GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Hydrogenovibrio halophilus DSM 15072

Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_019895362.1 A377_RS0106195 diaminobutyrate--2-oxoglutarate transaminase

Query= BRENDA::Q93R93
         (395 letters)



>NCBI__GCF_000384235.1:WP_019895362.1
          Length = 417

 Score =  192 bits (489), Expect = 1e-53
 Identities = 141/414 (34%), Positives = 213/414 (51%), Gaps = 29/414 (7%)

Query: 8   DWRALLEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVV 67
           DW    E+E    S  Y     + V+GQ A+ WD  G EYID   G GV N GH NP++ 
Sbjct: 2   DWFEQYESEIRAYSRAY---PAVFVKGQNAKQWDETGKEYIDFYAGAGVLNFGHNNPKLK 58

Query: 68  EAVKRQ-AETLMAMPQTLPTPMRGEFYRTLT-AILPP---ELNRVFPVNSGTEANEAALK 122
            A+    AE  +     + T  + +F +     IL P   +    F   +GT A EAALK
Sbjct: 59  AAMMDYLAEDGVLHSLDMMTAAKRDFIQGFVETILQPRKMDYKLQFMGPTGTNAVEAALK 118

Query: 123 FARAHTGRKKFVAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYND-------- 174
            AR  TGR+  +A  +GF G T+G+L+ T    +R+     +  V   P+          
Sbjct: 119 LARKVTGRQNVIAFAQGFHGMTLGALACTANGYFRQAAGVPLNHVSHCPFETNVGGGLAM 178

Query: 175 VEALKRAVD------EETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQ 228
           ++ L+   D      E+ AA+++EP+Q EGGV  A+ E+L+   ++ ++ GALLI+D+IQ
Sbjct: 179 LDTLRALYDNTSGGAEKPAAILVEPIQAEGGVNVASAEWLQGLDKLAKDLGALLIVDDIQ 238

Query: 229 TGMGRTGKRFAFEHFGIVPDILTLAKALGG-GVPLGVAVMREEVARSMPKGGHGTTFGGN 287
            G GRTG+ F+F+  GI PDI+TLAK LGG G P+ + +++ E  +    G H  TF G 
Sbjct: 239 AGCGRTGQYFSFDEAGIDPDIITLAKGLGGLGTPIAMNLVKPEHDQHWQPGEHTGTFRGQ 298

Query: 288 PLAMAAGVAAIRYLERTRLWERAAELGPWF---MEKLRAIPSPKIREVRGMGLMVGLELK 344
            L+  AG  A+RY E  +L     + G      +E++          VRG G+M  L++ 
Sbjct: 299 NLSFVAGREALRYFEDDQLMNAVHDKGEIMVGALEQMAQTYPDAGFSVRGKGMMQALDVG 358

Query: 345 EKA-APYIARLEKEHRVL--ALQAGPTVIRFLPPLVIEKEDLERVVEAVRAVLA 395
           + A A  +AR   E  +L      G +VI+ +PPL I +++L   +E +   LA
Sbjct: 359 DGALAKAVARECFERGMLFGPCGVGGSVIKLIPPLTIPEDELVAGLEILSEALA 412


Lambda     K      H
   0.319    0.137    0.403 

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: 388
Number of extensions: 19
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: 395
Length of database: 417
Length adjustment: 31
Effective length of query: 364
Effective length of database: 386
Effective search space:   140504
Effective search space used:   140504
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 Jul 25 2024. The underlying query database was built on Jul 25 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