Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate AZOBR_RS12970 AZOBR_RS12970 aspartate aminotransferase
Query= BRENDA::Q02635 (400 letters) >FitnessBrowser__azobra:AZOBR_RS12970 Length = 401 Score = 584 bits (1506), Expect = e-171 Identities = 288/396 (72%), Positives = 319/396 (80%) Query: 1 MAFLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRG 60 M+ +A LSR+KPS TIAV+QKAREL A GRDVIGLGAGEPDFDTPDNIK AAI AI G Sbjct: 1 MSIIASRLSRIKPSPTIAVTQKARELAAAGRDVIGLGAGEPDFDTPDNIKDAAIKAIQAG 60 Query: 61 ETKYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVI 120 +TKYT V G P L++AI KF+REN L Y Q VG GGKQ+L+NA MATL PGDEV+I Sbjct: 61 DTKYTAVDGTPALKKAICAKFERENGLKYAPDQITVGVGGKQVLYNALMATLTPGDEVII 120 Query: 121 PAPYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAA 180 PAPYWVSYP+MV L GTPVFV E FKL+ DL++AITPKTKW + NSPSNPSGAA Sbjct: 121 PAPYWVSYPDMVELAEGTPVFVSCPAEQGFKLQPADLEKAITPKTKWLILNSPSNPSGAA 180 Query: 181 YSHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKA 240 Y+ +E+KALTDVL+KHP VWV+TDDMYEHL Y F TP +VEP LY+RTLT+NGVSK+ Sbjct: 181 YTRDEMKALTDVLVKHPQVWVMTDDMYEHLLYDGIEFVTPAQVEPALYDRTLTVNGVSKS 240 Query: 241 YAMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQG 300 YAMTGWRIGYA GP LIKAM +IQ Q TS SIAQ AAVEALNGPQDFI +F Sbjct: 241 YAMTGWRIGYAGGPKALIKAMGVIQSQSTSNPTSIAQAAAVEALNGPQDFIAERAAVFAQ 300 Query: 301 RRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGV 360 RRDLVVSMLNQAKGISCP PEGAFYVYPSCAG IGKT P GKVIETDEDFV+ LLE+EGV Sbjct: 301 RRDLVVSMLNQAKGISCPKPEGAFYVYPSCAGTIGKTTPDGKVIETDEDFVTYLLESEGV 360 Query: 361 AVVHGSAFGLGPNFRISYATSEALLEEACRRIQRFC 396 AVV GSAFGL P+FRISYATS LEEAC+RIQR C Sbjct: 361 AVVQGSAFGLAPHFRISYATSTEALEEACKRIQRAC 396 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: 598 Number of extensions: 16 Number of successful extensions: 1 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: 401 Length adjustment: 31 Effective length of query: 369 Effective length of database: 370 Effective search space: 136530 Effective search space used: 136530 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