Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_013683113.1 ARCVE_RS02015 aminotransferase
Query= curated2:O67781 (394 letters) >NCBI__GCF_000194625.1:WP_013683113.1 Length = 384 Score = 225 bits (574), Expect = 1e-63 Identities = 154/394 (39%), Positives = 221/394 (56%), Gaps = 21/394 (5%) Query: 5 LASRVSHLKPSPTLTITAKAKELRAKGVDVIGFGAGEPDFDTPDFIKEACIRALREGKTK 64 ++ RV LKPS K EL DVI G GEPDF P I+E I AL +G T Sbjct: 8 VSKRVQELKPSGI----RKFFELIIGRDDVISLGVGEPDFAVPWRIREEIIYALEKGITS 63 Query: 65 YAPSAGIPELREAIAEKLLKENKVEYKPSEIVVSAGAKMVLFLIFMAILDEGDEVLLPSP 124 Y + G+ ELREAIAE K VE ++++ G + + AIL+EG+ VL+P P Sbjct: 64 YTSNFGLKELREAIAEYYRKFG-VECSAESVLITTGVSEGVDIALRAILNEGEAVLVPEP 122 Query: 125 YWVTYPEQIRFFGGVPVEVPLKKEKGFQLSLEDVKEKVTE-RTKAIVINSPNNPTGAVYE 183 +V+Y GG V +P + F+LS E + E E + KAIVIN PNNPTG Y Sbjct: 123 CYVSYAPLSSLAGGEVVAIPTTPD--FKLSYELIDEYAKETKPKAIVINYPNNPTGVSYS 180 Query: 184 EEELKKIAEFCVERGIFIISDECYEYFVYGDAKFVSPASFSDEVKNITFTVNAFSKSYSM 243 ++EL++IA+ +E + +ISDE Y Y K +S AS + ++ +N FSK+++M Sbjct: 181 KKELEEIADAAIEHDMIVISDEIYAELSY-TFKHISIASLNG-MEERAIILNGFSKAFAM 238 Query: 244 TGWRIGYVACPEEYAKVIASLNSQSVSNVTTFAQYGALEALKNPKSKDFVNEMRNAFERR 303 TG RIGY P + + + ++ + AQ GALEAL+N +D + EMR + RR Sbjct: 239 TGLRIGYAIAPADILEGMLKIHQYCMLCAPVTAQIGALEALRN--GEDELEEMRAEYIRR 296 Query: 304 RDTAVEELSKIPGMDVVKPEGAFYIFPDFSAYAEKLG-GDVKLSEFLLEKAKVAVVPGSA 362 R+ V+ + K+ +DV P+GAFY FP E G + +E LL + VAVVPG+A Sbjct: 297 RNFFVKRVGKV--LDVKMPDGAFYAFPSI----ESTGLSSEEFAERLLFEKNVAVVPGNA 350 Query: 363 FG--APGFLRLSYALSEERLVEGIRRIKKALEEI 394 FG G++R +YA+S E+L E + RI + +EE+ Sbjct: 351 FGECGEGYIRCAYAVSMEKLREAVDRIVEFVEEL 384 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: 483 Number of extensions: 28 Number of successful extensions: 8 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: 384 Length adjustment: 30 Effective length of query: 364 Effective length of database: 354 Effective search space: 128856 Effective search space used: 128856 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