Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_106716187.1 CU100_RS08590 PLP-dependent aminotransferase family protein
Query= SwissProt::H3ZPL1 (417 letters) >NCBI__GCF_003010935.1:WP_106716187.1 Length = 411 Score = 297 bits (761), Expect = 3e-85 Identities = 170/409 (41%), Positives = 240/409 (58%), Gaps = 13/409 (3%) Query: 17 DYEKYFSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHA 76 D++ +S + M+ASE+RELLKL++ D+IS AGG+P P FP E I E VL+++A Sbjct: 3 DWDARYSARTGKMRASEVRELLKLLDQPDIISFAGGIPDPALFPKEAIKEAYSAVLDENA 62 Query: 77 AQALQYGTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDII 136 ALQY ++G+ PLR L + M + + +I+ T+GSQQALD +G++FI+PGD I Sbjct: 63 DAALQYSVSEGYKPLRQWLVQHM-AALGVACTIDNIIITTGSQQALDYLGKLFISPGDTI 121 Query: 137 VVEAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQ 196 + PTYL ALQAF YEP + ++ + D Q G +V++ Y F Sbjct: 122 LTTWPTYLGALQAFNAYEPRYDRLIPEGGNTTPDAYRTNAQ---AAGGRVRLAYLTGDFS 178 Query: 197 NPAGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWD-------EEGR 249 NP G T+ K R +L+ELA + D ++ED Y LRY GE + A D + R Sbjct: 179 NPTGETIGRKERVKLVELAHELDIPLIEDAAYRVLRYEGENAPSMLALDIEREGHIDRTR 238 Query: 250 VIYLGTFSKILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDK 309 V+Y G+FSK L PG R+GW+ A I KL + KQ+ DL + T +Q++ +V + D Sbjct: 239 VLYSGSFSKSLTPGLRVGWVCAAQPVIAKLVLIKQAADLHSPTINQMVI-HHVAERHFDA 297 Query: 310 HIPKIIEFYKPRRDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAK- 368 + K Y+ RRD ML AL MP+GV WT+PEGGMFVW TLP+G+D +L ++V + Sbjct: 298 QVEKARGHYRQRRDHMLGALARHMPEGVTWTRPEGGMFVWMTLPDGMDGAALLARSVEQI 357 Query: 369 GVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKEEMKK 417 VA+VPG AF A NT+RLNF+ E I G++RL I EM + Sbjct: 358 RVAFVPGVAFHADGTGGNTIRLNFSLPNAEAIETGMQRLGGLIGREMDR 406 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: 444 Number of extensions: 26 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: 411 Length adjustment: 31 Effective length of query: 386 Effective length of database: 380 Effective search space: 146680 Effective search space used: 146680 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