Align Aromatic-amino-acid aminotransferase 2; ARAT-II; AROAT; EC 2.6.1.57 (characterized)
to candidate 352902 BT3375 aspartate aminotransferase (NCBI ptt file)
Query= SwissProt::H3ZPU1 (389 letters) >FitnessBrowser__Btheta:352902 Length = 386 Score = 287 bits (734), Expect = 4e-82 Identities = 141/383 (36%), Positives = 238/383 (62%), Gaps = 3/383 (0%) Query: 3 LSDRLEMVNPSEIRKLFDLAQGIEGIISLGIGEPDFDTPEHIKEYAKEALDKGLTHYSPN 62 LS+ ++PS R+LF+LAQ + +I +G+PD + IKE +A+ +G T YSPN Sbjct: 4 LSEITNSISPSLTRRLFNLAQKYDNVIDFTLGDPDIHPHDKIKEAGCKAILEGRTRYSPN 63 Query: 63 IGILELREAVAEKFKKHNGIDADPKTQIMITVGTNQQILMGLATFLKDNEEVLIPSPMFV 122 G+LELRE ++ ++K I+ +P +IM+TVG + + + L L +EV+IP+P ++ Sbjct: 64 AGLLELREIISSRYKLQYNIEYNPTNEIMVTVGGMEGLYLTLLAILNRGDEVIIPAPYWI 123 Query: 123 SYAPAVILAGGKPVEVPTYEENEFRLSVDELEKYVTPKTRALIINTPNNPTGAVLTKKDL 182 +Y V + G+P+ N+ +S++ + K +TPKT+A+I+NTP+NP+G +++ + Sbjct: 124 NYVQMVCMCSGEPIITAPVSTNDLSISIENIRKAITPKTKAIILNTPSNPSGRIISDDSI 183 Query: 183 EEIADFAVEHDLMILSDEVYEYFVYDGVKNYSIASLDGMFERTITMNGFSKTFAMTGWRL 242 ++IA A+E+DL++++DEVY+ +YD SI + D M ERT+ +N SK F MTGWRL Sbjct: 184 QQIAQIAIENDLIVITDEVYKTLLYDNAHFKSIVTCDKMKERTVVINSLSKEFCMTGWRL 243 Query: 243 GFLAAPEWVVEKMVRFQMYNATCPVTFIQYAAAKALRDERSWQAVEEMRREYERRRNLVW 302 G++AAP ++ M FQ A C QYAA +ALR+ + A M E+ RRN++ Sbjct: 244 GYIAAPSELISVMTMFQENIAACAPLPSQYAAIEALRNSEKYSA--GMIEEFTLRRNVLL 301 Query: 303 KRLNEMGLPTV-KPKGAFYIFPRIKDTGLSSKEFSELMIKEAKVVVVPGSAFGQAGEGYV 361 + + ++ TV P+G FY IK TGL S+EF+ ++++ +V VVPG +G E ++ Sbjct: 302 EEVAKIKTITVDAPQGTFYAMLNIKSTGLKSEEFAYALLEKEQVAVVPGITYGDCCEDFI 361 Query: 362 RISYATAYEKLEEAMDRMEKVLK 384 RI++ K++E + R+++ ++ Sbjct: 362 RIAFTLDIYKIKEGIQRLKRFVE 384 Lambda K H 0.318 0.135 0.387 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: 356 Number of extensions: 11 Number of successful extensions: 2 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: 389 Length of database: 386 Length adjustment: 30 Effective length of query: 359 Effective length of database: 356 Effective search space: 127804 Effective search space used: 127804 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