Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate 207852 DVU2364 aminotransferase, classes I and II
Query= SwissProt::H3ZPL1 (417 letters) >MicrobesOnline__882:207852 Length = 388 Score = 298 bits (763), Expect = 2e-85 Identities = 156/392 (39%), Positives = 241/392 (61%), Gaps = 16/392 (4%) Query: 29 MKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQALQYGTTKGF 88 ++ S IRE+LK+ D+IS AGGLP P++FPV+ + E VL + ++ALQY TT+G+ Sbjct: 10 VQRSYIREILKVTARPDIISFAGGLPHPDSFPVQGVAEAAAAVLAESGSEALQYSTTEGY 69 Query: 89 TPLRLALAEWMRERY---DIPISKVDIMTTSGSQQALDLIGRVFINPGDIIVVEAPTYLA 145 PLR EW+ RY I +S +I+ T+GSQQALDL+ + I+ G +V+E P YL Sbjct: 70 LPLR----EWISARYARQGIEVSPDEILITTGSQQALDLVAKTTIDRGAPVVIERPGYLG 125 Query: 146 ALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNPAGVTMNE 205 A+Q F +Y +F + L G++V+ L +E K ++ Y +P+FQNP+G+T +E Sbjct: 126 AIQCFSFYGAQFRTVDLTPLGVDVEALR-------REAKGARLFYAVPSFQNPSGITYDE 178 Query: 206 KRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSKILAPGFR 265 R+ + + ++ ++VEDNPYGELR+ G PV PI+ W E V+ LG+FSK+++PG R Sbjct: 179 PTRREVAAIMAETGCMLVEDNPYGELRFMGTPVAPIRKWAESPSVL-LGSFSKVVSPGLR 237 Query: 266 IGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIPKIIEFYKPRRDAM 325 IGW A +R + AKQ+ DL T F+Q + +++ +D+HI I + Y +R M Sbjct: 238 IGWACAPAELMRHMVTAKQASDLHTPMFTQRLLHRFLVDNDVDEHIASIRKRYGAQRQCM 297 Query: 326 LKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVK 385 + A+ + P+ V T+PEGGMF+W LPEG+ ++ + KA+ + VA+VPG F+ Sbjct: 298 MDAIRKHFPECVTVTEPEGGMFLWCGLPEGVTSEHLFHKAIERKVAFVPGCPFYVD-GTD 356 Query: 386 NTMRLNFTYVPEEKIREGIKRLAETIKEEMKK 417 RLNF+ ++ I EGI RL + EE+ + Sbjct: 357 TGFRLNFSNASQDDIVEGIARLGACLTEELAR 388 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: 453 Number of extensions: 16 Number of successful extensions: 5 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: 388 Length adjustment: 31 Effective length of query: 386 Effective length of database: 357 Effective search space: 137802 Effective search space used: 137802 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 09 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