Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_066326841.1 BLR17_RS05750 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >NCBI__GCF_900100165.1:WP_066326841.1 Length = 396 Score = 379 bits (973), Expect = e-110 Identities = 203/395 (51%), Positives = 261/395 (66%), Gaps = 3/395 (0%) Query: 4 LSDTLARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTK 63 LSD + + SQT+A+ AREL A G+D+I L GEPDF+TPD IK AAK+AID + Sbjct: 5 LSDRINNLATSQTLAMAALARELKAQGKDIISLSLGEPDFNTPDFIKEAAKKAIDENYST 64 Query: 64 YTAVDGIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIPAP 123 Y+ VDG ELK AIC KF+R+NGL Y P+Q+ V TG KQ LYN LN GDEVI+PAP Sbjct: 65 YSPVDGYAELKDAICRKFKRDNGLDYKPSQIVVSTGAKQSLYNIAQVMLNDGDEVILPAP 124 Query: 124 YWVSYPDMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTR 183 YWVSY ++V L+GG PV V +ET FK+TPEQLEAAITP+TK F+SP NP+G+ Y R Sbjct: 125 YWVSYFEIVKLSGGVPVEVPTSVETDFKITPEQLEAAITPKTKMMWFSSPCNPSGSVYNR 184 Query: 184 AELAALCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCM 243 EL AL +VL ++P +++++D++YEH+ F F + A I PG+++RT+T NGV+KA+ M Sbjct: 185 EELTALAKVLEKYPNIYVVADEIYEHINFSG-TFCSIASI-PGMFERTVTVNGVAKAFAM 242 Query: 244 TGWRIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRRD 303 TG+RIGY P + +A IQ Q TS SIAQ A + A+ L +AF RRD Sbjct: 243 TGYRIGYIGAPEFIAKACTKIQGQVTSGANSIAQRATITAVDADPSVLNHMVQAFHSRRD 302 Query: 304 LVVSMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAVV 363 LVV +L E G+ PEGAFYV+PD+S GKT G +I D + LL E VA V Sbjct: 303 LVVGLLKEIPGIKINVPEGAFYVFPDVSSFFGKT-LKGTEIKDANDVSMYLLAEANVATV 361 Query: 364 FGAAFGLSPNFRISYATADEVLREACARIQAFCAG 398 G AFG R SYAT+DE+L+EA RI+ AG Sbjct: 362 TGDAFGNPNCIRFSYATSDELLKEALKRIKDALAG 396 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: 456 Number of extensions: 15 Number of successful extensions: 4 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: 396 Length adjustment: 31 Effective length of query: 369 Effective length of database: 365 Effective search space: 134685 Effective search space used: 134685 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 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