GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapL in Klebsiella variicola At-22

Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (characterized)
to candidate WP_008804517.1 KVAR_RS10890 amidohydrolase

Query= SwissProt::D5E0A1
         (375 letters)



>NCBI__GCF_000025465.1:WP_008804517.1
          Length = 385

 Score =  211 bits (536), Expect = 4e-59
 Identities = 132/367 (35%), Positives = 192/367 (52%), Gaps = 10/367 (2%)

Query: 5   EFVKIRRELHKIPELGFQEVKTQRFLLDYINTLPQERLEVKTWKTGLFVKVHGTN-PTKT 63
           E V  RRE H  PELG+QE +T R + + + +     L+V     G  V     N P   
Sbjct: 10  EAVGWRREFHAAPELGYQEQETSRRVAELLASFG---LQVHRGLAGTGVVATLENGPGPV 66

Query: 64  IGYRADIDGLPITEETNYSFQSQHEGLMHACGHDMHMAIGLGVLTYFAQ-HEIKDNVLFI 122
           IG RAD+D LPITE  + S++S+  G+MHACGHD H A+ L    + AQ  +    V F+
Sbjct: 67  IGLRADMDALPITELGSVSYRSRRPGVMHACGHDGHTAMLLAAAAHLAQTRQFSGTVHFV 126

Query: 123 FQPAEEGPGGAQPMLQSDIMKEWLPDFIFALHVAPEYPVGSIALKEGLLFANTSELFIDL 182
           FQPAEE  GGA+ M++  + + +  D I+ALH  P  P+G +AL +G + A+     I L
Sbjct: 127 FQPAEENLGGARKMVEEGLFERFPMDAIYALHNWPGIPLGEVALSDGAMMASLDAFEITL 186

Query: 183 KGKGGHAAYPHTTNDMVVAACQLVSQLQTIVARNVDPLDSAVITVGKIQGGTVQNIIAER 242
           +GK  HAA P +  D +VAA QL+  LQTI +R + P DSAV+++ +I GG   N++ + 
Sbjct: 187 RGKSCHAAMPESGADPIVAAAQLIMALQTIPSRRLSPQDSAVVSITQINGGEAINVLPDT 246

Query: 243 ARIEGTIRTLSPESMTRVKERIEAIVKGVEVGYQCETAIDYGCMYHQVYNHHEVTREFME 302
             + GT R LS     RV+E IE+ V         +  I +   Y    NH    ++  E
Sbjct: 247 VVLRGTFRCLSNRVRARVRELIESYVATQPQVSDVQGEISWFPGYPVTKNHALQAQQVRE 306

Query: 303 FAKEQTDVDVIECKEA--MTGEDFGYMLKDIPGFMFWLGVQSE---YGLHHAKLQPHEGA 357
            A      + +   +A  M  EDF  ML+  PG  FW+G   E     LH+A    ++  
Sbjct: 307 VAVATLGAEAVRWNQAPSMASEDFACMLEACPGAYFWIGTDGETPSKPLHNASYDFNDAL 366

Query: 358 IDIAISL 364
           I   +++
Sbjct: 367 ISPGVAM 373


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: 358
Number of extensions: 14
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: 385
Length adjustment: 30
Effective length of query: 345
Effective length of database: 355
Effective search space:   122475
Effective search space used:   122475
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 Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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