Align Aromatic-amino-acid aminotransferase 2; ARAT-II; AROAT; EC 2.6.1.57 (characterized)
to candidate SMc01578 SMc01578 aspartate aminotransferase
Query= SwissProt::H3ZPU1 (389 letters) >FitnessBrowser__Smeli:SMc01578 Length = 400 Score = 251 bits (640), Expect = 3e-71 Identities = 148/396 (37%), Positives = 235/396 (59%), Gaps = 22/396 (5%) Query: 3 LSDRLEMVNPSEIRKLFDLAQGIEG----IISLGIGEPDFDTPEHIKEYAKEALDKGLTH 58 L+D L V PS + A+ ++ +I LG GEPDFDTP++IK+ A +A+D+G T Sbjct: 4 LADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETK 63 Query: 59 YSPNIGILELREAVAEKFKKHNGIDADPKTQIMITVGTNQQILMGLATFLKDNEEVLIPS 118 Y+P GI ELREA+A+KFK+ N +D Q ++ G Q + L +EV+IP+ Sbjct: 64 YTPVSGIPELREAIAKKFKRENNLDYTA-AQTIVGTGGKQILFNAFMATLNPGDEVVIPA 122 Query: 119 PMFVSYAPAVILAGGKPVEVPTYEENEFRLSVDELEKYVTPKTRALIINTPNNPTGAVLT 178 P +VSY V L GG PV VPT +EN F+L ++L++ +TPKT+ + N+P+NP+GA + Sbjct: 123 PYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYS 182 Query: 179 KKDLEEIADFAVEH-DLMILSDEVYEYFVYDGVKNYSIASLD-GMFERTITMNGFSKTFA 236 ++L+ + D ++H + +L+D++YE+ Y + + ++ G++ERT+TMNG SK +A Sbjct: 183 HEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYA 242 Query: 237 MTGWRLGFLAAPEWVVEKMVRFQMYNATCPVTFIQYAAAKALRDERSWQAVEEMRREYER 296 MTGWR+G+ A P +++ M Q + + Q+AA +AL + + + + ++ Sbjct: 243 MTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDF--IGRNKEIFQG 300 Query: 297 RRNLVWKRLNE-MGLPTVKPKGAFYIFPR----IKDTGLSSK------EFSELMIKEAKV 345 RR+LV LN+ G+ P+GAFY++P I T S K +F +++ V Sbjct: 301 RRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGV 360 Query: 346 VVVPGSAFGQAGEGYVRISYATAYEKLEEAMDRMEK 381 VV GSAFG G + RISYAT+ LEEA R+++ Sbjct: 361 AVVHGSAFG-LGPNF-RISYATSEALLEEACRRIQR 394 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: 377 Number of extensions: 19 Number of successful extensions: 6 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: 400 Length adjustment: 31 Effective length of query: 358 Effective length of database: 369 Effective search space: 132102 Effective search space used: 132102 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 Aug 03 2021. The underlying query database was built on Aug 03 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