Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_012673667.1 SULAZ_RS05275 aspartate aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000021545.1:WP_012673667.1 Length = 399 Score = 329 bits (844), Expect = 8e-95 Identities = 165/393 (41%), Positives = 252/393 (64%), Gaps = 10/393 (2%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 RI++LP YVFA +++LKA+ R++G D+IDLGMGNPD +++ ++ + H Y Sbjct: 7 RIKRLPQYVFAVVNDLKARLRKEGEDIIDLGMGNPDLPPAPHIIEKLCESAKKKTTHRYS 66 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 +G R+AIT++Y +RY V LDP+ E + +GSKEGL+HL +A + PGD+ +VPSP Sbjct: 67 MSQGIPRLRKAITDFYKKRYDVDLDPEKEVIMTIGSKEGLAHLMLAMLEPGDIAMVPSPR 126 Query: 131 YPAHFRGPVIAGGTVHSLIL-------KPENDWLIDLTAIPEEVARKAKILYFNYPSNPT 183 YP H+ PVIAG +V ++ L + + +L ++ E+ +AK+L N+P+NPT Sbjct: 127 YPIHYYAPVIAGASVLTVPLPLEGSDSEKQEQFLKNIYETYEDSYPEAKVLILNFPNNPT 186 Query: 184 GATAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSK 243 T EFF+EIVAFA+K + ++HDL Y +L +DGY+ S+L++ GAKDI VE ++++K Sbjct: 187 TMTVDLEFFKEIVAFAKKKNLWIIHDLAYGDLCYDGYKAPSILQVEGAKDIAVETYSMTK 246 Query: 244 TYNMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYR 303 ++MAGWRV FV+GN ++ L+ LK+ LDYG F +Q A+ AL+ + + + Y Sbjct: 247 GFSMAGWRVAFVLGNETLVYNLKRLKSYLDYGTFTPIQVASIIALEGDYSVVEKARDTYS 306 Query: 304 TRRDFLIQGLGELGWDVPKTKATMYLWVKCPV---GMGSTDFALNLLQQTGVVVTPGNAF 360 R D L++GL + GW V K KATM+LW K P +GS +F+ LL + V V PG F Sbjct: 307 KRLDILVEGLNKAGWPVEKPKATMFLWAKIPEKFRHLGSIEFSKLLLTEGKVAVAPGIGF 366 Query: 361 GVAGEGYVRISLIADCDRLGEALDRIKQAGIRY 393 G GEGYVR +++ + R+ +A+ IK+ +Y Sbjct: 367 GEHGEGYVRFAVVENEKRIRQAISNIKKLMKKY 399 Lambda K H 0.321 0.140 0.427 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: 448 Number of extensions: 17 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: 403 Length of database: 399 Length adjustment: 31 Effective length of query: 372 Effective length of database: 368 Effective search space: 136896 Effective search space used: 136896 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 (21.8 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