Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_085772716.1 B1812_RS17405 aminotransferase class V-fold PLP-dependent enzyme
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_002117405.1:WP_085772716.1 Length = 397 Score = 214 bits (545), Expect = 3e-60 Identities = 134/382 (35%), Positives = 204/382 (53%), Gaps = 9/382 (2%) Query: 7 KKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEN-DTFLITGS 65 + L +PGPT +P V AM + HR+ + +L++ +LKKVF TE F+ S Sbjct: 9 RNFLFVPGPTNLPDRVQRAMMVASEDHRSPIFPDLVKPLFPQLKKVFETEKAHAFIFPAS 68 Query: 66 GTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKE 125 GT + AI+N + GDKVL G F + ++ E ++ + WG +PE ++E Sbjct: 69 GTGGWEAAITNTLSPGDKVLAQRFGQFSHLWIDLANRLGLEVVKQERPWGTGNDPELIEE 128 Query: 126 IL--DKYDDIKAVTVVHNETSTGARNPIKEIGEVVK--DYDALYIVDTVSSLGGDYVNVD 181 L DK +IKAV HNET+TG + I + + + + AL VD VSS+ ++D Sbjct: 129 TLKADKNHEIKAVFATHNETATGVTSDIGAVRKAIDAAKHPALLFVDGVSSVASLPFHMD 188 Query: 182 KFHIDICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVGFYLDLLAYKKYYEEKKQT 241 K+ +D+ V+GSQK P GL + S KA E K N + ++ K E Sbjct: 189 KWGVDVIVSGSQKGFMLPAGLLLMAASPKAVEAGKSNKSRRAYFEFQDMIKN--NETGYF 246 Query: 242 PYTPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKE-RARSVT 300 PYTPS+ L + L +L ++ EEG++ KRH LA RA +EA G++ AKE + S T Sbjct: 247 PYTPSIPLLHGLKESLAILFEEGLDQVYKRHHHLASGCRAAVEAWGLKTCAKEPKWNSDT 306 Query: 301 VTSAKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKEVLATLACVE 360 VT+ PEG + +K +YN+ + G +AGK+FRIGH+G E +L +A E Sbjct: 307 VTAIVVPEGFDAAKVIATAYKRYNLALGAGLSEVAGKVFRIGHLGDLNELMLLGAIAGAE 366 Query: 361 LALKELGFEVKE-SGVEVAKEV 381 +A+ + G +++ SGV A+ V Sbjct: 367 MAMLDNGIKIQPGSGVAAAQAV 388 Lambda K H 0.316 0.135 0.379 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: 333 Number of extensions: 19 Number of successful extensions: 6 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: 385 Length of database: 397 Length adjustment: 31 Effective length of query: 354 Effective length of database: 366 Effective search space: 129564 Effective search space used: 129564 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: 50 (23.9 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