Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_006748824.1 THITH_RS04895 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000227685.2:WP_006748824.1 Length = 400 Score = 231 bits (590), Expect = 2e-65 Identities = 135/380 (35%), Positives = 212/380 (55%), Gaps = 6/380 (1%) Query: 8 KLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGSG 66 + LM PGP+ V P VL AM+ P+IGH + ++E+ L+ F T N T ++ G Sbjct: 11 RTLMGPGPSDVNPRVLAAMSRPIIGHLDPAFIAMMEEVRTMLQSAFKTRNALTLPVSAPG 70 Query: 67 TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEI 126 +A M+ +N+++ GDKV+ + G FG R V+ G A+ +D +WG+ + V++ Sbjct: 71 SAGMETCFANLVEPGDKVIVCINGVFGGRMKENVERCGGTAVTVDDDWGNPVSLDKVEDA 130 Query: 127 LDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 L + D + + VH ETSTGA + ++ + E+ +D L +VD V+SLGG ++VD + +D Sbjct: 131 LKAHPDARVLAFVHAETSTGAESDVRALCELAHRHDCLALVDAVTSLGGSPLHVDDWGVD 190 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYY---EEKKQTP 242 +GSQKCL+ PGL+ ++ SE+A E I+ +V ++LDL Y+ + K+ Sbjct: 191 AIYSGSQKCLSCTPGLSPVSFSERAVERIRSRRSRVQSWFLDLNLVMGYWIGSDGKRAYH 250 Query: 243 YTPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVT 302 +T +N YAL+ AL ++ EEG+E RH R +A RAGLEAMG+ E R + Sbjct: 251 HTAPINALYALHEALVILHEEGLEASWARHRRHHEALRAGLEAMGLHFLVDEAHRLPQLN 310 Query: 303 SAKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMG-ICGEKEVLATLACVEL 361 + PEG++++ R L +Y + + G AG+I+RIG MG E+ VL L +E Sbjct: 311 AVLVPEGVDEAGVRAALLERYGLEIGAGLGPYAGRIWRIGLMGHAANERNVLVCLGALEA 370 Query: 362 ALKELGFEVKESGVEVAKEV 381 L E G V V A+ V Sbjct: 371 ILAETGAAVPGKAVPAARAV 390 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: 377 Number of extensions: 13 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: 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 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