Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_015944380.1 DHAF_RS15445 diaminopimelate aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >NCBI__GCF_000021925.1:WP_015944380.1 Length = 388 Score = 149 bits (375), Expect = 2e-40 Identities = 117/380 (30%), Positives = 173/380 (45%), Gaps = 22/380 (5%) Query: 24 RELAAAGRDVIGLGAGEPDFDTPDNI-KAAAKRAIDAGRTKYTAVDGIPELKRAICEKFE 82 +EL AG+ +I L G PD I K A+ +D G YT G + ++ Sbjct: 22 KELEKAGKQLINLSIGSPDRSPSAEIRKVLAEGVLDGGSYGYTLTRGTESFRSGCARWYK 81 Query: 83 RENGLKYTPAQVTVGTGGKQI-LYNALVATLNPGDEVIIPAPYWVSYPDMVLLAGGTPVS 141 G+ P + + G Q L + +A +PGD +IP P + Y ++LAGG V+ Sbjct: 82 ERFGVNLDPEKEVLPLMGSQDGLAHIFLALCDPGDVALIPDPGYPIYTAGLVLAGGEKVA 141 Query: 142 VAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTRAELAALCEVL--MRHPQV 199 + E GF +E + + K N P+NPT A A L+ EV+ R ++ Sbjct: 142 LPLREENGFLPDLSAIEDEVAQQAKIMFLNYPNNPTAAV---APLSFFEEVVDFARRNRI 198 Query: 200 WIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCMTGWRIGYAAGPVELIR 259 + D Y L FD + + Q+ PG + + + VSK Y + G R+G+A G E+I Sbjct: 199 VVCHDAAYSELAFDGYRPVSFLQV-PGAKEVGIEFHSVSKTYNLAGVRLGFAVGNGEIIG 257 Query: 260 AMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRRDLVVSMLNEAKGVTCPN 319 A+ ++S A A ALS QE + NR A+Q RRD+ V +A G + P+ Sbjct: 258 ALAELKSNIDYGVFEPALQAGAYALSASQENVEQNRRAYQERRDIWVKGCAQA-GWSMPS 316 Query: 320 PEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAVVFGAAFGL--SPNFRIS 377 P G+ +++ + D +FA AL E GV VV G AFG RI Sbjct: 317 PRGSMFIWAPV-----------PTAQDSRSFAFALAREAGVIVVPGVAFGEYGEGYVRIG 365 Query: 378 YATADEVLREACARIQAFCA 397 EVL+EA R+Q F A Sbjct: 366 MVQDQEVLQEAVRRVQEFLA 385 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: 357 Number of extensions: 24 Number of successful extensions: 6 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: 388 Length adjustment: 31 Effective length of query: 369 Effective length of database: 357 Effective search space: 131733 Effective search space used: 131733 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