Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_110205831.1 DNK54_RS04735 acetylornithine transaminase
Query= curated2:Q89RB7 (404 letters) >NCBI__GCF_003194585.1:WP_110205831.1 Length = 396 Score = 261 bits (666), Expect = 3e-74 Identities = 152/383 (39%), Positives = 209/383 (54%), Gaps = 21/383 (5%) Query: 25 VVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRAFHNDQ 84 +VL++GEG VWD DGN YLD L + GH HP ++ A+ +Q L S F + Sbjct: 24 LVLAKGEGATVWDADGNEYLDLLGGIAVNLLGHAHPALIEAVTQQLGTLGHVSNFFTSGP 83 Query: 85 LAPFYEEIAALTGSH-KVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCADNFH 143 E + AL G +V NSG EA E+A K R+ G + ++ FH Sbjct: 84 QVELAERLLALLGQDGRVFLSNSGTEANEAAFKITRRTG---------RTHVVATEGGFH 134 Query: 144 GRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQGEAGVI 203 GRT+G + ++ R F P +P+GDAAALE A+T T A ++EPIQGEAGV Sbjct: 135 GRTMGALALTSKAAYRDPFAPLPGDVTFVPYGDAAALEAAVTDQTAAVVLEPIQGEAGVN 194 Query: 204 IPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEG-----IEADVTLLGKAL 258 +PP+ Y +VRE+ + + ++ LDEIQTG+GRTG+ A QH G + D+ L K L Sbjct: 195 VPPSDYLARVREITSRHGALMWLDEIQTGVGRTGRWFAHQHPGLAPEPVTPDLITLAKGL 254 Query: 259 AGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGA 318 GG P+ A ++ L+PGQHG+TFGGNP+A A A A +RV EE ++ A G Sbjct: 255 GGGL-PIGATIALGAAGDLLQPGQHGTTFGGNPVATAAALAVLRVAEEESLLARAEALGE 313 Query: 319 RLLEGLKDIRANTVREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHTIRIA 378 RL GL D R V EVRG GL++ ++L E R+ A G G + + H IR+A Sbjct: 314 RLRAGLADPR---VSEVRGLGLLIGLDLAQE--RSAEVAAAALGAGFIINNPTPHRIRLA 368 Query: 379 PPLVITSDEVDWALEQFATTLTQ 401 PPLV+T + D L + L Q Sbjct: 369 PPLVLTDAQADRFLAAWPGILDQ 391 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: 465 Number of extensions: 24 Number of successful extensions: 5 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: 396 Length adjustment: 31 Effective length of query: 373 Effective length of database: 365 Effective search space: 136145 Effective search space used: 136145 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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