Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_043917065.1 jaqu_RS01005 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >NCBI__GCF_000877395.1:WP_043917065.1 Length = 400 Score = 652 bits (1683), Expect = 0.0 Identities = 318/400 (79%), Positives = 349/400 (87%) Query: 1 MAFLSDTLARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAG 60 MAFLSDTLARVKPS TIAVT KAREL AAGRDVIGLGAGEPDFDTPDNIKAAAK AIDAG Sbjct: 1 MAFLSDTLARVKPSPTIAVTTKARELKAAGRDVIGLGAGEPDFDTPDNIKAAAKAAIDAG 60 Query: 61 RTKYTAVDGIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVII 120 +TKYTA DGIPELK+AIC+KF+R+NGL YTPAQV+VGTGGKQILYNAL+ATLN GDEV+I Sbjct: 61 KTKYTAPDGIPELKQAICDKFKRDNGLDYTPAQVSVGTGGKQILYNALMATLNDGDEVVI 120 Query: 121 PAPYWVSYPDMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAA 180 PAPYWVSYPDMVLLAGGTPV + +TG+K+TPEQLE AIT RTKW IFNSPSNPTGA Sbjct: 121 PAPYWVSYPDMVLLAGGTPVFIEGPSQTGYKITPEQLEEAITDRTKWLIFNSPSNPTGAG 180 Query: 181 YTRAELAALCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKA 240 YT E+ L +VLMRHP VW+M+DDMYEHL + DFDF TPAQ+EPGLYDRTLT NGVSKA Sbjct: 181 YTAEEIKGLTDVLMRHPHVWVMTDDMYEHLTYGDFDFATPAQVEPGLYDRTLTVNGVSKA 240 Query: 241 YCMTGWRIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQR 300 Y MTGWRIGYAAGP LI AM +QSQSTSNPCSI+Q+AA+EAL G Q+F+ N F+R Sbjct: 241 YSMTGWRIGYAAGPEHLIAAMRKVQSQSTSNPCSISQWAAVEALEGTQDFIPVNNAMFKR 300 Query: 301 RRDLVVSMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGV 360 RRDLVVSMLNEA+GV CP PEGAFYVYP I GCIGKTSAGGA+I DDEAFA+ALLEE GV Sbjct: 301 RRDLVVSMLNEAEGVQCPTPEGAFYVYPSIHGCIGKTSAGGARIDDDEAFATALLEEEGV 360 Query: 361 AVVFGAAFGLSPNFRISYATADEVLREACARIQAFCAGLS 400 AVV GAAFGLSP FR+SYAT+DE L EAC RIQ FCAGL+ Sbjct: 361 AVVHGAAFGLSPAFRVSYATSDEALTEACTRIQRFCAGLT 400 Lambda K H 0.318 0.134 0.399 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: 669 Number of extensions: 23 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 ( 7.4 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 Sep 24 2021. The underlying query database was built on Sep 17 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