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.
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:
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