Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_009547332.1 CCE_RS13545 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000017845.1:WP_009547332.1 Length = 372 Score = 223 bits (569), Expect = 5e-63 Identities = 121/340 (35%), Positives = 203/340 (59%), Gaps = 3/340 (0%) Query: 8 KLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGSG 66 +LLM PGP+ P +L+AM+LP IGH Y +++ + L+ V+ TEN+ T I+G+G Sbjct: 15 RLLMGPGPSNANPRILSAMSLPAIGHLDPFYLEMMDQIQDLLRYVWQTENELTISISGTG 74 Query: 67 TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEI 126 +A M+ +++N+++ GD VL V G FG R ++ Y + + WG+ +KE Sbjct: 75 SAGMEASLANVVEPGDVVLIGVMGYFGHRLVDMATRYGADVKTISKPWGENFSLAELKEA 134 Query: 127 LDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 ++ + + +V+ ETSTG R P++ +GE+ ++++ L +VD V+SLGG D++ +D Sbjct: 135 IETHKPT-ILGLVNAETSTGVRQPLEGVGELCREHNCLLLVDAVTSLGGVPFYADQWGVD 193 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVG-FYLDLLAYKKYYEEKKQTPYTP 245 + + SQK L PPGL+ T+S++A E ++K V +YLD+ +Y+ E ++ +T Sbjct: 194 LAYSCSQKGLGCPPGLSPFTMSDRAIEKLQKRTTPVSNWYLDMNLLSQYWGEPRKYHHTA 253 Query: 246 SVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSAK 305 N+ Y L AL L++EEG+EN +RH++ A+ GLE +G+ ++ R T+T+ + Sbjct: 254 PCNMNYGLREALALIVEEGLENCWQRHQQNAELLWEGLEKLGLVCHVEKAFRLPTLTTVR 313 Query: 306 YPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMG 345 PEG+ L +YNI + GG LAGK++RIG MG Sbjct: 314 IPEGVNGKAVSSYLLKEYNIEIGGGLGELAGKVWRIGLMG 353 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: 330 Number of extensions: 15 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: 372 Length adjustment: 30 Effective length of query: 355 Effective length of database: 342 Effective search space: 121410 Effective search space used: 121410 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