Align Serine O-acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate WP_011337925.1 RSPH17029_RS08305 homoserine O-succinyltransferase
Query= SwissProt::A0A120HUS7 (271 letters) >NCBI__GCF_000015985.1:WP_011337925.1 Length = 305 Score = 125 bits (315), Expect = 8e-34 Identities = 76/260 (29%), Positives = 120/260 (46%), Gaps = 3/260 (1%) Query: 5 PLKIGILNVMHDKADTKTRLQHVLTHTAIPVDLHFYYPMTHYAGRTVPEAVSSILDPLDI 64 PL+IG+LN+M K T+ + ++ T + +D H T E + + P Sbjct: 35 PLRIGLLNLMPKKIQTENQFARLIGATPLQIDFQLIRMTEHQTKNTAAEHMEAFYRPFQE 94 Query: 65 HEVATMDGFIITGSPIETLEFDQVHYIAEVRTLLKTLSQHVPNQLYLCWGGMVALNYFFG 124 + DG IITG+PIE L+F V Y E+ ++ +V + +CWGGM + +F Sbjct: 95 VKHEKFDGLIITGAPIEHLDFADVTYWDELCEVMDWTQTNVQSTFGVCWGGMAMIYHFHR 154 Query: 125 ISKLILPHKLFGVYPQTILEP-HPLLKGLKNDFKSPHARYAEMDVRGIHADPRLTINATT 183 + K L K FG + + P P L+G +DF P +R+ EM I A P L + Sbjct: 155 VQKHRLQAKAFGCFRHRNVAPTSPYLRGFSDDFVIPVSRWTEMRQAEIDAAPGLRTLLAS 214 Query: 184 TKGKLFMVTEPTDTQTFVFSHIEYDRWGLDSEYKREVAAHPEIDYVRAKHYYHHKNDYDH 243 + +V +P ++F+H EYD L EY R+VA I+ +YY + Sbjct: 215 DEAGPCLVEDPGHRALYIFNHFEYDSDTLKQEYDRDVANGKPINV--PANYYPDDDPSKP 272 Query: 244 PKFNWKKTQRTIFDNWIQHV 263 P W+ ++ NWI + Sbjct: 273 PLNRWRSHAHLLYGNWINEI 292 Lambda K H 0.322 0.138 0.434 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: 258 Number of extensions: 13 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: 271 Length of database: 305 Length adjustment: 26 Effective length of query: 245 Effective length of database: 279 Effective search space: 68355 Effective search space used: 68355 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 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 16 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