Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_028585625.1 G494_RS0117930 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::A0A6F8T0V6 (393 letters) >NCBI__GCF_000429965.1:WP_028585625.1 Length = 402 Score = 376 bits (965), Expect = e-109 Identities = 192/393 (48%), Positives = 260/393 (66%), Gaps = 4/393 (1%) Query: 3 LAKRVASLTPSATLAITAKAKELKAAGYDVIGLGAGEPDFNTPQHIIAAAIKTMNEGHTK 62 LA RV + PS TLA+ AKAK L+A G DV+ GEPDF TP HI AA + +++GHT+ Sbjct: 8 LADRVLQIAPSPTLAVNAKAKALRATGADVLNFSVGEPDFPTPAHICAAGKQAIDDGHTR 67 Query: 63 YTPSGGLPALKEEIIKKFARDQGLSYEPAEIIVCVGAKHALYTLFQVLLDEGDEVIIPTP 122 YTP G+ L+E I ++F D G Y+P +I VC G KH LY LFQ L+ GDE++IP P Sbjct: 68 YTPVPGVLELREAISQRFKEDHGWDYDPDQIQVCCGGKHGLYNLFQAALNPGDEILIPAP 127 Query: 123 YWVSYPEQVKLAGGVPVYVEGLEENDFKMTPDQLKQAITPKTKAVIINSPSNPTGMIYTA 182 YWVSYP V+LAGGVPV V EE F + P L++ +TPKT+ +++NSPSNPTG + ++ Sbjct: 128 YWVSYPPMVQLAGGVPVIVPLDEEKGFDLDPATLEKYVTPKTRGIVLNSPSNPTGAVLSS 187 Query: 183 EELKALGEVCLAHGVLIVSDEIYEKLIYGGAKHVSIAELSPELKEQTIIINGVSKSHSMT 242 L+A+ + L + L+VSD+IYE L Y I ++ P +KEQ II+NGVSKS SMT Sbjct: 188 RALEAVAALALENDWLVVSDDIYETLTYEQGVLPHILDVEPAIKEQLIILNGVSKSFSMT 247 Query: 243 GWRIGYAAGPKDIIQAMTDLASHSTSNPTSIAQYAAIAAYSGPQEPVEQMRQAFEERLNI 302 GWRIGY+AGP +I+AM + S STSNP + +QYAA+AA SGPQ+ + M++AF R Sbjct: 248 GWRIGYSAGPLHLIKAMNKIQSQSTSNPAAPSQYAALAALSGPQDFPKVMQEAFAPRRAY 307 Query: 303 IYDKLVQIPGFTCIKPQGAFYLFPN--ARKAADMAGCRTVDEFVAA--LLEEAKVALVPG 358 + + L IPG +C+ P G+FY+FPN A VD A LL+EA +A VPG Sbjct: 308 MVETLNSIPGVSCVSPGGSFYVFPNFSAYYGKAFYNHAIVDSLSLADYLLDEAMIATVPG 367 Query: 359 SGFGAPDYVRLSYATSLEALETAIERIRRFMEA 391 FGA D++R S+ATS+E L + R+++ +EA Sbjct: 368 VAFGADDFIRFSFATSMEVLCEGMTRLKKALEA 400 Lambda K H 0.316 0.133 0.380 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: 455 Number of extensions: 18 Number of successful extensions: 2 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: 393 Length of database: 402 Length adjustment: 31 Effective length of query: 362 Effective length of database: 371 Effective search space: 134302 Effective search space used: 134302 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