GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapL in Klebsiella michiganensis M5al

Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (characterized)
to candidate BWI76_RS16785 BWI76_RS16785 peptidase M20

Query= SwissProt::D5E0A1
         (375 letters)



>FitnessBrowser__Koxy:BWI76_RS16785
          Length = 383

 Score =  201 bits (512), Expect = 2e-56
 Identities = 128/371 (34%), Positives = 192/371 (51%), Gaps = 16/371 (4%)

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

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

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

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

Query: 243 ARIEGTIRTLSPESMTRVKERIEAIVKGVEVGYQCETAIDYGCMYHQVYNHHEVTREFME 302
             + GT R L  +   RV+  IE+ V       + E AI +   Y    NH    ++  E
Sbjct: 247 VVLRGTFRCLDNQVRARVRGLIESYVAAQPQVSEVEGAIAWYPGYPVTTNHPAEAQKVRE 306

Query: 303 FAKEQTDVDVIEC--KEAMTGEDFGYMLKDIPGFMFWLGVQSEYG---LHHA------KL 351
            A        +      +M  EDF  ML+  PG  FW+G   E     LH+A      +L
Sbjct: 307 VATALLGESAVSWNGNPSMASEDFACMLEACPGAYFWIGADGETASKPLHNAGYDFNDEL 366

Query: 352 QPHEGAIDIAI 362
            PH  A+  A+
Sbjct: 367 LPHGVALWTAL 377


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: 371
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: 383
Length adjustment: 30
Effective length of query: 345
Effective length of database: 353
Effective search space:   121785
Effective search space used:   121785
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