Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate AO356_24005 AO356_24005 aspartate aminotransferase
Query= BRENDA::Q02635 (400 letters) >lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24005 AO356_24005 aspartate aminotransferase Length = 403 Score = 361 bits (927), Expect = e-104 Identities = 184/398 (46%), Positives = 246/398 (61%), Gaps = 1/398 (0%) Query: 3 FLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGET 62 +L+ + RV SA A +A L+ GRD++ L GEPDFDTP +IK+AA AI G T Sbjct: 4 YLSKRVQRVSLSANAAAKSRATALRDAGRDILDLTTGEPDFDTPAHIKQAAYAAIAAGAT 63 Query: 63 KYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPA 122 KYTP G+ LR A+ +K + EN LDY A ++ G KQI+FNAF ATL+ GDEV++P Sbjct: 64 KYTPTPGVKALRVAVQRKLRTENQLDYPLASIVIANGAKQIIFNAFAATLDDGDEVLVPT 123 Query: 123 PYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYS 182 PYW S+P+ V GG PVF+ + KL L++ I +T+W + NSP NPSGA YS Sbjct: 124 PYWPSFPDSVRFNGGEPVFIECGLDQGCKLTPRQLEQHIGERTRWLILNSPGNPSGAVYS 183 Query: 183 HEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYA 242 EL+ L VL +H HV +L D++YEH+ + + V P L R L + GVSK YA Sbjct: 184 EAELQGLAQVLRRHAHVLILLDELYEHIRFDGRPSQNLLNVAPDLQSRCLLVGGVSKTYA 243 Query: 243 MTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRR 302 MTGWRIG+ AGP L AM ++Q Q TSGA+S+ Q AA+ A G DF+ ++ RR Sbjct: 244 MTGWRIGFGAGPQALTDAMTVVQSQSTSGASSVGQAAALAAFEGGLDFLPEQVAAYRQRR 303 Query: 303 DLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAV 362 D++VS L +G+ P G F+V+ CAGL+G+ P G+ +E D D V+ LL+ EGVA Sbjct: 304 DVLVSTLRNVEGLEVLEPHGGFFVFVCCAGLLGRYRPDGQRLEHDADVVAYLLD-EGVAG 362 Query: 363 VHGSAFGLGPNFRISYATSEALLEEACRRIQRFCAACR 400 V GSA+GL P FR+S AT+ + EA RRI C R Sbjct: 363 VAGSAYGLSPWFRLSIATATETVAEAGRRIAHACGQLR 400 Lambda K H 0.318 0.134 0.402 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: 430 Number of extensions: 16 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: 400 Length of database: 403 Length adjustment: 31 Effective length of query: 369 Effective length of database: 372 Effective search space: 137268 Effective search space used: 137268 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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