Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_106716053.1 CU100_RS06990 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_003010935.1:WP_106716053.1 Length = 364 Score = 221 bits (563), Expect = 3e-62 Identities = 128/344 (37%), Positives = 185/344 (53%), Gaps = 2/344 (0%) Query: 10 LMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFLITGSGTAA 69 ++ GP PEVL A+ PV+ + + EKL+K TE ++ G Sbjct: 1 MLTTGPVPAYPEVLEALGSPVLYDYHPAFQTFYAEVTEKLRKALRTETTPVIMQGEAILG 60 Query: 70 MDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEILDK 129 ++ A + +I D VLN+V+G +G F Y E I V + D+ +P+ V+E L + Sbjct: 61 IEAAAAALIAADDVVLNLVSGPYGREFDTWAGRYGKEVIEQAVPYDDVIDPQVVREALAR 120 Query: 130 YDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHIDICV 189 DI V++ H+ET G NP+ EIG +V + A IVD VSS GG V+ ++ H DI + Sbjct: 121 RPDISVVSLCHHETPCGTLNPLNEIGAIVASHGACLIVDAVSSFGGMSVHPEEAHADIFI 180 Query: 190 TGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYYEEKKQTPYTPSVN 248 T KCL + PGL+ I +SE+AW I+ N D +L LLA++ E K P TPSV+ Sbjct: 181 TSPSKCLGSTPGLSLIALSERAWAKIQANPDAPRNSFLSLLAWRNASEPGKPFPVTPSVS 240 Query: 249 LTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERA-RSVTVTSAKYP 307 YAL+ ALD +EG EN RH A TR GL +G+ L+ K+ A S T T K P Sbjct: 241 EIYALDAALDRHAQEGPENVWARHAVTAAITRKGLFELGLPLWPKQEAFCSPTATVFKVP 300 Query: 308 EGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKE 351 +G+ D R L + + I+V+ G+ GK+ R+GHMG E + Sbjct: 301 QGVSDVALRDRLLHDHGILVSLGRGETTGKVLRVGHMGASAEPD 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: 275 Number of extensions: 11 Number of successful extensions: 3 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: 364 Length adjustment: 30 Effective length of query: 355 Effective length of database: 334 Effective search space: 118570 Effective search space used: 118570 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 Jul 26 2024. The underlying query database was built on Jul 25 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