Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_051347374.1 B076_RS12450 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000483485.1:WP_051347374.1 Length = 360 Score = 229 bits (585), Expect = 7e-65 Identities = 130/358 (36%), Positives = 204/358 (56%), Gaps = 5/358 (1%) Query: 11 MIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGSGTAA 69 M PGP+ V P +L+AMA P IGH ++ ++++ + LK F TEN+ T ++ G+A Sbjct: 1 MGPGPSDVHPRILSAMARPTIGHLDPEFVRMMDELKQLLKYAFQTENEMTMPVSAPGSAG 60 Query: 70 MDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEILDK 129 M+ +N+++ GDKV+ + G FG R V+ G + + +WG P V+ L + Sbjct: 61 METCFANLVEPGDKVIVCINGVFGMRMKENVERTGGICVEVHDDWGSAVSPAKVESALKE 120 Query: 130 YDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHIDICV 189 + D K V VH ETSTGA + +K I ++ +D L IVD V+SLGG + VD++ +D Sbjct: 121 HSDAKIVAFVHAETSTGACSDVKAICDIAHQHDCLTIVDAVTSLGGVELKVDEWGVDAIY 180 Query: 190 TGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYYEE--KKQTPYTPS 246 +G+QKCL+ PGL+ ++ +E A + ++ KV ++LDL Y+ + K+ +T Sbjct: 181 SGTQKCLSCTPGLSPVSFNEAALQKVRNRKTKVQSWFLDLNLVMGYWGQGAKRAYHHTAP 240 Query: 247 VNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSAKY 306 VN YAL+ +L ++ EG+EN RH + + +AGLE MGI +E R + S Sbjct: 241 VNALYALHESLVMLKNEGLENSWARHAAMHEKLKAGLEEMGITFVVEESVRLPQLNSVWI 300 Query: 307 PEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKE-VLATLACVELAL 363 PEG +D+ R L N YN+ + G AGK++RIG MG ++E VL LA ++ L Sbjct: 301 PEGFDDATVRSELLNTYNLEIGAGLGDFAGKVWRIGLMGFSAKEENVLFCLAALKKVL 358 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: 336 Number of extensions: 12 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: 360 Length adjustment: 30 Effective length of query: 355 Effective length of database: 330 Effective search space: 117150 Effective search space used: 117150 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: 49 (23.5 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