Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_011384845.1 AMB_RS12385 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000009985.1:WP_011384845.1 Length = 400 Score = 148 bits (374), Expect = 2e-40 Identities = 117/371 (31%), Positives = 191/371 (51%), Gaps = 12/371 (3%) Query: 9 LLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFL-ITGSGT 67 L+M GP +PP+V A +L +I H + ++E + VF T + + + G + Sbjct: 22 LMMGAGPVPIPPKVAMANSL-IINHLGDTMNAVIEQVKTMGRYVFQTNSPHVMGVAGPAS 80 Query: 68 AAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEIL 127 AAM+MAI+N+++ G +VL+I G F R A + G+ RLD E V++ L Sbjct: 81 AAMEMAIANLVEPGTRVLSICNGLFSRRLAEMADRVGGDVTRLDAPDKRAISAEDVEKAL 140 Query: 128 DKYDDIKAVTVVHNETSTGARN-PIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 K + +TVV ETS N + EI + K Y L IVD V +L + +D++ +D Sbjct: 141 -KTGRFQILTVVQGETSNTVWNRDLVEICRLGKQYGCLNIVDAVCTLSTMPMEMDEWMVD 199 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIK-KNDDKVGFYLDL-LAYKKYYEEKKQTPYT 244 +TG QK L++ PG++ I SE+A+ I+ +N + LD LA++ ++ YT Sbjct: 200 AIITGGQKGLSSIPGVSLIAFSEEAFARIEARNSPMAHWCLDARLAHQFWHNHSYH--YT 257 Query: 245 PSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSA 304 V+ AL+ AL L+ +E + R +RH + +KA + G+EAMG++L E +R +V Sbjct: 258 APVSGILALHEALRLIGDETLPGRFRRHAQCSKALQNGVEAMGLKLLIAEDSRLNSVVGI 317 Query: 305 KYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGE-KEVLATLACVELAL 363 + PE I + R I+S + + ++G I RIG MG + TL + A+ Sbjct: 318 ELPEVISADQVRHIMSQVHKVEISGA---FGLPIVRIGQMGEQSRAPNLFRTLHALGSAM 374 Query: 364 KELGFEVKESG 374 + G +V G Sbjct: 375 RAAGGKVDMPG 385 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: 321 Number of extensions: 22 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: 385 Length of database: 400 Length adjustment: 31 Effective length of query: 354 Effective length of database: 369 Effective search space: 130626 Effective search space used: 130626 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 09 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