Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_092487417.1 BM299_RS17360 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_900115975.1:WP_092487417.1 Length = 383 Score = 320 bits (820), Expect = 4e-92 Identities = 164/378 (43%), Positives = 242/378 (64%), Gaps = 3/378 (0%) Query: 7 KKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFLITGSG 66 K LMIPGPT VPP V+ AM P+ GHR++D+ + ++ I KL+K+F T+N+ +++T SG Sbjct: 4 KSYLMIPGPTPVPPSVVAAMTAPMFGHRSEDFQAMHKEIIGKLQKLFQTQNEIYVLTSSG 63 Query: 67 TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEI 126 T M+ A++N + GDKVL +V G FGER++ + Y E I L+ EWG +P+AV+E Sbjct: 64 TGGMESAVANTVSPGDKVLTLVGGKFGERWSELANQYGAEVIELNYEWGTCVDPQAVQEQ 123 Query: 127 LDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 L DIK V NETSTG N I+ +G++V AL++VD VS +GG + VD++++D Sbjct: 124 LAANPDIKVVFATQNETSTGVTNDIEALGKIVAQTPALFVVDGVSGVGGIEIKVDEWNVD 183 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVGFYLDLLAYKKYYEEKKQTPYTPS 246 I TGSQK L PPGLA ++S+KAW+ I++N +Y LL +K Y K T YTP+ Sbjct: 184 ILTTGSQKSLMLPPGLAIQSISDKAWKKIEENKSP-RYYFSLLKARKQY-PKWNTAYTPA 241 Query: 247 VNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSAKY 306 V+L LN ALD++L EG++N RH+ + ATRA + A+G+ L + S VTS Sbjct: 242 VSLFVGLNAALDMILNEGLDNVYARHKLMRDATRAAIRALGLNLMTDDAYASPVVTSVYA 301 Query: 307 PEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKEVLATLACVELALKEL 366 PEGI R +L +YNI AGGQ L KI RI HMG + +++ ++ +E+AL+++ Sbjct: 302 PEGIGADDIRKVLKQEYNITFAGGQAKLKNKILRIAHMGFADKMDIIIAVSGLEMALQKV 361 Query: 367 GFEVK-ESGVEVAKEVLL 383 G+ V+ +GV+ A++V L Sbjct: 362 GYPVELGAGVKAAQQVFL 379 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: 382 Number of extensions: 16 Number of successful extensions: 2 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: 383 Length adjustment: 30 Effective length of query: 355 Effective length of database: 353 Effective search space: 125315 Effective search space used: 125315 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