Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_043747187.1 AMB_RS22510 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_000009985.1:WP_043747187.1 Length = 390 Score = 217 bits (552), Expect = 5e-61 Identities = 141/385 (36%), Positives = 214/385 (55%), Gaps = 15/385 (3%) Query: 5 QMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTS-G 63 ++LM PGP+ V +VL A A+ IGH F ++ EL L+ +++N++ + G Sbjct: 11 RILMGPGPSDVHPRVLAAQARPTIGHLDPAFVGMMDELKGLLQAAFRSDNEMTFAVSGPG 70 Query: 64 TGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKTL 123 + MEA +N + PGD V+V NG FG R + + G ++ WG +DP + Sbjct: 71 SAGMEACFVNLIEPGDTVVVCVNGVFGGRMKENVERCGARAVVVEDAWGTPVDPAKVEAA 130 Query: 124 LEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAIDDL 183 L+A+++ +KAL H+ETSTGV +D A+ A A AHG AL IVD VTSLG PV +D Sbjct: 131 LKANAN--VKALAFVHAETSTGVESDAGALCALAHAHG-ALAIVDTVTSLGGIPVLVDQW 187 Query: 184 GLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYET--ATIPRFYLD---LKKYKKSTDEDS 238 G D V SGSQK PPGL V+ S++A QA ++ + ++LD L Y + + Sbjct: 188 GADAVYSGSQKCLSAPPGLSPVTFSSRAVQALKSRKTKVQSWFLDLTLLTAYWGGGAKRT 247 Query: 239 SPFTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNA 298 T P+N +YGL SL M+ EGLDA ++RH+ A + ++A+ L L + + Sbjct: 248 YHHTAPVNALYGLHESLVMLHEEGLDAAWSRHRAMHEALKAGLEAMGLGLLVAEQSRLPQ 307 Query: 299 ITAV-APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLG-FVCDRDILSCIGAL 356 + AV P GV+ +R+ + +F + + G L GK++RIG +G R +++C+ AL Sbjct: 308 LNAVTVPEGVDEAAVRAQLLARFGLEIGAGLGALAGKVWRIGLMGQSATPRHVMACLTAL 367 Query: 357 EATLIELGYEGVTPGSGVAAAAGVL 381 E+ L E V PG+G AAA+ L Sbjct: 368 ESVL----GEKVKPGAGPAAASRAL 388 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: 330 Number of extensions: 27 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 384 Length of database: 390 Length adjustment: 30 Effective length of query: 354 Effective length of database: 360 Effective search space: 127440 Effective search space used: 127440 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