Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate YP_004141244.1 Mesci_2041 class V aminotransferase
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_000185905.1:YP_004141244.1 Length = 401 Score = 231 bits (590), Expect = 2e-65 Identities = 140/376 (37%), Positives = 218/376 (57%), Gaps = 7/376 (1%) Query: 7 LMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTEN-DVLMLTTSGTG 65 L IPGPT +P+ V AM R+ DF +++ L +LK + +TE V + SGTG Sbjct: 8 LFIPGPTNIPDAVRRAMNVPMQDMRAPDFPELVLPLFRDLKQIFKTETGSVFIFPGSGTG 67 Query: 66 AMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKTLLE 125 A EA+I N L+ GDRVL+ G+F WV +A+ GL V+ + EWG+ + + ++ L Sbjct: 68 AWEAAISNTLNRGDRVLMSRFGQFSHLWVDMAERLGLKVDCVDVEWGEGVPLDAYRQRLG 127 Query: 126 ADSDKTIKALIITHSETSTGVLNDLAAINAAAK--AHGGALMIVDAVTSLGATPVAIDDL 183 D IKA+ TH+ET+TGV +D+A + AA AH AL+ VD V+S+G+ +D+ Sbjct: 128 DDKGHEIKAVFATHNETATGVTSDIAGVRAALDETAHD-ALLFVDGVSSIGSIDFRMDEW 186 Query: 184 GLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSPFTP 243 G+D+ +GSQKG M+P GLG ++VSAK +A++ + + R Y + + S+ P+TP Sbjct: 187 GVDLAITGSQKGLMLPAGLGILAVSAKGLEAHKQSHMERCYFSFEDMQASSKTGFFPYTP 246 Query: 244 PINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNA-ASNAITA- 301 P L+ GL+ASL ++ AEGL+ IF RH R R + A L L A + S+ ++A Sbjct: 247 PTQLLLGLRASLDLIFAEGLEQIFARHHRLAEGVRRGVHAWGLKLCANEEKWWSDTVSAI 306 Query: 302 VAPLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEATLI 361 V V+A ++ + ++ + G + G++FRIGHLG + + L+ + + E +L Sbjct: 307 VVSEDVDARQVIANGYSRYRTSFGAGLSKVAGRVFRIGHLGDLNEVMCLAALASAEMSLR 366 Query: 362 ELGYEGVTPGSGVAAA 377 + G + GSGVAAA Sbjct: 367 DAGAR-IEAGSGVAAA 381 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: 341 Number of extensions: 16 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: 401 Length adjustment: 31 Effective length of query: 353 Effective length of database: 370 Effective search space: 130610 Effective search space used: 130610 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