Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate BWI76_RS11670 BWI76_RS11670 aspartate aminotransferase family protein
Query= curated2:Q89RB7 (404 letters) >FitnessBrowser__Koxy:BWI76_RS11670 Length = 406 Score = 233 bits (593), Expect = 1e-65 Identities = 130/379 (34%), Positives = 203/379 (53%), Gaps = 6/379 (1%) Query: 20 YEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRA 79 Y P + RGEG +WD G Y+D + + GH HP+++ A+ EQA + T Sbjct: 18 YAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNG 77 Query: 80 FHNDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCA 139 + N+ + +++ T + +V NSGAEA E+A+K RK+ ++ G +++ I+ Sbjct: 78 YTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFG--SEKSGIVAFK 135 Query: 140 DNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQGE 199 + FHGRTL V P F P P + + D + + I NT A +VEP+QGE Sbjct: 136 NAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDNTCAVIVEPMQGE 195 Query: 200 AGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKALA 259 GV+ A + +RELC A+N +L+ DE+QTG+GRTG+L A H G+ D+ KAL Sbjct: 196 GGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKALG 255 Query: 260 GGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGAR 319 GGF P+ A+L++ + G HG+T+GGNPLACAVA + ++ ++ Sbjct: 256 GGF-PIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQRHQW 314 Query: 320 LLEGLKDIRA--NTVREVRGRGLMLAVELHPE-AGRARRYCEALQGKGILAKDTHGHTIR 376 E L I A +E+RG GL++ L E AG+A+ +G++ + +R Sbjct: 315 FCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLMILIAGANVVR 374 Query: 377 IAPPLVITSDEVDWALEQF 395 AP L+I+ DEV+ L++F Sbjct: 375 FAPALIISEDEVNSGLDRF 393 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: 403 Number of extensions: 21 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: 404 Length of database: 406 Length adjustment: 31 Effective length of query: 373 Effective length of database: 375 Effective search space: 139875 Effective search space used: 139875 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 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