Align Serine acetyltransferase, plasmid; SAT; EC 2.3.1.30 (characterized)
to candidate BPHYT_RS21290 BPHYT_RS21290 serine acetyltransferase
Query= SwissProt::Q59967 (319 letters) >FitnessBrowser__BFirm:BPHYT_RS21290 Length = 308 Score = 338 bits (867), Expect = 1e-97 Identities = 174/296 (58%), Positives = 217/296 (73%), Gaps = 4/296 (1%) Query: 14 RSWGLDSIVSALSQASTDPLPHHLLSDQFYPLPSRESLGLILHGLRSVLFPRHFGDPELS 73 ++WGL+ IV+ L +AS + L LPSRE++ I+ GLR+ LFP H+G P+L+ Sbjct: 7 QNWGLEQIVADL-RASREQLHRTRHPLGIRELPSREAVVNIVAGLRAALFPTHYGAPDLT 65 Query: 74 VETTHYFIGNTLDKTLNLLNEQIRRELWLQHVTQGTPEATPAVLSQHASELTQAFAQALP 133 ET Y++G+TL+ TL LL EQIRR L TP+ L A ++ + F LP Sbjct: 66 DETVDYYVGHTLESTLRLLAEQIRRALRFLPEFGETPDVD---LQARAFDIAREFGTQLP 122 Query: 134 EIKRLLDSDVNAAYLGDPAAQSISEILFCYPGITAITFHRLAHRLYQLGLPLLARITAEV 193 I+ LL SD+ AA+ GDPAAQ I+EIL CYPG+ A+T HRLAH L++LG+PLLAR E+ Sbjct: 123 GIRALLVSDIQAAFTGDPAAQHITEILLCYPGVWAMTHHRLAHALHRLGVPLLARFINEI 182 Query: 194 SHSETGIDIHPGAAIGGSFFIDHGTGVVIGETCVIGDRVRIYQAVTLGAKSFPRDETGAL 253 +HS TGIDIHPGA IG SFFIDHGTGVVIGET +IG+RVR+YQAVTLGAKSF D G L Sbjct: 183 AHSATGIDIHPGATIGPSFFIDHGTGVVIGETAIIGERVRVYQAVTLGAKSFAADLDGTL 242 Query: 254 IKGQARHPVIEDDVVIYAGATLLGRITVGRGSTIGGNVWLTRSVPAGSFISQAQIR 309 +KG ARHP++EDDVVIYAGAT+LGR+T+GRGS IGGNVWLT SVP GS +SQ +IR Sbjct: 243 VKGNARHPIVEDDVVIYAGATILGRVTIGRGSVIGGNVWLTHSVPPGSSVSQGKIR 298 Lambda K H 0.320 0.137 0.405 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: 360 Number of extensions: 20 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: 319 Length of database: 308 Length adjustment: 27 Effective length of query: 292 Effective length of database: 281 Effective search space: 82052 Effective search space used: 82052 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