Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Pf6N2E2_1496 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::Q02635 (400 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1496 Length = 403 Score = 355 bits (912), Expect = e-102 Identities = 183/398 (45%), Positives = 244/398 (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 YLSKRVQRVSLSANAAAKSRATALREAGRDILDLTTGEPDFDTPTHIKQAAYAAIAAGAT 63 Query: 63 KYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPA 122 KYTP G+ LR A+ +K EN LDY ++ G KQI+FNAF ATL+ GDEV++P Sbjct: 64 KYTPTPGVKALRVAVQRKLCTENQLDYPLESIVIANGAKQIIFNAFAATLDDGDEVLVPT 123 Query: 123 PYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYS 182 PYW S+P+ V GG PVF+ E KL + L++ I +T+W + NSP NPSGA YS Sbjct: 124 PYWPSFPDSVRFNGGEPVFIECGLEQGCKLTPQQLEQHIGERTRWLILNSPGNPSGAVYS 183 Query: 183 HEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYA 242 EL+ L VL +H HV +L D++YEH+ + + V P L R L + GVSK YA Sbjct: 184 EAELQGLAQVLRRHAHVLILLDELYEHIRFDGRAAQNLLNVAPDLQARCLLVGGVSKTYA 243 Query: 243 MTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRR 302 MTGWRIG+ AGP L AM ++Q Q TSGA+S+ Q AA+ A G +F+ ++ RR Sbjct: 244 MTGWRIGFGAGPQALSDAMTVVQSQSTSGASSVGQAAALAAFEGGLEFLPEQVAAYRQRR 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 DGLVSTLRTVEGLEVLEPHGGFFVFVRCAGLLGRYRPDGQRLEHDADVVAYLLD-EGVAG 362 Query: 363 VHGSAFGLGPNFRISYATSEALLEEACRRIQRFCAACR 400 V GSA+GL P FR+S AT+ + EA RRI C R Sbjct: 363 VAGSAYGLSPWFRLSIATATETVAEAGRRIAHACRQLR 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: 426 Number of extensions: 19 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:
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