Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate AZOBR_RS14010 AZOBR_RS14010 homoserine O-succinyltransferase
Query= SwissProt::Q2GAJ2 (301 letters) >FitnessBrowser__azobra:AZOBR_RS14010 Length = 307 Score = 412 bits (1059), Expect = e-120 Identities = 193/304 (63%), Positives = 234/304 (76%), Gaps = 4/304 (1%) Query: 1 MPIRIADNLPARRTLEAEGVIVMSETEAARQDIRPMRIALLNLMPDKITTETQIARLLGA 60 MPIRI ++LPA L+ EGV+VM E +A RQDIRP+R LLNLMPDKI TETQIARLLG Sbjct: 1 MPIRIPNDLPAFTALQTEGVMVMQEADAIRQDIRPLRFGLLNLMPDKIRTETQIARLLGN 60 Query: 61 TPLQVDLELVRISDHVSKNTSAGHISAFYRPWDDVRAEKYDGLIVTGAPVETIPYEEVSY 120 TPLQV+L L+RI++HV +NT+A H+SAFYR W+D R E +DG I+TGAPVET+P+EEVSY Sbjct: 61 TPLQVELSLIRITNHVPRNTAADHMSAFYRSWEDARRETFDGFIITGAPVETMPFEEVSY 120 Query: 121 WDELRRIFDWSQSNVHRTLSVCWGAMAALYHFHGIEKHGLPTKASGVFRHVNHAPASPWM 180 WDEL +FDW+QS+VH L++CW A AA++HFHG+ KH LP KASGVFRH N APASP++ Sbjct: 121 WDELCSVFDWTQSHVHACLNICWAAQAAVHHFHGVPKHLLPRKASGVFRHRNRAPASPYL 180 Query: 181 RGLPDVFDVPVSRWSEVRREDLPEGRGLSVLADSAETGLCLIDDPAMRTLHMFNHLEYDT 240 GL D +PVSRW+EVR +DLP GL VL DS ETG CL++D A R+LHMFNH+EYDT Sbjct: 181 CGLSDGVPIPVSRWTEVREDDLPPESGLRVLLDSPETGPCLLEDAAHRSLHMFNHIEYDT 240 Query: 241 LTLAGEYARDEGK----YLPRNYFPGDDPQAMPANTWRGHGHLLYGNWINETYQTTPYDL 296 TL EY RD K +P YFP DDP P N WR H HLL+ NWIN+ YQTTP++L Sbjct: 241 DTLRNEYVRDVAKDAATPVPHGYFPDDDPSQPPENRWRSHAHLLFANWINQIYQTTPFEL 300 Query: 297 ADIG 300 + IG Sbjct: 301 SRIG 304 Lambda K H 0.320 0.137 0.430 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: 388 Number of extensions: 12 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: 301 Length of database: 307 Length adjustment: 27 Effective length of query: 274 Effective length of database: 280 Effective search space: 76720 Effective search space used: 76720 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: 48 (23.1 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