Align Alanine--glyoxylate aminotransferase; AGT; Serine--pyruvate aminotransferase; SPT; EC 2.6.1.44; EC 2.6.1.51 (characterized)
to candidate WP_043747187.1 AMB_RS22510 alanine--glyoxylate aminotransferase family protein
Query= SwissProt::P31030 (392 letters) >NCBI__GCF_000009985.1:WP_043747187.1 Length = 390 Score = 269 bits (687), Expect = 1e-76 Identities = 155/365 (42%), Positives = 213/365 (58%), Gaps = 3/365 (0%) Query: 21 PHRLLLGPGPSNLPPRVLAAGGLQMIGHMHEEMYQVMDEIKQGIQYAFQTRNALTLAVSG 80 P R+L+GPGPS++ PRVLAA IGH+ +MDE+K +Q AF++ N +T AVSG Sbjct: 9 PLRILMGPGPSDVHPRVLAAQARPTIGHLDPAFVGMMDELKGLLQAAFRSDNEMTFAVSG 68 Query: 81 SGHCALETALFNLLEPGDAFLVGANGIWGQRAAEVGERIGARVHPMIKDPGSHYTLQEVE 140 G +E NL+EPGD +V NG++G R E ER GAR + G+ +VE Sbjct: 69 PGSAGMEACFVNLIEPGDTVVVCVNGVFGGRMKENVERCGARAVVVEDAWGTPVDPAKVE 128 Query: 141 ECLAQHKPV-LLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSVASLGGAPIYMDQQG 199 L + V L H E+STGV L H + L +VD+V SLGG P+ +DQ G Sbjct: 129 AALKANANVKALAFVHAETSTGVESDAGALCALAHAHGALAIVDTVTSLGGIPVLVDQWG 188 Query: 200 IDVLYSGSQKALNAPPGTSLISFSDKAKSKIYARKTKPFSFYMDVQLLANIWGCDGKPRM 259 D +YSGSQK L+APPG S ++FS +A + +RKTK S+++D+ LL WG G R Sbjct: 189 ADAVYSGSQKCLSAPPGLSPVTFSSRAVQALKSRKTKVQSWFLDLTLLTAYWG-GGAKRT 247 Query: 260 YHHTTPVIGIFALRESLALLVEQGLEKSWQRHREVAQHLYRRLQELGLQLFVKDPALRLP 319 YHHT PV ++ L ESL +L E+GL+ +W RHR + + L L+ +GL L V + + RLP Sbjct: 248 YHHTAPVNALYGLHESLVMLHEEGLDAAWSRHRAMHEALKAGLEAMGLGLLVAEQS-RLP 306 Query: 320 TVTTVIVPASYRWRDIVSYVMHHFGIEITGGLGPSADKVLRIGLLGCNATRENVDRLATA 379 + V VP + + ++ FG+EI GLG A KV RIGL+G +AT +V TA Sbjct: 307 QLNAVTVPEGVDEAAVRAQLLARFGLEIGAGLGALAGKVWRIGLMGQSATPRHVMACLTA 366 Query: 380 LREAL 384 L L Sbjct: 367 LESVL 371 Lambda K H 0.322 0.138 0.420 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: 404 Number of extensions: 19 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: 392 Length of database: 390 Length adjustment: 31 Effective length of query: 361 Effective length of database: 359 Effective search space: 129599 Effective search space used: 129599 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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