Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate Pf6N2E2_5813 Transcriptional regulator, GntR family domain / Aspartate aminotransferase (EC 2.6.1.1)
Query= SwissProt::H3ZPL1 (417 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5813 Length = 388 Score = 246 bits (628), Expect = 9e-70 Identities = 144/398 (36%), Positives = 218/398 (54%), Gaps = 21/398 (5%) Query: 22 FSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQAL- 80 FSE+ +K+S IRE+L + +V+S AGGLPA P + AA L Sbjct: 3 FSERVSRLKSSLIREILAAAQRPEVMSFAGGLPAEAMLPKV-----------EWAAMPLS 51 Query: 81 --QYGTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDIIVV 138 QYG ++G LR ALA R + ++ SGSQQ LDL ++ I+ G +++ Sbjct: 52 MGQYGMSEGEPALREALAAQARA-LGVACEASQVLVVSGSQQTLDLAAKLHIDVGTEVML 110 Query: 139 EAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNP 198 EAPTYLAALQ F+ + + + +PL+ +G ++ L +L E + +Y IPTFQNP Sbjct: 111 EAPTYLAALQIFQLFGADCITVPLEADGPDLKALRARL-----ERHRPAFIYLIPTFQNP 165 Query: 199 AGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSK 258 + V +E +R + L ++ ++ED PY EL + G PI + + IY GT SK Sbjct: 166 SAVRYSEAKRDAVAALLDEFGVTLIEDEPYRELTFDGGSATPIVSRLRKASWIYTGTVSK 225 Query: 259 ILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIPKIIEFY 318 L PG R+G++ A P L KQS DL TN Q A +++ +H+ ++ +FY Sbjct: 226 TLLPGLRVGYLIASPDLFPHLLRLKQSADLHTNRIGQWQALQWIGTEQYRRHLSELRDFY 285 Query: 319 KPRRDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAF 378 + RRD ALE+ D W P+GG+F W TL + +DT+ +L A+A VA++PGE F Sbjct: 286 RDRRDRFQAALEKHFTDLADWNIPQGGLFFWLTLKQPLDTRTLLAAALAADVAFMPGEPF 345 Query: 379 FAHRDV-KNTMRLNFTYVPEEKIREGIKRLAETIKEEM 415 F D +RLNF+++ ++ EG+KRLA ++E + Sbjct: 346 FPEPDQHPGHLRLNFSHIDPARLDEGLKRLAGVVREAL 383 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: 419 Number of extensions: 22 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 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