Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_013840109.1 DESRU_RS00105 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_000215085.1:WP_013840109.1 Length = 385 Score = 316 bits (809), Expect = 8e-91 Identities = 169/385 (43%), Positives = 246/385 (63%), Gaps = 5/385 (1%) Query: 1 MDNKQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLT 60 M +K+ L+IPGPTPVP +V+ AM++ IGHRS F ++ +T LK + QTEN V +L Sbjct: 2 MKDKKYLLIPGPTPVPPRVVEAMSRPIIGHRSAGFQAVMERVTGKLKKVFQTENHVFILG 61 Query: 61 TSGTGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDF 120 +SGTGA+EA++ N + PGD+VL + GKFG+R+ ++A+ +G V+ + WG +D N Sbjct: 62 SSGTGALEAAVANLVHPGDKVLALSCGKFGERFAELARIYGGNVDFVDFGWGYDIDLNVV 121 Query: 121 KTLLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAI 180 K L D D IK ++ T +ETST V ND+ + A A++ VDAV+ L A + Sbjct: 122 KRKL--DEDSAIKVVLATQNETSTAVQNDIEGLGKLV-AQYDAVLAVDAVSGLAAIDLKT 178 Query: 181 DDLGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSP 240 D+ +D+V SGSQK +M+PPGL F+SVS KAW E T P +Y DLKK KKS + ++ Sbjct: 179 DEWNVDMVVSGSQKAFMLPPGLAFISVSDKAWAKIEKNTSPVYYFDLKKAKKSIAKWNTA 238 Query: 241 FTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNAIT 300 +T P++++YGL+A+L M+ EGL +F RH ATR A++ L L L APD AS A+T Sbjct: 239 YTTPVSMVYGLEAALDMILEEGLPQVFARHALLAKATRAAVQGLGLELLAPDECASKAVT 298 Query: 301 AV-APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEAT 359 AV +P+ V+A+ +R + K++ + AGGQ+ +KGKIFRI H+G+ D++ I ALE Sbjct: 299 AVQSPMVVDADTLRKVLLKEYGVTFAGGQEMMKGKIFRIAHMGYAGKMDVIIAIAALEMA 358 Query: 360 LIELGYEGVTPGSGVAAAAGVLAKG 384 L + GY+ G+GV A V G Sbjct: 359 LGKCGYKAEL-GAGVREAQMVFVGG 382 Lambda K H 0.317 0.134 0.386 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: 353 Number of extensions: 16 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: 384 Length of database: 385 Length adjustment: 30 Effective length of query: 354 Effective length of database: 355 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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