Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_057509166.1 ABB28_RS13775 aspartate aminotransferase family protein
Query= curated2:Q89RB7 (404 letters) >NCBI__GCF_001431535.1:WP_057509166.1 Length = 408 Score = 257 bits (656), Expect = 5e-73 Identities = 155/380 (40%), Positives = 212/380 (55%), Gaps = 7/380 (1%) Query: 20 YEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRA 79 Y+P VVL RG+G VWD+ G Y+D + + GH P + AA+VEQA +L TS Sbjct: 19 YKPRQVVLERGQGARVWDSQGREYIDLAAGIAVCGLGHNDPDLTAALVEQAGKLWHTSNV 78 Query: 80 FHNDQLAPFYEEIA-ALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVC 138 F++ EE+ A + +V NSGAEA E AIK VRKW +G P D+ I+ Sbjct: 79 FYSAPPLHLAEELVKASRFAERVFLCNSGAEANEVAIKMVRKWASS-QGRPADRRVIVTF 137 Query: 139 ADNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVA-FLVEPIQ 197 +FHGRTL V + P+ + + P GFR + F D LE A+ VA ++EP+Q Sbjct: 138 RGSFHGRTLAAVTATAQPKYQEGYEPLPQGFRYVDFNDEVQLETAMAAGDVAAVMLEPVQ 197 Query: 198 GEAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKA 257 GE GV+ G+ +VRELC + +LVLDEIQ G+GRTG L A +G+ D+ L KA Sbjct: 198 GEGGVMPARPGFLKRVRELCDQHGALLVLDEIQAGMGRTGTLFAHWQDGVVPDMVTLAKA 257 Query: 258 LAGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQG 317 L GGF P+ A+L+ +V T++ G HG+TFGGNPLA AVAR A+R L + + N RQ Sbjct: 258 LGGGF-PIGAMLAGPKVAETMQFGAHGTTFGGNPLAAAVARVALRKLASDEIAANVDRQS 316 Query: 318 ARLLEGLKDIRA--NTVREVRGRGLMLAVELHPE-AGRARRYCEALQGKGILAKDTHGHT 374 L EG + I A +VRGRGLML L + G+A + G+L Sbjct: 317 RALREGFERINAEFGVFGQVRGRGLMLGAVLSKDHLGQAGVILDHAAEHGLLTLQAGPDV 376 Query: 375 IRIAPPLVITSDEVDWALEQ 394 +R P L IT +E+ L++ Sbjct: 377 LRFVPSLNITDEEIAEGLKR 396 Lambda K H 0.319 0.136 0.405 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: 443 Number of extensions: 21 Number of successful extensions: 6 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: 404 Length of database: 408 Length adjustment: 31 Effective length of query: 373 Effective length of database: 377 Effective search space: 140621 Effective search space used: 140621 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 (21.8 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