Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_013450502.1 CALNI_RS01845 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_000183405.1:WP_013450502.1 Length = 383 Score = 298 bits (763), Expect = 2e-85 Identities = 159/374 (42%), Positives = 234/374 (62%), Gaps = 3/374 (0%) Query: 4 KQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSG 63 K+ L+ PGPTPVPEKVLL MA I HR+ +FS I E+ LK + T DVL+L SG Sbjct: 3 KRYLLSPGPTPVPEKVLLDMAMPMIHHRTSEFSNIFKEVREGLKPIFGTRQDVLILAGSG 62 Query: 64 TGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKTL 123 T AMEA+++N L+ GD+VLV N GKFG RWV++A T+GL V I EWG+++ P+ ++ Sbjct: 63 TAAMEAAVVNTLNEGDKVLVVNAGKFGKRWVEIATTYGLDVITIDIEWGRSVKPDQVESK 122 Query: 124 LEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAIDDL 183 L A + IKA+++ SETST + + I L+IVD +TS+G +D+ Sbjct: 123 LIAHPE--IKAVLVQASETSTTAYHPIEEIGKIVSLRDETLLIVDGITSVGVYETKMDEW 180 Query: 184 GLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSPFTP 243 G+D++ +GSQK +M+PPGL +++S KAW+ E + IP+FYL+LKK +KS E+++ +TP Sbjct: 181 GIDILITGSQKAFMLPPGLALIALSEKAWKFTEKSRIPKFYLNLKKERKSQLENTTSWTP 240 Query: 244 PINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNAITAVA 303 ++L+ GL++ L++M EGL ++ RH ATR + A+ L A D +++A V Sbjct: 241 AVSLIIGLKSVLEIMNKEGLPNVYKRHALCAEATRKGLMAMGFELLAKDIPSNSATGIVL 300 Query: 304 PLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEATLIEL 363 P G + K MR+K + AGGQDHLKGKI R+ HLG+ D + + +LE + Sbjct: 301 PEGFDGGKFVKLMREKAGLTFAGGQDHLKGKILRVSHLGYHDFFDTIIALSSLEIGFSQF 360 Query: 364 GYEGVTPGSGVAAA 377 G + V G+GV A Sbjct: 361 GLK-VELGAGVKVA 373 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: 322 Number of extensions: 9 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: 384 Length of database: 383 Length adjustment: 30 Effective length of query: 354 Effective length of database: 353 Effective search space: 124962 Effective search space used: 124962 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 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