Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_029907839.1 P166_RS0100985 phosphoserine transaminase
Query= SwissProt::Q9RME2 (361 letters) >NCBI__GCF_000711315.1:WP_029907839.1 Length = 367 Score = 314 bits (804), Expect = 3e-90 Identities = 162/356 (45%), Positives = 230/356 (64%), Gaps = 4/356 (1%) Query: 7 NFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRELLQIPN 66 NF+AGP ALP+ L + Q+ +L +T MSV+ +SHRS + V E+A+ +R+LL I Sbjct: 8 NFSAGPGALPETVLNQVQESILTLPETGMSVLGMSHRSDWFSSVLEEAETNIRQLLGIGE 67 Query: 67 DYQILFLQGGASLQFTMLPMNLLTK-GTIGNYVLTGSWSEKALKEAKLLGETHIAASTKA 125 ++ +LFLQGGA+ QF+M+P+ LL G Y+ TG W +KA+ EA+ G+ S +A Sbjct: 68 EFHVLFLQGGATQQFSMIPITLLRNTGREAEYLQTGYWGKKAIVEAEKEGKVKTLWSGQA 127 Query: 126 NSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSRPLKV 185 + Y+ +PD +E +E AYLH SN T+ G Q+ + P + DMSSD LSRP+ Sbjct: 128 DGYKRLPDDAELSFSEQAAYLHYASNETVEGLQFHRVLGPDSVPRVCDMSSDFLSRPVDA 187 Query: 186 NQFGMIYAGAQKNLGPSGVTVVIVKKDLLNTKVEQ--VPTMLQYATHIKSDSLYNTPPTF 243 ++F +IYA AQKN+GP+GVTVV++KK LL++ EQ +P+ L Y H+ + S YNTPP F Sbjct: 188 DRFSIIYAHAQKNIGPAGVTVVLIKKSLLDSAQEQPNLPSFLDYRNHVATHSNYNTPPVF 247 Query: 244 SIYMLRNVLDWIKD-LGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVTF 302 +IY+ V WIKD +GG E + N KA+++Y ID+S GFY G + K RS MN TF Sbjct: 248 AIYVTLLVTRWIKDVVGGLENMENINHRKAELLYQAIDDSQGFYQGWSRKEDRSYMNATF 307 Query: 303 NLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFK 358 NL EL Q+FL +A + GF GL+GHRS+GG RAS+YN + + A L + M F+ Sbjct: 308 NLTTPELEQRFLQEAAQAGFSGLDGHRSLGGVRASLYNGLTVPAVEQLLDFMSTFE 363 Lambda K H 0.316 0.132 0.372 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: 367 Number of extensions: 12 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: 361 Length of database: 367 Length adjustment: 29 Effective length of query: 332 Effective length of database: 338 Effective search space: 112216 Effective search space used: 112216 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