Align Serine O-acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate GFF1439 PGA1_c14560 homoserine O-succinyltransferase MetA
Query= SwissProt::A0A120HUS7 (271 letters) >FitnessBrowser__Phaeo:GFF1439 Length = 305 Score = 141 bits (356), Expect = 1e-38 Identities = 80/260 (30%), Positives = 128/260 (49%), Gaps = 3/260 (1%) Query: 5 PLKIGILNVMHDKADTKTRLQHVLTHTAIPVDLHFYYPMTHYAGRTVPEAVSSILDPLDI 64 PL+IG+LN+M K T+ + ++ T + +DL H T E ++ P Sbjct: 35 PLRIGLLNLMPKKIQTENQFARLIGATPLQIDLSLIRMTEHQTRNTAAEHMAEFYRPFQE 94 Query: 65 HEVATMDGFIITGSPIETLEFDQVHYIAEVRTLLKTLSQHVPNQLYLCWGGMVALNYFFG 124 + DG IITG+PIE LEF+ V Y E+ + +V + +CWGGM +NYF G Sbjct: 95 IKDQRFDGLIITGAPIEHLEFEDVTYWDELCEVFDWTQTNVHSTFGVCWGGMAMINYFHG 154 Query: 125 ISKLILPHKLFGVYPQTILEP-HPLLKGLKNDFKSPHARYAEMDVRGIHADPRLTINATT 183 + K +L HK+FG + L+P P L+G +D P +R+ E+ I A P L + Sbjct: 155 VKKHLLDHKVFGCFRHQNLDPASPYLRGFSDDCVIPVSRWTEIRQSEIDARPGLRSLLGS 214 Query: 184 TKGKLFMVTEPTDTQTFVFSHIEYDRWGLDSEYKREVAAHPEIDYVRAKHYYHHKNDYDH 243 ++ +P+ ++F+H EYD L EY R+VA+ I+ +YY + Sbjct: 215 QDAGPCLIEDPSHRALYIFNHFEYDSDTLKQEYDRDVASGTPINV--PMNYYPDDDPSRK 272 Query: 244 PKFNWKKTQRTIFDNWIQHV 263 P+ W+ ++ NWI + Sbjct: 273 PQNRWRSHAHLLYGNWINDI 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: 242 Number of extensions: 9 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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