Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_011799827.1 PNAP_RS01975 PLP-dependent aminotransferase family protein
Query= SwissProt::H3ZPL1 (417 letters) >NCBI__GCF_000015505.1:WP_011799827.1 Length = 406 Score = 300 bits (769), Expect = 4e-86 Identities = 164/391 (41%), Positives = 237/391 (60%), Gaps = 12/391 (3%) Query: 23 SEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQALQY 82 + +A M S IRE+LK+ E +IS AGGLP+P+TFPV ++VL + ALQY Sbjct: 6 ARRAQKMNPSVIREILKVTEKPGIISFAGGLPSPKTFPVSAFSAACEKVLREDGHAALQY 65 Query: 83 GTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDIIVVEAPT 142 ++G+ PLR +A + D + ++ T+GSQQ LDLI +V I+ G ++VE PT Sbjct: 66 AASEGYAPLREMVASMLPWNVDPAL----VLITTGSQQGLDLIAKVLIDEGSRVLVETPT 121 Query: 143 YLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNPAGVT 202 YL ALQAF EPE V + DD G+++ +L + + + Y +P FQNP G T Sbjct: 122 YLGALQAFTPMEPEIVSVASDDGGVDI-------ADLAAKAEGARFFYVLPNFQNPTGRT 174 Query: 203 MNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSKILAP 262 M E+RR L A++ +VEDNPYG+L + P P+ A + EG +YLG+FSK+LAP Sbjct: 175 MPEERRAALSAEAARLGLPLVEDNPYGDLWFDTPPPLPLTARNPEG-CVYLGSFSKVLAP 233 Query: 263 GFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIPKIIEFYKPRR 322 G R+G++ A KL AKQ+ DL + F+Q + + ++ G+LD+H+P I YK +R Sbjct: 234 GLRLGFMVAPASIFPKLLQAKQAADLHSPGFNQRLVAEVMKDGFLDRHVPTIRALYKSQR 293 Query: 323 DAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHR 382 DAML A+ MP+GV+W P GGMF+W LPEG++ +L +AV + VA+VPG AF+A + Sbjct: 294 DAMLAAMVREMPEGVEWNTPAGGMFLWVRLPEGMNAIELLPRAVERNVAFVPGWAFYADQ 353 Query: 383 DVKNTMRLNFTYVPEEKIREGIKRLAETIKE 413 T+RL+F +I GI LA I+E Sbjct: 354 PDARTLRLSFVTSSVAQIDIGIAALAGAIRE 384 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: 460 Number of extensions: 23 Number of successful extensions: 4 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: 406 Length adjustment: 31 Effective length of query: 386 Effective length of database: 375 Effective search space: 144750 Effective search space used: 144750 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 Apr 10 2024. The underlying query database was built on Apr 09 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