Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_089301141.1 CHB84_RS09325 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_900188115.1:WP_089301141.1 Length = 365 Score = 201 bits (511), Expect = 3e-56 Identities = 118/347 (34%), Positives = 189/347 (54%), Gaps = 12/347 (3%) Query: 6 VKKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITG 64 V +LL+ PGP+ PE ++ P++GH ++ +LL++T ++L+ V+ T+N T ++G Sbjct: 3 VDRLLLGPGPSNPYPEASQGLSQPLLGHLDPEFLSLLDETNDRLRAVWGTQNPRTLPLSG 62 Query: 65 SGTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVK 124 +G+ M+ A +N ++ GD V+ V G FGER ++ Y E +R+D +WG P V+ Sbjct: 63 TGSIGMEAAFANAVRPGDVVVIAVNGLFGERMVDVAGRYGAEVVRVDHDWG---RPIDVQ 119 Query: 125 EILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYD--ALYIVDTVSSLGGDYVNVDK 182 +LD + + V VH ETSTG R+ I + V + D AL + D V+S+ G V +D+ Sbjct: 120 RVLDAHPRPRLVGAVHAETSTGVRSDIGALARAVHERDDAALVLADCVTSIAGIPVEIDE 179 Query: 183 FHIDICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVGFYLDLLAYKKYYEEK---- 238 + +D+ G+QKC+ PGLA TVSE+AW + +YLDL Y Sbjct: 180 WGVDLAYAGTQKCIGVAPGLAPFTVSERAWH--SRVASPPTWYLDLGLIGNYVSGTDGGA 237 Query: 239 KQTPYTPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARS 298 + +T + +L+ L +L+EG+ RH + GL AMG+ELFA E R Sbjct: 238 RVYHHTAPTAMIASLHAGLGRILDEGLGEVYARHASAGQRLADGLRAMGLELFAAEGHRL 297 Query: 299 VTVTSAKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMG 345 +T+ + PEG++ +K R L +Y I + G A ++RIG MG Sbjct: 298 PELTTVRVPEGVDSAKVRTQLLEEYGIEIGAGAGPYAASVWRIGLMG 344 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: 313 Number of extensions: 7 Number of successful extensions: 5 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: 365 Length adjustment: 30 Effective length of query: 355 Effective length of database: 335 Effective search space: 118925 Effective search space used: 118925 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