Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate BWI76_RS24235 BWI76_RS24235 aminotransferase
Query= SwissProt::H3ZPL1 (417 letters) >FitnessBrowser__Koxy:BWI76_RS24235 Length = 393 Score = 297 bits (761), Expect = 3e-85 Identities = 164/399 (41%), Positives = 246/399 (61%), Gaps = 12/399 (3%) Query: 18 YEKYFSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAA 77 +++ + +A +K S +RELLK + VISL GG+PAPE F E + ++V+ Sbjct: 2 HDRRLAARAGELKPSAVRELLKHSKLPGVISLGGGIPAPELFDTEGLNLAVQQVMNGRFN 61 Query: 78 QALQYGTTKGFTPLRLALAEWMRER-YDIPISKVDIMTTSGSQQALDLIGRVFINPGDII 136 A QYG T+G+ PLR A++E + R P S V I TSGSQQ+LD++ R ++PGD I Sbjct: 62 DAFQYGLTEGYPPLRQAVSELCQARGVACPASHVYI--TSGSQQSLDIVARTLLDPGDAI 119 Query: 137 VVEAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQ 196 VVE PTYLAALQ F+ + + + DD+GM V+ L + L E +VK VY +PTF Sbjct: 120 VVERPTYLAALQVFQLAQANILSVDTDDDGMLVEQLADLL-----ETTRVKAVYLVPTFG 174 Query: 197 NPAGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEE----GRVIY 252 NP G T++E RR+RL+ELA ++DF+I+ED+PYGE+ ++ E +P+ + E +V+Y Sbjct: 175 NPGGKTLSEARRRRLVELAKKHDFVIIEDDPYGEISFTDEVRRPLYQYAVELGCEDQVVY 234 Query: 253 LGTFSKILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIP 312 TFSKILAPG RIGWI ++ I KQ+ DL TN SQVI +Y+ L+ I Sbjct: 235 TSTFSKILAPGMRIGWIVMPDWLAQQTVIVKQAADLHTNMLSQVITAEYLSMNRLESQIA 294 Query: 313 KIIEFYKPRRDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAY 372 I E Y+ + A+ ALE + + +++++P+GGMF+WA DT ++K + GV Y Sbjct: 295 LIREDYRKKCVALADALESQLGEHLEFSRPKGGMFLWARFRYPFDTMEWMKKTLENGVVY 354 Query: 373 VPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETI 411 VPGEAF+ T+RL+++ V + + ++RLA+++ Sbjct: 355 VPGEAFYNDNPDTRTLRLSYSTVSADGLMTAVERLAKSL 393 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: 423 Number of extensions: 17 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: 393 Length adjustment: 31 Effective length of query: 386 Effective length of database: 362 Effective search space: 139732 Effective search space used: 139732 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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