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_RS07340 BWI76_RS07340 amidohydrolase

Query= curated2:B1YJ90
         (370 letters)



>FitnessBrowser__Koxy:BWI76_RS07340
          Length = 392

 Score =  192 bits (487), Expect = 2e-53
 Identities = 124/341 (36%), Positives = 180/341 (52%), Gaps = 15/341 (4%)

Query: 5   IEMRRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKGLTGNRTIGY 64
           I +R  LH  PE   +EF T   +  ++  +    V+    +TGV   +      RTIG 
Sbjct: 17  IAIRHYLHAHPELSLEEFNTSELVAGKLTEWGYT-VTRGLAKTGVVGTLSKGDSPRTIGL 75

Query: 65  RADIDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALGLLRRIVELPVMDD--VVFLFQ 122
           RAD+D LPI EAT LP+ S   G MHACGHD H +I L   + I       +  V  +FQ
Sbjct: 76  RADMDALPIFEATDLPWASTVAGKMHACGHDGHTTILLAAAKYIASPACQFNGTVHLIFQ 135

Query: 123 PAEEGPGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREVHITIYG 182
           PAEE  GGA+ MIK  LFE++    ++GLH  P  PVG +    G   ASA  V ITI G
Sbjct: 136 PAEEAIGGADLMIKDGLFERFPCERIFGLHNMPGLPVGKLGFYAGNFMASADTVKITITG 195

Query: 183 QSGHAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDAGIRENVIAGRAL 242
             GH A P  T+D +V  AAL+M LQ+IV+R++ P   +V+++G   AGI  NVI    +
Sbjct: 196 YGGHGAHPERTVDPIVTGAALVMNLQSIVARNVPPGATAVVSVGTFQAGIASNVIPENVV 255

Query: 243 LDGTMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVNDQRVVDKFSSFV 302
           ++ ++RA+     + L +R++++      S+G   +++  + Y  + N     D+ + F 
Sbjct: 256 MELSVRAMKPEIRDLLIKRIKELADFTAKSYGASSEVEVFDSYPVLTNS----DEETEFA 311

Query: 303 KMNA-------NYIECDAAM-TGEDFGFMLKEIPGMMFWLG 335
           K  A         +E  + M   EDF FML++ PG  F LG
Sbjct: 312 KALALEVFGEEGVLESISPMNASEDFAFMLQKRPGCYFLLG 352


Lambda     K      H
   0.323    0.140    0.417 

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: 379
Number of extensions: 13
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: 370
Length of database: 392
Length adjustment: 30
Effective length of query: 340
Effective length of database: 362
Effective search space:   123080
Effective search space used:   123080
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 (21.9 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