Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_027720641.1 H589_RS0102885 pyridoxal phosphate-dependent aminotransferase
Query= curated2:A5FRC5 (388 letters) >NCBI__GCF_000425265.1:WP_027720641.1 Length = 391 Score = 199 bits (507), Expect = 9e-56 Identities = 120/389 (30%), Positives = 203/389 (52%), Gaps = 13/389 (3%) Query: 1 MKLSKRIENLPPYLFVQISKKIAEKRAKGEDVISFAIGDPDLPTPKHILAELCKAAEDPS 60 MK+SKR+ P + ++ K E RA+G++++S A+G+PD PTP+H+ E K A D Sbjct: 1 MKISKRLMRAKPSATLAVNAKAQELRAQGKEIVSLAVGEPDFPTPQHV-CEAMKKAVDDG 59 Query: 61 NHRYPETEGLPVLRKAMAEWYQKRFGVKLNPDTEVLPLIGSKEGIGHAAWCFLDPGDIAL 120 HRY GLP LR+A+A++Y + +GVK D ++ G K+ + + +D GD L Sbjct: 60 FHRYTAVPGLPELRRAVADYYGRFYGVKATADNTIIS-NGGKQSLYNLFMALIDQGDEVL 118 Query: 121 VPNPAYPVYAISSQLAGAEVFNLPLNKGNNFLPNLEAIPQNILSKAKVLWINYPNNPTGA 180 +P P + Y +LA +P + FL ++ + + K+L IN P+NPTG Sbjct: 119 IPAPYWVSYPAMVELADGVPVIVPTTAESGFLAQIKDLEACCTERTKLLVINTPSNPTGG 178 Query: 181 VAGLSFFQEVANFAAKHNLAVCHDGPYSEIAF--DGYKPVSFLEADGAKDVGIEFHSLSK 238 + E+AN+A + + D Y + + Y +S +DV I +LSK Sbjct: 179 HYPQAHLDEIANWAKSKGIFIVSDEVYDRLVYAPAEYSTLSTFWEKNPEDVAI-VGALSK 237 Query: 239 SYNMTGWRIGMAVGNAKMIDALRRFKSNLDSGIPQAIQLMAIAALNGSQEIINQNCAIYQ 298 S+ MTGWR+G A+ + ++ A+ + + S + Q AIAA +GS + I++ ++ Sbjct: 238 SFCMTGWRVGTALAHPDLVKAMVKIQGQSTSNVNTMAQKAAIAAFDGSWDFIDEMRDVFH 297 Query: 299 RRRDRLVEALRN-IGMEVTAPKASLYIWAPVPESYT-----SASFATELLDKTGVVVTPG 352 RRRD E + + G+ P + Y++ + YT SAS T++L++ G+ + PG Sbjct: 298 RRRDIAHEIITSWPGVVCPKPDGAFYLFPVLENFYTEETPDSASMCTKILEEVGIALVPG 357 Query: 353 TGYGTAGEGYIRLSLTVPDEQIEKGIAKL 381 + +G + IR S V DE ++ + K+ Sbjct: 358 SAFG--DDRCIRFSYAVDDEVLKTSLGKI 384 Lambda K H 0.317 0.135 0.401 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: 363 Number of extensions: 20 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: 388 Length of database: 391 Length adjustment: 30 Effective length of query: 358 Effective length of database: 361 Effective search space: 129238 Effective search space used: 129238 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 (21.6 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