Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_028989557.1 G579_RS0106655 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q82WA8 (397 letters) >NCBI__GCF_000423825.1:WP_028989557.1 Length = 394 Score = 501 bits (1291), Expect = e-146 Identities = 251/395 (63%), Positives = 310/395 (78%), Gaps = 6/395 (1%) Query: 3 LSQRVQAIKPSPTLAVTAKAARLKAEGKNIIGLGAGEPDFDTPLHIKDAAITAIRNGFTK 62 LS+RVQAIKPSPTLAVTA+AARLKA G++I+ LGAGEPDFDTP +IK+AAI AIR+GFTK Sbjct: 5 LSRRVQAIKPSPTLAVTARAARLKAAGRDIVSLGAGEPDFDTPDYIKEAAIQAIRDGFTK 64 Query: 63 YTAVGGTASLKQAIISKFKRENSLEFMPGEILVSSGGKQSFFNLVLATIDPGDEVIIPAP 122 YTAV GT LKQAII KF R+N F P +ILVS GGKQS FNL A ++PGDEVI+PAP Sbjct: 65 YTAVDGTPGLKQAIIDKFARDNGFHFAPEQILVSVGGKQSIFNLCQALLNPGDEVIVPAP 124 Query: 123 YWVSYPDIVLIAEGKPVFIDTGIEEKFKISPDQLEKAITPRTRMFVVNSPSNPSGSVYSL 182 YWVSY DI ++AE +PV ++TG++ FKI+P+QL AITP+TR+ +NSPSNP+G+ Y+ Sbjct: 125 YWVSYTDIAILAEARPVILETGMDSGFKITPEQLAAAITPQTRLLFINSPSNPTGAAYTA 184 Query: 183 EELQALGAVLRKYPDILIATDDMYEHILLSGDGFVNILNACPDLKARTVVLNGVSKAYAM 242 EL ALG VLR++P +LIATDDMYE IL + FVNI NACPDL RTVVLNGVSKAYAM Sbjct: 185 AELAALGEVLRRHPRVLIATDDMYEKILFTEAPFVNIANACPDLLPRTVVLNGVSKAYAM 244 Query: 243 TGWRIGYCGGPAAIITAMENIQSQSTSNPNSIAQVAAEAALNGDQSCMVPMIEAFRERNQ 302 TGWRIGYC GP +I AM N+QSQSTSNP SIAQ AAEAAL+GDQS + PM++AFRER+ Sbjct: 245 TGWRIGYCAGPRELIQAMTNVQSQSTSNPCSIAQKAAEAALSGDQSVLAPMLQAFRERHD 304 Query: 303 FLTNALNSIAGIHCLLSEGAFYAFVDVRQAISRLNTQQILQNSSDIAFCNYVLEKAEVAA 362 ++ L + G+ C S+G FYAF +A++R LQ + DI +LE+AEVA Sbjct: 305 YVVARLQDMPGVACRPSQGTFYAFPSFHEAMAR------LQLADDITLAERLLEEAEVAL 358 Query: 363 VPGSAFGCEGYMRLSFATSMDNLQEAVKRIASLLS 397 VPGSAFG +GY+R+S+ATSMDNL++A+ RI + L+ Sbjct: 359 VPGSAFGADGYLRISYATSMDNLRKALDRIEAFLT 393 Lambda K H 0.318 0.133 0.380 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: 444 Number of extensions: 12 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: 397 Length of database: 394 Length adjustment: 31 Effective length of query: 366 Effective length of database: 363 Effective search space: 132858 Effective search space used: 132858 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 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