Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_078428470.1 BK574_RS09735 aminotransferase class V-fold PLP-dependent enzyme
Query= curated2:O67781 (394 letters) >NCBI__GCF_002019605.1:WP_078428470.1 Length = 394 Score = 363 bits (932), Expect = e-105 Identities = 185/392 (47%), Positives = 260/392 (66%), Gaps = 6/392 (1%) Query: 5 LASRVSHLKPSPTLTITAKAKELRAKGVDVIGFGAGEPDFDTPDFIKEACIRALREGKTK 64 LA RVS L PS TL ITAKAK LR +G DVIG GAGEPDF+TP +I +A ++++ EG TK Sbjct: 3 LAKRVSTLTPSSTLAITAKAKALREQGHDVIGLGAGEPDFNTPQYIIDAAVKSMEEGHTK 62 Query: 65 YAPSAGIPELREAIAEKLLKENKVEYKPSEIVVSAGAKMVLFLIFMAILDEGDEVLLPSP 124 Y PS G+ +L++AI K + + Y +EI+V +GAK L+ +F AILDEGDEV++P+P Sbjct: 63 YTPSGGLSKLKDAIIGKFKDDQNITYSANEIIVCSGAKHALYTLFQAILDEGDEVIIPTP 122 Query: 125 YWVTYPEQIRFFGGVPVEVPLKKEKGFQLSLEDVKEKVTERTKAIVINSPNNPTGAVYEE 184 YWV+YPEQ++ GG PV + K+ F+++++ ++ + ++TKA ++NSP+NPTG++Y E Sbjct: 123 YWVSYPEQVKLAGGNPVYIEGKESNEFKVTVDQLEAAINDKTKAFILNSPSNPTGSMYSE 182 Query: 185 EELKKIAEFCVERGIFIISDECYEYFVYGDAKFVSPASFSDEVKNITFTVNAFSKSYSMT 244 +E+K + + C++ I I+SDE YE VY A +S A S+E+K T +N SKS+SMT Sbjct: 183 DEMKALGDVCLKHDILIVSDEIYEKLVYDGAVHISIAQLSNELKEQTVIINGVSKSHSMT 242 Query: 245 GWRIGYVACPEEYAKVIASLNSQSVSNVTTFAQYGALEALKNPKSKDFVNEMRNAFERRR 304 GWRIGY A E K + +L S S SN T AQYG + A V +MR AFE R Sbjct: 243 GWRIGYAAGNSEVIKAMTNLASHSTSNPTANAQYGTIAAYTEDDGS--VEKMRQAFEERL 300 Query: 305 DTAVEELSKIPGMDVVKPEGAFYIFPDFSAYAEKLGGDVKLSEF---LLEKAKVAVVPGS 361 ++L IPG+ VKP+GAFY+FP+ A G D + ++ LL+K KVA+VPGS Sbjct: 301 HKVYDQLIAIPGLSCVKPKGAFYLFPNAKEAASICGFD-NVDDWVTALLDKEKVALVPGS 359 Query: 362 AFGAPGFLRLSYALSEERLVEGIRRIKKALEE 393 FGAP +RLSYA S E + E + RI + +E+ Sbjct: 360 GFGAPENVRLSYATSLEAIQEALERIARFIEK 391 Lambda K H 0.317 0.135 0.383 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: 450 Number of extensions: 18 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: 394 Length of database: 394 Length adjustment: 31 Effective length of query: 363 Effective length of database: 363 Effective search space: 131769 Effective search space used: 131769 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