GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Epibacterium ulvae U95

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_090220307.1 CV091_RS16395 PLP-dependent aminotransferase family protein

Query= SwissProt::H3ZPL1
         (417 letters)



>NCBI__GCF_002796795.1:WP_090220307.1
          Length = 399

 Score =  288 bits (737), Expect = 2e-82
 Identities = 164/404 (40%), Positives = 238/404 (58%), Gaps = 16/404 (3%)

Query: 16  LDYEKYFSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKH 75
           +++E+  + +   MKASEIRELLKL++  +VIS AGG+P PE FP E     + EVL + 
Sbjct: 1   MEFERLLASRHHFMKASEIRELLKLLDQPEVISFAGGIPDPEFFPREAFQRASAEVLTQ- 59

Query: 76  AAQALQYGTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDI 135
            A+ LQY  ++G   LR  L   M +   +P    +I+ TSGSQQALD IG++F++PGD 
Sbjct: 60  -AEPLQYSISEGDLGLRQQLKAHMAD-LGVPCGVENILITSGSQQALDYIGKLFLSPGDT 117

Query: 136 IVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTF 195
            +VE+PTYL AL AF  YEP + ++ +          E      +  G  VK  Y +P F
Sbjct: 118 ALVESPTYLGALAAFNAYEPRYDRLQVQGNQSP----EVSTAAAQAAGSCVKFAYVVPDF 173

Query: 196 QNPAGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWD-------EEG 248
            NP G T+    R+ LL+ A+  D  ++ED  Y  LRY GE +  I + +          
Sbjct: 174 SNPTGETLGCGAREALLDRATTLDCAVIEDAAYQALRYEGEAIPSILSLELKRTGDINRC 233

Query: 249 RVIYLGTFSKILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLD 308
           R +Y G+FSK LAPG R+GWI A    I ++ + KQ+ DL + T +Q++    +  G+  
Sbjct: 234 RTLYCGSFSKTLAPGLRVGWIVAAKPLIDQMVLIKQASDLHSPTLNQMLVSHVLSEGF-P 292

Query: 309 KHIPKIIEFYKPRRDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAV-A 367
            H+  + + Y+ RRD ML AL  +MPDGV W++PEGGMFVW TLP  ID   +L++A+  
Sbjct: 293 AHLEYLRKSYRERRDVMLNALTSYMPDGVHWSQPEGGMFVWLTLPPHIDGAALLKRALEQ 352

Query: 368 KGVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETI 411
           + +A+VPG+AF A     NT RL+F+    + IREG++RLA  +
Sbjct: 353 EKIAFVPGQAFHADGSGANTARLSFSCGKPDSIREGVQRLARVL 396


Lambda     K      H
   0.318    0.137    0.398 

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: 399
Number of extensions: 21
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: 417
Length of database: 399
Length adjustment: 31
Effective length of query: 386
Effective length of database: 368
Effective search space:   142048
Effective search space used:   142048
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 26 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