Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate 8500978 DvMF_1715 aminotransferase class V (RefSeq)
Query= BRENDA::P74281 (384 letters) >FitnessBrowser__Miya:8500978 Length = 389 Score = 224 bits (570), Expect = 4e-63 Identities = 120/356 (33%), Positives = 196/356 (55%), Gaps = 3/356 (0%) Query: 1 MDNKQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLT 60 M +K L+ PGPTP PE+V LAMA I HR F I+A + L+ L T VL + Sbjct: 1 MLDKPRLLTPGPTPTPERVRLAMAHDMIHHRKPAFKAIMAAVQPKLRELFGTAQPVLPMA 60 Query: 61 TSGTGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDF 120 SG+G M A++ PG++V+V GKFG RW ++A GL V + +WG+ + P + Sbjct: 61 CSGSGVMTAAVHGLFRPGEKVIVVEGGKFGQRWREIAAVRGLNVVSVVVDWGRPVTPAEV 120 Query: 121 KTLLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAI 180 + L D +++ SETSTG L+ + I A A L++VD ++++ +P + Sbjct: 121 EAALNEHPDAA--GVLVQLSETSTGTLHPVREI-ARLTAGRDTLLVVDGISAVSISPCPM 177 Query: 181 DDLGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSP 240 D+ G+D + +GSQKG M+PPGLG +++S +AW+ +T FY + + + ++ + Sbjct: 178 DEWGIDCLLTGSQKGLMLPPGLGLIALSERAWRKADTVPPSCFYFNFRGELANLEKQQTL 237 Query: 241 FTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNAIT 300 FT P++L+ GL SL M + GL+ ++ + T R + A+ L + + Sbjct: 238 FTTPVSLIIGLNESLDMFREVGLETVYRKQWALTQMARRGVTAMGLEPLVKEGYTWGLTS 297 Query: 301 AVAPLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGAL 356 + P GV A + ++F + MA GQDH+K +I RIGH+G++ D+ + + AL Sbjct: 298 VLLPEGVPATGVLRVAAERFGVIMAAGQDHMKERIIRIGHMGWLDWADLAAGLHAL 353 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: 332 Number of extensions: 10 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: 389 Length adjustment: 30 Effective length of query: 354 Effective length of database: 359 Effective search space: 127086 Effective search space used: 127086 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 09 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