Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_011881973.1 2-aminoethylphosphonate aminotransferase
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_000016205.1:WP_011881973.1 Length = 354 Score = 144 bits (362), Expect = 5e-39 Identities = 111/369 (30%), Positives = 181/369 (49%), Gaps = 25/369 (6%) Query: 6 MLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQ---TENDVLMLTTS 62 +L+ PGP + E+V ++ + + HR +F + E A L ++ E +++T S Sbjct: 2 LLLNPGPVTLSERVRRSLLQPDLCHRESEFFDLQDEARARLVAAYELDPAEWAAVLMTGS 61 Query: 63 GTGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKT 122 GT A+E+ I + ++LV NG +G+R ++A +G+A + +K EW +A D + Sbjct: 62 GTAAVESMIAALVPQDGKLLVIENGVYGERITQIATQYGIAHDVLKHEWMQAPDVAEVAA 121 Query: 123 LLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAIDD 182 L+A + + H ET+TG LNDL AI +A G M+VD V+S GA + Sbjct: 122 RLDAGG---YSHVAVIHHETTTGRLNDLGAIADVCRAR-GVRMLVDGVSSFGAEAIDFGG 177 Query: 183 LGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSPFT 242 +D VA+ + K PG FV V A + T +YLDL + K D+ ++PFT Sbjct: 178 GVIDAVAATANKCLHGVPGAAFVIVRRSALTKAASRT---YYLDLGRLAKLQDQRNTPFT 234 Query: 243 PPINLMYGL-QASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNAITA 301 P ++ Y L +A + +A G A R++ + + + A +PL PD +S + A Sbjct: 235 PSVHAYYALVEALREFDEAGGWRARHARYKALADQVQAGLAARGMPLVLPDGESSVVLRA 294 Query: 302 V-APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEATL 360 P GV E + ++ + + A GQ L ++FRI S +GA+EA Sbjct: 295 YRLPQGVAYEALHDGLKARGFVIYA-GQGGLSKELFRI------------STMGAIEAAD 341 Query: 361 IELGYEGVT 369 +E EG T Sbjct: 342 VERLLEGFT 350 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: 247 Number of extensions: 15 Number of successful extensions: 7 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: 354 Length adjustment: 30 Effective length of query: 354 Effective length of database: 324 Effective search space: 114696 Effective search space used: 114696 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: 49 (23.5 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