Align Alanine--glyoxylate aminotransferase; AGT; Serine--pyruvate aminotransferase; SPT; EC 2.6.1.44; EC 2.6.1.51 (characterized)
to candidate H281DRAFT_04750 H281DRAFT_04750 aspartate aminotransferase
Query= SwissProt::P31030 (392 letters) >FitnessBrowser__Burk376:H281DRAFT_04750 Length = 407 Score = 186 bits (471), Expect = 1e-51 Identities = 120/358 (33%), Positives = 185/358 (51%), Gaps = 10/358 (2%) Query: 24 LLLGPGPSNLPPRVLAAGGLQMIGHMHEEMYQVMDEIKQGIQYAFQTRNALTLAVSGSGH 83 L++G GP +P V A + +I H+ M +V+ ++K +Y FQT + L V+G G Sbjct: 31 LMMGAGPVPIPAAVAKANTI-VINHLGATMVKVIGQVKTMARYVFQTNSKWVLGVAGPGS 89 Query: 84 CALETALFNLLEPGDAFLVGANGIWGQRAAEVGERIGARVHPMIKDPGSHYTLQEVEECL 143 A+E A+ NL G L NG + R AE+G R+GARV + + +L E+ E + Sbjct: 90 AAMEMAISNLAWEGTRVLSIKNGFFSGRMAEMGRRVGARVTELEVADRTVASLDEIAEAI 149 Query: 144 AQHKPVLLFLTHGESSTGVLQ-PLDGFGELCHRYKCLLLVDSVASLGGAPIYMDQQGIDV 202 + +P ++ + GE+S V L L L++VD+V +L P+ MD GID Sbjct: 150 RRERPEIVTVVQGETSNTVWNYQLKDIAALAKAAGALVIVDAVCTLSTMPLAMDAWGIDA 209 Query: 203 LYSGSQKALNAPPGTSLISFSDKAKSKIYARKTKPFSFYMDVQLLANIWGCDGKPRMYHH 262 + +G QK L++ PG SLI+FSD A ++ R + +D L N W G YH+ Sbjct: 210 VITGGQKGLSSIPGVSLIAFSDAAWERVKGRTAPNAHWCLDASLAENFWHNAG----YHY 265 Query: 263 TTPVIGIFALRESLALLVEQGLEKSWQRHREVAQHLYRRLQELGLQLFVKDPALRLPTVT 322 T PV G+ AL E+L L+ + LEK + RH + + L + LGLQL+ A RL +V Sbjct: 266 TAPVSGVLALHEALRLVCAETLEKRFARHLKCSVALQEGVTALGLQLYA-PVACRLNSVV 324 Query: 323 TVIVPASYRWRDIVSYVMHHFGIEITGGLGPSADKVLRIGLLGCNATRENVDRLATAL 380 + VPA D+ +++ +EI+G G ++RIG +G N+ R AL Sbjct: 325 GIEVPAGLSPGDVCAHISRQHQVEISGSFGL---PIVRIGQMGEQCREHNLFRTLHAL 379 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: 327 Number of extensions: 23 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: 407 Length adjustment: 31 Effective length of query: 361 Effective length of database: 376 Effective search space: 135736 Effective search space used: 135736 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