Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate Pf1N1B4_351 Phosphoserine aminotransferase (EC 2.6.1.52)
Query= BRENDA::P23721 (362 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_351 Length = 292 Score = 322 bits (826), Expect = 6e-93 Identities = 164/294 (55%), Positives = 202/294 (68%), Gaps = 2/294 (0%) Query: 69 VLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVTVDGL 128 VLF GG QFA +PLN+L + TADY+D G W+ AI+EA +Y NV D Sbjct: 1 VLFLQGGASQQFAQIPLNLLPESGTADYIDTGIWSQKAIEEASRYGHVNVAATAKPYDYF 60 Query: 129 RAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPIDVSR 188 A+ EW+LS +AAY+HY PNETI G+ P+ G DV + AD SS ILSRP+DVSR Sbjct: 61 -AIPGQNEWKLSKDAAYVHYAPNETIGGLEFQWIPETG-DVPLVADMSSDILSRPVDVSR 118 Query: 189 YGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTFAWYL 248 +G+IYAGAQKNIGP+G+ + IVREDLLG A CP++L+Y + DNGSM+NTPPT AWYL Sbjct: 119 FGMIYAGAQKNIGPSGIVVNIVREDLLGHARSICPTMLNYKVAADNGSMYNTPPTLAWYL 178 Query: 249 SGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQLADSA 308 SGLVF+WLK GGV + K+N+ K LY ID S Y N + K++RS MNVPF+LAD Sbjct: 179 SGLVFEWLKEQGGVEAIGKLNEVKQRTLYDFIDASGLYSNPINKSDRSWMNVPFRLADDR 238 Query: 309 LDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362 LDK FL + GL LKGHR VGGMRASIYNA+ + V AL +M EFE+ HG Sbjct: 239 LDKPFLAGADERGLLNLKGHRSVGGMRASIYNAVDIVAVNALVSYMAEFEKEHG 292 Lambda K H 0.319 0.136 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: 339 Number of extensions: 11 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: 362 Length of database: 292 Length adjustment: 28 Effective length of query: 334 Effective length of database: 264 Effective search space: 88176 Effective search space used: 88176 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