Align aspartate transaminase (EC 2.6.1.1); aspartate-prephenate aminotransferase (EC 2.6.1.78); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_106718519.1 CU100_RS21000 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q02635 (400 letters) >NCBI__GCF_003010935.1:WP_106718519.1 Length = 400 Score = 642 bits (1657), Expect = 0.0 Identities = 311/400 (77%), Positives = 350/400 (87%) Query: 1 MAFLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRG 60 MAFLADALSRVK SATIA++QKAR+LKA+GRDVI L GEPDFDTPDN+K+AAI AI RG Sbjct: 1 MAFLADALSRVKISATIAITQKARDLKAEGRDVISLSVGEPDFDTPDNVKEAAIAAIRRG 60 Query: 61 ETKYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVI 120 ETKYTPVSGIP+LREAI +KFKREN LDY A+QTIV TGGK +++NA ++TLNPGDEV+ Sbjct: 61 ETKYTPVSGIPQLREAIVRKFKRENELDYKASQTIVSTGGKHVIYNALLSTLNPGDEVIC 120 Query: 121 PAPYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAA 180 APYWVSYPEMV+LCGGTPV V Q N FKL+ EDL+RAITPKTKW + NSPSNPSGAA Sbjct: 121 VAPYWVSYPEMVSLCGGTPVIVSAIQANEFKLQPEDLERAITPKTKWIIMNSPSNPSGAA 180 Query: 181 YSHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKA 240 YS +E+K LTDVL++HPHVWVLTDDMYEHLTYGDF+F TPV+VEP LY+RTLTMNGVSKA Sbjct: 181 YSWDEMKKLTDVLVRHPHVWVLTDDMYEHLTYGDFKFVTPVQVEPNLYDRTLTMNGVSKA 240 Query: 241 YAMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQG 300 YAMTGWRIGYAAGP+ LIKAMDM+QGQQTSG +SI+QWAAVEAL+G Q+ + K+ F+G Sbjct: 241 YAMTGWRIGYAAGPIELIKAMDMVQGQQTSGTSSISQWAAVEALDGTQEHLPVFKKAFEG 300 Query: 301 RRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGV 360 RRDL+VSMLNQ + CP PEGAFYVYPSCA IGKTAPSGKVIE DEDFVSELL TE V Sbjct: 301 RRDLIVSMLNQTNLLECPKPEGAFYVYPSCAAAIGKTAPSGKVIENDEDFVSELLSTEAV 360 Query: 361 AVVHGSAFGLGPNFRISYATSEALLEEACRRIQRFCAACR 400 A VHGSAFGLGPNFRISYATS+A LEEA +RIQRFCA R Sbjct: 361 AAVHGSAFGLGPNFRISYATSDANLEEAGKRIQRFCANLR 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: 585 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: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 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 Jul 26 2024. The underlying query database was built on Jul 25 2024.
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