Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_012282232.1 HM1_RS05100 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_000019165.1:WP_012282232.1 Length = 387 Score = 351 bits (901), Expect = e-101 Identities = 183/382 (47%), Positives = 261/382 (68%), Gaps = 3/382 (0%) Query: 1 MDNKQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLT 60 M K+ LM+PGPTPVP ++L A+++ I HR F ++I E+T +++ +QT+NDVL+L Sbjct: 1 MFEKEYLMLPGPTPVPPRLLRALSEPLINHRGPSFKRLIDEVTEGIRYAYQTKNDVLILP 60 Query: 61 TSGTGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDF 120 +SGTG MEA+I+NFLSPGD+VL + G FGDR+ +A+T+G V+++ EWG A+D N Sbjct: 61 SSGTGGMEAAIVNFLSPGDKVLALSIGAFGDRFATIAQTYGCIVDKVDFEWGTAVDLNVV 120 Query: 121 KTLLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAI 180 K L AD +K KA+++TH+ETSTGV NDL ++ H AL++VD+V+ LG V Sbjct: 121 KAKLAADVNKEYKAILVTHNETSTGVCNDLKGLSEIRGDH-PALILVDSVSGLGVMEVKT 179 Query: 181 DDLGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSP 240 D+ GLDV+ + +QKG+MIPPG+ FVSVS +AW AYE +T P+FY DL KK ++ +P Sbjct: 180 DEWGLDVIVTAAQKGFMIPPGVAFVSVSPRAWAAYEKSTAPKFYWDLGSAKKFLEKGQTP 239 Query: 241 FTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNAIT 300 TP I + GL+ +LQ+ + +G +A+F + + + TR +KAL L L A D AS A+T Sbjct: 240 VTPAIPQLTGLREALQLFREKGREAVFAKQRYLRDITRAGVKALGLKLLADDAVASAAVT 299 Query: 301 AV-APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEAT 359 AV AP G+EA+ I MR+ ++ +AGGQ L+ KIFRIGHLG+ D+L+ + ALE T Sbjct: 300 AVWAPEGIEAKAINKRMREAHNVVLAGGQKKLENKIFRIGHLGYGQHLDVLATVAALEMT 359 Query: 360 LIELGYEGVTPGSGVAAAAGVL 381 L ELGY V G+GV AA V+ Sbjct: 360 LKELGYP-VELGAGVKAAQEVI 380 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: 391 Number of extensions: 20 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: 384 Length of database: 387 Length adjustment: 30 Effective length of query: 354 Effective length of database: 357 Effective search space: 126378 Effective search space used: 126378 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