Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate GFF2657 PS417_13545 arginine aminotransferase
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__WCS417:GFF2657 Length = 664 Score = 228 bits (580), Expect = 5e-64 Identities = 138/375 (36%), Positives = 207/375 (55%), Gaps = 15/375 (4%) Query: 19 VNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELREALA 78 ++ A + QG D++ L+ G+PDF TP + +AA AL +G T Y G P LREA+A Sbjct: 20 IHHAAFQAASQGEDIIILSVGDPDFATPSFITDAAVSALREGDTHYTEIPGRPALREAIA 79 Query: 79 EKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGV 138 ++ + +++ E I G + ALF +L GDEV+VL P +V+Y ++ +G Sbjct: 80 ARYSKTLARALSAENVITVAGAQNALFVTSLCLLQAGDEVLVLDPMYVTYEATLKASGAT 139 Query: 139 VVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDF 198 +V V PE GF D + + AITPRT+A+ ++PNNPTG V + L+A+A LA+ D Sbjct: 140 LVRVPCSPESGFRLDAQLLGAAITPRTRAIFFSNPNNPTGVVLNLQELQAIADLAIARDL 199 Query: 199 YLVSDEIYEHLLYEGEHFS----PGRVAPEHTLTVNGAAKAFAMTGWRIGYACG-PKEVI 253 ++V DE+YE L+++GE+ S PG E + + +K+ AMTGWRIG+ P+ V Sbjct: 200 WVVVDEVYESLVFDGEYHSLAALPGMA--ERCVVIGSLSKSHAMTGWRIGWIIATPQMVA 257 Query: 254 KAMASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTAL-GL 312 A V S P + + AT L + + ++ RE YRRRRDL++ GL+A G+ Sbjct: 258 HAETLVLSMLYGLPGFVMEAATAAVLAHDDVTQGM----REIYRRRRDLVMAGLSACPGI 313 Query: 313 KAVRPSGAFYVLMDTSPIAPDEVRAAERLL-EAGVAVVPGTDFA--AFGHVRLSYATSEE 369 K P +VL+D + A RL EAGV+V+ F A G VRLS+ EE Sbjct: 314 KVQAPQAGMFVLVDVRGTGLGSLDFAWRLFREAGVSVLDAAAFGAPAQGFVRLSFTLGEE 373 Query: 370 NLRKALERFARVLGR 384 L +A +R A + + Sbjct: 374 RLSEACQRIAHFVAK 388 Lambda K H 0.317 0.133 0.379 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: 542 Number of extensions: 23 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 385 Length of database: 664 Length adjustment: 34 Effective length of query: 351 Effective length of database: 630 Effective search space: 221130 Effective search space used: 221130 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 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