Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_012971153.1 ALVIN_RS09725 phosphoserine transaminase
Query= SwissProt::Q59196 (362 letters) >NCBI__GCF_000025485.1:WP_012971153.1 Length = 372 Score = 294 bits (753), Expect = 2e-84 Identities = 158/364 (43%), Positives = 219/364 (60%), Gaps = 4/364 (1%) Query: 3 KRAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALL 62 + A NF+ GP ALP VL + G+SI+ +SHR + + + + L ALL Sbjct: 9 RNALNFSGGPGALPAVVLAETRQAIDAVPEIGLSILGVSHRSDWFAGLIEQTERDLRALL 68 Query: 63 GNPTGYKVLFIQGGASTQFAMIPMNFLK-EGQTANYVMTGSWASKALKEAKLIGDTHVAA 121 P + VL +QGGA+ QF+MIPM L+ G+ A Y+ TG W++K++ A+L GD V Sbjct: 69 DLPDSHAVLMLQGGATLQFSMIPMLLLRGSGRVAEYLRTGYWSAKSIAPARLEGDVRVLW 128 Query: 122 SSE--ASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDIL 179 E + + LP E++ AAYLH SNET+EG QF P V + DMSSD L Sbjct: 129 DGERQGAGFRRLPTADELECSPEAAYLHYVSNETVEGVQFHHIPGLDGVRRVCDMSSDFL 188 Query: 180 SRPFDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNT 239 SRP D +F LVYA AQKNLGP+GVT+V++R L+ + P +P +L Y +++ S+YNT Sbjct: 189 SRPCDPERFDLVYAHAQKNLGPAGVTLVVIRRALLDQVPPGIPDILDYRAHLQARSIYNT 248 Query: 240 PPSFGIYMVNEVLKWI-EERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDM 298 PP IY+V+ VL+W+ E+ GGLE + NR KA+ +Y+ ID+ Y G RS M Sbjct: 249 PPVMAIYVVSRVLRWLREDIGGLERMDALNRHKAACLYEVIDRYPDVYTGWAHPADRSRM 308 Query: 299 NITFRLASEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFK 358 N+ FRL + E E +F+ +E GF GLKGHRS+GG+RASIYN + + E L +FM F Sbjct: 309 NVVFRLPTPEREADFLHRAESAGFSGLKGHRSLGGIRASIYNGMSLAAVERLAKFMTDFA 368 Query: 359 RSRG 362 R G Sbjct: 369 RHGG 372 Lambda K H 0.316 0.132 0.378 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: 348 Number of extensions: 20 Number of successful extensions: 4 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: 372 Length adjustment: 30 Effective length of query: 332 Effective length of database: 342 Effective search space: 113544 Effective search space used: 113544 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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