Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_012169089.1 AZC_RS02835 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >NCBI__GCF_000010525.1:WP_012169089.1 Length = 394 Score = 255 bits (652), Expect = 1e-72 Identities = 152/388 (39%), Positives = 211/388 (54%), Gaps = 12/388 (3%) Query: 10 RVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTKYTAVDG 69 R+ AV +A LAA GRD+I LG G+PDF TP++I AA +A+ G+ YT G Sbjct: 10 RIGEENAFAVLARATTLAAQGRDIINLGIGQPDFRTPEHIVEAAVKALKDGQHGYTPSVG 69 Query: 70 IPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIPAPYWVSYP 129 I L+ A+ + ++ P V + GGK +Y A++ PG E++ P P + Y Sbjct: 70 IQPLREAVARDLHKRFDVEVDPGLVMIMPGGKVTMYAAILLFGEPGAEILYPDPGFPIYR 129 Query: 130 DMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTRAELAAL 189 M+ G TP+ V E GF + E+ A ITP+T+ I NSP+NPTG +AE+ L Sbjct: 130 SMIEYTGATPIPVPIREENGFAFSAEETLALITPKTRLLIINSPANPTGGVTPKAEIDKL 189 Query: 190 CEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCMTGWRIG 249 + L HP V +MSD++Y+ +FD T P + DR + NG SK Y MTGWR+G Sbjct: 190 VKGLADHPHVALMSDEIYDQFLFDGERHQT-LLAYPEIRDRLILLNGWSKTYAMTGWRLG 248 Query: 250 YAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRRDLVVSML 309 Y+ P L + + + S + QYA + AL GPQE +A F +RR LVV L Sbjct: 249 YSIWPQALYDKVRKLSVNAWSCVNAATQYAGIAALEGPQEPVAAMLAEFDKRRRLVVEGL 308 Query: 310 NEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAVVFGAAFG 369 N GVTC P+GAFY +P++S G TSA +A ASALLE+ GVA + G FG Sbjct: 309 NALPGVTCAKPKGAFYAFPNVSR-TGWTSA--------KALASALLEDAGVATIGGPDFG 359 Query: 370 LSPN--FRISYATADEVLREACARIQAF 395 + R+SYA + E + A R+ AF Sbjct: 360 VHGEGYIRLSYANSAENIARALERMGAF 387 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: 453 Number of extensions: 26 Number of successful extensions: 3 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: 394 Length adjustment: 31 Effective length of query: 369 Effective length of database: 363 Effective search space: 133947 Effective search space used: 133947 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 Apr 10 2024. The underlying query database was built on Apr 09 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