GapMind for Amino acid biosynthesis

 

Aligments for a candidate for PPYAT in Dyella japonica UNC79MFTsu3.2

Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate N515DRAFT_1217 N515DRAFT_1217 transcriptional regulator, GntR family

Query= reanno::acidovorax_3H11:Ac3H11_1015
         (396 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1217 N515DRAFT_1217
           transcriptional regulator, GntR family
          Length = 468

 Score =  186 bits (471), Expect = 2e-51
 Identities = 112/386 (29%), Positives = 188/386 (48%), Gaps = 12/386 (3%)

Query: 10  VETSAIRELFKLLGKPGIISFAGGFPDSAMFDVEGIRAASNAALAEEPGAALQYGATEGY 69
           V   A++E+  +L +  ++      P  A+     + AA + +L   P A L Y   +G 
Sbjct: 87  VNNPALQEVLDMLARSDVLPLHSATPSPALLPQAALTAALSRSLRHHPAAVLDYAPPQGL 146

Query: 70  NPLREQLAAFMTSKGAKDVAADNLIVTTGSQQALDLLGKTLISPGDKVIVEGPTFLATIQ 129
             LR Q+A      GA  V+ D +++T G+ + + L  +TL  PGD V+VE PT+   +Q
Sbjct: 147 PALRRQIARRYAQLGAA-VSPDEIVITAGAMEGISLALRTLAEPGDVVLVETPTYHGILQ 205

Query: 130 CFRLYGAELISAP-IDGNGVKTDELEKLIAEHKPKFVYLIPTFGNPSGAMLSLERRKAVL 188
                  +++  P + G G+    L++L+ +++ +   L+P F NP G++     ++A+L
Sbjct: 206 AVAALRLKVLEVPNLPGQGIDVARLDQLLQQNRVRAAVLVPNFNNPLGSVTGDAAKQALL 265

Query: 189 EMAVKHNTLIVEDDPYGDLYFGDAPPPSLLNLSATVPGSRELLVHCGSLSKVLSPGLRVG 248
               +H T+++EDD YGDL +    P  L         +R  L+ CGS SK LSPGLR+G
Sbjct: 266 ASCARHGTVVIEDDVYGDLAWSGERPSPLRRWD-----TRGNLISCGSFSKSLSPGLRLG 320

Query: 249 WMIAPAELLGKATMCKQFSDAHTSTFAQATAAQYLKAGRMPGTLANVRKVYAERAQAMGD 308
           W IA           K FS    ++  Q   A+YL+   +   L  +R+  A+ AQ + +
Sbjct: 321 W-IAAGAWTDALVRAKYFSTVGAASLPQLAMAEYLQKHDLERHLRRLRRALADNAQRLHE 379

Query: 309 ALRKELGDAIEFVQPQGGLFVWARLTGAGGKVADGNVLAKRAIEKGVAFVPGTPFFCANP 368
           A+ +         +P+GGL +W +L   G    DG +L + A+E+G+   PG  F     
Sbjct: 380 AISRHWPAGTRASEPRGGLSLWLQLPEGG----DGQMLFEAALEQGIGTSPGVLFSSRGD 435

Query: 369 DHATFRLSFATADVDKIREGVARLGQ 394
                RLS       ++ + + +LGQ
Sbjct: 436 YGDCLRLSCGMPWDARLEQALKKLGQ 461


Lambda     K      H
   0.319    0.136    0.394 

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: 495
Number of extensions: 32
Number of successful extensions: 6
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: 396
Length of database: 468
Length adjustment: 32
Effective length of query: 364
Effective length of database: 436
Effective search space:   158704
Effective search space used:   158704
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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