Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate 351941 BT2413 homoserine O-succinyltransferase (NCBI ptt file)
Query= BRENDA::Q03BU2 (271 letters) >FitnessBrowser__Btheta:351941 Length = 305 Score = 143 bits (361), Expect = 4e-39 Identities = 78/259 (30%), Positives = 133/259 (51%), Gaps = 3/259 (1%) Query: 5 PLKIGILNVMHDKADTKTRLQHVLTHTAIPVDLHFYYPMTHYAGRTVPEAVSSILDPLDI 64 PL+I ILN+M K T+T L +L++T + V++ F +H + T E + + + Sbjct: 35 PLRIVILNLMPLKITTETDLVRLLSNTPLQVEISFMKIKSHTSKNTPIEHMQTFYTDFEQ 94 Query: 65 HEVATMDGFIITGSPIETLEFDQVHYIAEVRTLLKTLSQHVPNQLYLCWGGMVALNYFFG 124 DG IITG+P+E ++F++V Y E+ + HV + LY+CW L + +G Sbjct: 95 MRNEKYDGMIITGAPVEQMDFEEVTYWEEITEIFDWARTHVTSTLYICWAAQAGLYHHYG 154 Query: 125 ISKLILPHKLFGVYPQTILEP-HPLLKGLKNDFKSPHARYAEMDVRGIHADPRLTINATT 183 + K L K+FG++ +LEP H + +G + F PH+R+ E+ I P LT+ + + Sbjct: 155 VPKYPLDQKMFGIFEHRVLEPFHSIFRGFDDCFYVPHSRHTEVRREDILKVPELTLLSES 214 Query: 184 TKGKLFMATEPTDTQTFVFSHIEYDRWGLDSEYKREVAAHPEIDYVRAKHYYHHKNDYDH 243 ++MA + FV H EY + LD+EY+R++ I+ R +YY + Sbjct: 215 KDAGVYMAMARGGREFFVTGHSEYSPYTLDTEYRRDLGKGLPIEIPR--NYYVDDDPDKG 272 Query: 244 PKFNWKKTQRTIFDNWIQH 262 P W+ +F NW+ + Sbjct: 273 PLVRWRAHANLLFSNWLNY 291 Lambda K H 0.322 0.138 0.433 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: 250 Number of extensions: 16 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 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