Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate Synpcc7942_2160 Synpcc7942_2160 alanine-glyoxylate aminotransferase
Query= metacyc::MONOMER-15919 (385 letters) >FitnessBrowser__SynE:Synpcc7942_2160 Length = 384 Score = 203 bits (516), Expect = 8e-57 Identities = 114/351 (32%), Positives = 200/351 (56%), Gaps = 3/351 (0%) Query: 3 IDAVKKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFL 61 ++ ++LL+ PGP+ P VL A++ P IGH + L+ + L+ ++ T+N T Sbjct: 19 LELPERLLLGPGPSNAHPAVLEAISRPPIGHLDPKFLELMTEVQGLLRYIWQTDNRLTIP 78 Query: 62 ITGSGTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPE 121 ++G+G+AAM+ I+N ++ GD VL V G FG R ++ Y + + WGD+ Sbjct: 79 VSGTGSAAMEATIANSVEPGDVVLVGVMGYFGNRLVDMAGRYGADVRTIHKPWGDVFSLA 138 Query: 122 AVKEILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVD 181 +++ L+++ + + +VH ETSTGA P+ +G++ +++D L ++DTV+SLG +D Sbjct: 139 ELRQALEEHRP-QILALVHAETSTGAEQPLAGVGDLCREFDCLLLIDTVTSLGAVPTLLD 197 Query: 182 KFHIDICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVG-FYLDLLAYKKYYEEKKQ 240 ++ +D+ + SQK L+ PPG++ T+ +A E + + KV +YLD+ +Y+ + Sbjct: 198 EWGVDLAYSCSQKGLSCPPGVSPFTMGPRAEEKLARRKGKVANWYLDMSLLNQYWGSDRV 257 Query: 241 TPYTPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVT 300 +T VN+ + + AL L+ +EGIE KRH A+ AGLE +G+ R T Sbjct: 258 YHHTAPVNMNFGIREALRLIADEGIETVWKRHRDNAEYLWAGLEDLGLTCHVPVENRLPT 317 Query: 301 VTSAKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKE 351 +T+ + PEG++ L +++ I + GG LAGK++RIG MG +E Sbjct: 318 LTTVRIPEGVDGKAVSRQLLDEHGIEMGGGLGELAGKVWRIGLMGYNSRRE 368 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: 311 Number of extensions: 19 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: 384 Length adjustment: 30 Effective length of query: 355 Effective length of database: 354 Effective search space: 125670 Effective search space used: 125670 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