Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_086511813.1 BZY95_RS20880 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_002151265.1:WP_086511813.1 Length = 406 Score = 253 bits (645), Expect = 9e-72 Identities = 147/381 (38%), Positives = 219/381 (57%), Gaps = 9/381 (2%) Query: 4 KQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSG 63 + L IPGP+PVP+++L AM+ I HR +F + EL A LK + +TE V++ SG Sbjct: 11 RHFLQIPGPSPVPDRILRAMSLPTIDHRGPEFGALGLELLAKLKQVFKTEGPVMIYPASG 70 Query: 64 TGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAE----WGKALDPND 119 TGA EA++ N LSPGDRVL+ G F W K+A L E I W + + + Sbjct: 71 TGAWEAALANVLSPGDRVLMYETGHFAALWHKMALRLQLEPEFIGLPGYEGWRQGVQADM 130 Query: 120 FKTLLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGG-ALMIVDAVTSLGATPV 178 + L D++ +KA+ + H+ETSTGV +D+AA+ A A G AL++VD ++ L + Sbjct: 131 IEARLREDAEHRLKAVCVVHNETSTGVTSDIAAVRRAIDAAGHPALLLVDTISGLASADY 190 Query: 179 AIDDLGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDS 238 D+ G+DV SGSQKG M+PPG+ F ++S KA A +T+PR + + ++ Sbjct: 191 RHDEWGVDVTISGSQKGLMLPPGISFNALSDKAIAASRESTMPRSFWAWDEILEANRNGY 250 Query: 239 SPFTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNA 298 P+TP NL+YGL +L M+ EGL+ +F RHQR R A++A L + D A + Sbjct: 251 WPYTPSTNLLYGLNEALDMLLDEGLEHVFARHQRWAAGVRTAVEAWGLEIQCQDPALYSP 310 Query: 299 IT--AVAPLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGAL 356 + V P GV+A+ +R + ++FD+++ G KGK+FRIGHLG D +++ +G Sbjct: 311 VLTGVVMPDGVDADAVRKIIYERFDLSLGMGLGKAKGKMFRIGHLGDCNDLTLIATLGGC 370 Query: 357 EATLIELGYEGVTPGSGVAAA 377 EA + G GSGVAAA Sbjct: 371 EAGMKLCGVP--LAGSGVAAA 389 Lambda K H 0.317 0.134 0.386 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: 387 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: 384 Length of database: 406 Length adjustment: 31 Effective length of query: 353 Effective length of database: 375 Effective search space: 132375 Effective search space used: 132375 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 (21.7 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