Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_086511813.1 BZY95_RS20880 aminotransferase class V-fold PLP-dependent enzyme
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_002151265.1:WP_086511813.1 Length = 406 Score = 214 bits (544), Expect = 5e-60 Identities = 133/392 (33%), Positives = 210/392 (53%), Gaps = 29/392 (7%) Query: 7 KKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFLITGSG 66 + L IPGP+ VP +L AM+LP I HR ++ L + + KLK+VF TE + SG Sbjct: 11 RHFLQIPGPSPVPDRILRAMSLPTIDHRGPEFGALGLELLAKLKQVFKTEGPVMIYPASG 70 Query: 67 TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVE-----------WG 115 T A + A++N++ GD+VL TG+F + + A+RL +E W Sbjct: 71 TGAWEAALANVLSPGDRVLMYETGHFAALWHKM-------ALRLQLEPEFIGLPGYEGWR 123 Query: 116 DMAEPEAVKEIL--DKYDDIKAVTVVHNETSTGARNPIKEIGEVV--KDYDALYIVDTVS 171 + + ++ L D +KAV VVHNETSTG + I + + + AL +VDT+S Sbjct: 124 QGVQADMIEARLREDAEHRLKAVCVVHNETSTGVTSDIAAVRRAIDAAGHPALLLVDTIS 183 Query: 172 SLGGDYVNVDKFHIDICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVGFYLDLLAY 231 L D++ +D+ ++GSQK L PPG++ +S+KA +++ F+ A+ Sbjct: 184 GLASADYRHDEWGVDVTISGSQKGLMLPPGISFNALSDKAIAASRESTMPRSFW----AW 239 Query: 232 KKYYEEKKQ--TPYTPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIE 289 + E + PYTPS NL Y LN ALD++L+EG+E+ RH+R A R +EA G+E Sbjct: 240 DEILEANRNGYWPYTPSTNLLYGLNEALDMLLDEGLEHVFARHQRWAAGVRTAVEAWGLE 299 Query: 290 LFAKERA-RSVTVTSAKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICG 348 + ++ A S +T P+G++ R I+ ++++ + G GK+FRIGH+G C Sbjct: 300 IQCQDPALYSPVLTGVVMPDGVDADAVRKIIYERFDLSLGMGLGKAKGKMFRIGHLGDCN 359 Query: 349 EKEVLATLACVELALKELGFEVKESGVEVAKE 380 + ++ATL E +K G + SGV A E Sbjct: 360 DLTLIATLGGCEAGMKLCGVPLAGSGVAAALE 391 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: 364 Number of extensions: 16 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: 406 Length adjustment: 31 Effective length of query: 354 Effective length of database: 375 Effective search space: 132750 Effective search space used: 132750 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