++  G +S    ++K   TG + +V   N
Sbjct: 3   LAEQLIRWRRELHQYPELSLQEVDTTARIRDWLQSGGISLLPYDLK---TGAVAEVGSGN 59

Query: 60  PEKVIGYRADIDGLPITEETGYEFASVHEGMMHACGHDLHTTIGLG--LLTAAVTERIDD 117
             KVI  RADID LPI E     F S++ G+MHACGHD+HT++ LG  LL      ++  
Sbjct: 60  --KVIALRADIDALPIEEAASVPFRSLNAGVMHACGHDIHTSVILGAALLLKQREAQLAG 117

Query: 118 DLVFLFQPAEEGPGGALPMLESEELKEWKPNIILGLHIAPEYPVGTIATKEGLLFANTSE 177
            +  LFQPAEE  GGA  ++ +  L+    + I G+H  P  PVG  AT+ G  +AN   
Sbjct: 118 RVRILFQPAEESFGGAKTLIRAGVLEG--VSAIFGMHNEPGLPVGEFATRGGAFYANVDR 175

Query: 178 LYVDLKGKGGHAAYPHTANDMIVAASHLVTQLQSVISRNVNPLDSAVITIGKITGGTVQN 237
               + GKG HAA PH   D I+ AS LVT LQSV SR VN LDS V+++ +I GG   N
Sbjct: 176 FVFKVTGKGAHAARPHEGKDAILLASQLVTLLQSVASREVNTLDSVVLSVTRIQGGNTWN 235

Query: 238 IIAEKSRLEGTIRTLSVESMSRVKSRIEAIVAGIEASFQCEAIIDYGAMYHQVYNHEALT 297
           ++ E   LEGT+RT S E   RVK+R+  I AG  ++F  +  + + A    + N E   
Sbjct: 236 VLPESVELEGTLRTHSSEVQQRVKARVSEIAAGFASAFGAQIDVFWYAGPTALVNDERWA 295

Query: 298 REFMQFVSEQTDMKVITCTEAMTGEDFGYMLQEIPGFMFWLGVNSEYGLHHAKLKPDEEA 357
             F   V++++  +       + GEDF   LQ IPG    +G  SE+GLHH    PDE  
Sbjct: 296 -AFASDVADKSGYRTHHADLHLGGEDFAVYLQHIPGAFVSIGSASEFGLHHPAFNPDERL 354

Query: 358 IEKA 361
           I  A
Sbjct: 355 IAPA 358


Lambda     K      H
   0.319    0.136    0.400 

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: 362
Number of extensions: 22
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: 376
Length of database: 373
Length adjustment: 30
Effective length of query: 346
Effective length of database: 343
Effective search space:   118678
Effective search space used:   118678
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