Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_013819317.1 METME_RS13600 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_000214665.1:WP_013819317.1 Length = 388 Score = 251 bits (641), Expect = 2e-71 Identities = 139/380 (36%), Positives = 215/380 (56%), Gaps = 4/380 (1%) Query: 1 MDNKQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTE-NDVLML 59 M + L IPGPT P +VL AM HRS F + L +LK + +TE + Sbjct: 1 MAGRNHLFIPGPTNTPHEVLSAMHVPMEDHRSPIFPNLFKPLLEDLKKVFRTEAGQCFVF 60 Query: 60 TTSGTGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPND 119 +GT E ++ N L+PGD+VL+ G+F W+ A+ G VE + EWGK + + Sbjct: 61 PATGTAGWEVALTNCLNPGDKVLIYRFGQFAHLWMDAARKLGFDVEAHEVEWGKGIPLDA 120 Query: 120 FKTLLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGG-ALMIVDAVTSLGATPV 178 + L+ D + IKA++ TH+ETSTGV +D+A + A A G AL+ VD V+S+ + Sbjct: 121 MEARLKEDKNHEIKAVLATHNETSTGVTSDIAGVRKAMDAAGHPALLFVDGVSSIASLEF 180 Query: 179 AIDDLGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDS 238 +DD G+D SGSQKG+M+P G ++ S KA A ET+T PR + LK + + Sbjct: 181 RMDDWGVDGAISGSQKGFMLPAGAAILAFSQKALAAVETSTFPRSFFSLKDQMNANKDGY 240 Query: 239 SPFTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNA 298 +P+TP +++GL+ +L ++ EG+D ++ RH R R A+ A L + A S+ Sbjct: 241 TPYTPSTPMLHGLRKALDLLLEEGMDNVYARHHRLGEGVRRAVAAWGLQICAQPGFESDT 300 Query: 299 ITA-VAPLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALE 357 +TA V P +A + ST K++I++ G + GK+FRIGH+G + D +L I +E Sbjct: 301 VTAIVVPADKDARHVISTAYNKYNISLGAGLTEVAGKVFRIGHIGDMNDVSLLGAIAGVE 360 Query: 358 ATLIELGYEGVTPGSGVAAA 377 +++ G++ + PGSGVAAA Sbjct: 361 MAMLDNGFD-IKPGSGVAAA 379 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: 359 Number of extensions: 19 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: 388 Length adjustment: 30 Effective length of query: 354 Effective length of database: 358 Effective search space: 126732 Effective search space used: 126732 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