Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_024850635.1 N745_RS0102880 phosphoserine transaminase
Query= SwissProt::Q59196 (362 letters) >NCBI__GCF_000526715.1:WP_024850635.1 Length = 367 Score = 319 bits (817), Expect = 8e-92 Identities = 169/358 (47%), Positives = 231/358 (64%), Gaps = 4/358 (1%) Query: 7 NFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALLGNPT 66 NF+AGP ALP VL++ Q + TGMS++ MSHR A + +V EA+A + LLG Sbjct: 8 NFSAGPGALPQSVLDQVQQSIIALPETGMSVLGMSHRSAWFLSVLEEAEANVRELLGIDD 67 Query: 67 GYKVLFIQGGASTQFAMIPMNFLK-EGQTANYVMTGSWASKALKEAKLIGDTHVAASSEA 125 + VLF+QGGA+ QF+MIP+ L+ G A Y+ TG W KA+ EAK G V S E Sbjct: 68 EFHVLFLQGGATQQFSMIPITLLRGSGLEAEYLQTGYWGQKAVAEAKKEGKVKVLWSGED 127 Query: 126 SNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDILSRPFDL 185 + Y LP +E+ +AAY H SNET+EG QF SVP + DMSSD LSRP + Sbjct: 128 AGYHRLPDDEELTFSKDAAYFHYVSNETVEGLQFHRVLGHDSVPRVCDMSSDFLSRPIEA 187 Query: 186 NQFGLVYAGAQKNLGPSGVTVVIVREDLV--AESPKHLPTMLRYDTYVKNNSLYNTPPSF 243 N+F ++YA AQKN+GP+GVTVV++++ ++ A +LP+ L Y V +S YNTPP F Sbjct: 188 NRFSIIYAHAQKNIGPAGVTVVLIKKSVLDSAREQGNLPSFLDYRNQVSAHSNYNTPPVF 247 Query: 244 GIYMVNEVLKWI-EERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNITF 302 IY+ V +WI +E GGL+ ++ NRKKA L+Y AID S GFY G + RS MN+ F Sbjct: 248 AIYVTLLVTRWIKDEVGGLKNMEAINRKKAELLYQAIDGSDGFYTGWARQEDRSLMNVAF 307 Query: 303 RLASEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFKRS 360 LA++ELE+ F++A+ + GF GL GHRS+GG+RASIYN + + E LV FM F+++ Sbjct: 308 NLATQELEQSFLQAAGEAGFSGLDGHRSLGGVRASIYNGLTISAAEQLVDFMSSFQQA 365 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: 339 Number of extensions: 13 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: 367 Length adjustment: 29 Effective length of query: 333 Effective length of database: 338 Effective search space: 112554 Effective search space used: 112554 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