Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_085120817.1 B9O00_RS02410 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_900177295.1:WP_085120817.1 Length = 399 Score = 262 bits (669), Expect = 1e-74 Identities = 149/383 (38%), Positives = 218/383 (56%), Gaps = 5/383 (1%) Query: 4 KQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSG 63 + L IPGPT VP++VL AM + I HR +F + + A ++ + +TE V++ SG Sbjct: 7 RHFLQIPGPTNVPDRVLRAMDRPTIDHRGPEFQALALRVLAGIRTIFKTEQPVVIYPASG 66 Query: 64 TGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKTL 123 TGA EA+++N LS GDRVL+ G F W +A+ GL E I +W DP + Sbjct: 67 TGAWEAALVNSLSAGDRVLMFETGHFASLWKALAERLGLQPEFIAGDWRHGADPAAIEAR 126 Query: 124 LEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHG-GALMIVDAVTSLGATPVAIDD 182 L D IKA+ + H+ETSTG ++ + A+ A A G AL++VD ++SL + D+ Sbjct: 127 LREDRGHAIKAVCVVHNETSTGCVSPIGAVRKAIDAAGHPALLMVDTISSLASIDYRHDE 186 Query: 183 LGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSPFT 242 G+DV GSQKG M+PPGL F +VS KA A +TA +PR Y D + + PFT Sbjct: 187 WGVDVTVGGSQKGLMLPPGLSFNAVSEKAVAASKTAGLPRSYWDWGEMLAINAKGFFPFT 246 Query: 243 PPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNA-ASNAITA 301 P NL+YGL A++ M+ EGL+ +F RH RH ATR A+++ L + + A S ++TA Sbjct: 247 PATNLLYGLDAAIDMLHEEGLERVFERHARHGEATRRAVRSWGLEVLCQEPAHYSGSLTA 306 Query: 302 V-APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEATL 360 V P G +A++ R T+ F++++ G L G++FRIGHLG D ++ +G +E L Sbjct: 307 VLMPAGHDADRFRGTVLDAFNMSLGNGLSKLAGRVFRIGHLGHFNDLTLIGTLGGVEMGL 366 Query: 361 IELGYEGVTPGSGVAAAAGVLAK 383 G GV AA LA+ Sbjct: 367 EVAGVP--HKAGGVQAAMDFLAQ 387 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: 374 Number of extensions: 14 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: 399 Length adjustment: 31 Effective length of query: 353 Effective length of database: 368 Effective search space: 129904 Effective search space used: 129904 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