Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_090216551.1 CV091_RS05515 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >NCBI__GCF_002796795.1:WP_090216551.1 Length = 405 Score = 613 bits (1581), Expect = e-180 Identities = 296/399 (74%), Positives = 339/399 (84%) Query: 2 AFLSDTLARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGR 61 +FLS+TL+RVKPS T+AVT KA +L AAG DVIGLGAGEPDF TPDNIKAAA AI+AG+ Sbjct: 7 SFLSETLSRVKPSPTMAVTAKAADLKAAGEDVIGLGAGEPDFTTPDNIKAAAIEAINAGK 66 Query: 62 TKYTAVDGIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIP 121 TKYTAVDGIPELK AIC KF+R+N L YTPAQV+V +GGK LYNAL+AT+NPGDEVIIP Sbjct: 67 TKYTAVDGIPELKAAICAKFKRDNDLSYTPAQVSVNSGGKHTLYNALMATINPGDEVIIP 126 Query: 122 APYWVSYPDMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAY 181 AP+WVSYPDMVLLAGGTPV+V +E FKLT QLEAAITP+TKWFIFNSPSNPTGA Y Sbjct: 127 APFWVSYPDMVLLAGGTPVTVETTLEANFKLTAAQLEAAITPKTKWFIFNSPSNPTGAGY 186 Query: 182 TRAELAALCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAY 241 T EL AL +VL+RHP VW+M+DDMYEHL +DDF F TPAQ+EPGLYDRTLTCNGVSKAY Sbjct: 187 TWDELKALTDVLLRHPHVWVMTDDMYEHLAYDDFKFCTPAQVEPGLYDRTLTCNGVSKAY 246 Query: 242 CMTGWRIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRR 301 MTGWRIGYAAGP LI AM +QSQSTSNPC+++Q+AA+EAL+GPQ++LA N E F RR Sbjct: 247 AMTGWRIGYAAGPQPLIAAMRKVQSQSTSNPCTVSQWAAVEALNGPQDYLAHNNETFVRR 306 Query: 302 RDLVVSMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVA 361 R+LV+SML+E G+ CP PEGAFYVYP I+G IGKT+ G I DDE FA+ALLE+ VA Sbjct: 307 RNLVISMLSEIDGIVCPTPEGAFYVYPSIAGLIGKTTPNGTVIKDDETFAAALLEDEKVA 366 Query: 362 VVFGAAFGLSPNFRISYATADEVLREACARIQAFCAGLS 400 VVFGAAFGLSPNFR+SYAT+DE L EAC RIQ FCA L+ Sbjct: 367 VVFGAAFGLSPNFRVSYATSDEALHEACTRIQRFCAALT 405 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: 643 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: 405 Length adjustment: 31 Effective length of query: 369 Effective length of database: 374 Effective search space: 138006 Effective search space used: 138006 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