Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_245779653.1 BM299_RS04985 aspartate aminotransferase family protein
Query= SwissProt::P38021 (401 letters) >NCBI__GCF_900115975.1:WP_245779653.1 Length = 471 Score = 244 bits (622), Expect = 5e-69 Identities = 155/411 (37%), Positives = 218/411 (53%), Gaps = 62/411 (15%) Query: 32 ALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKD--------QADKITLTSRAFH 83 A G V D EGN Y+D L Y ++N GH HP++I+A++ QA T+T+ H Sbjct: 57 AEGTRVWDSEGNAYLDFLGGYGSLNIGHNHPRVIEAVEQVRELPNILQASIPTITAALLH 116 Query: 84 NDQLGPFYEKTAKLT-GK-EMILPMNTGAEAVESAVKAARRWAYEVKGVADNQAEIIACV 141 N A +T GK + N+GAEAVE A+K AR A + I C Sbjct: 117 N---------LAVITPGKLKRSFLCNSGAEAVEGALKLAR--------AATGRKTFIYCR 159 Query: 142 GNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAITP-NTAAFLFEPIQG 200 +FHG++ A+S++ E+Y+ F P+L + +P+GD++ALR+A+ AAF+ EP+QG Sbjct: 160 NSFHGKSFGALSVTGREKYRELFEPLLFDCREVPFGDIDALRKALRKYQAAAFIVEPVQG 219 Query: 201 EAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDGIVPDMYILGKAL 260 E GI +PP G+L EAA C++ LFIADEIQTG GRTG FAC + + PD+ L K+L Sbjct: 220 EGGINMPPRGYLSEAARACRDAGTLFIADEIQTGFGRTGAMFACQHENVEPDVMCLAKSL 279 Query: 261 GGGVFPISCIAADREIL-----GVFNPGSHGSTFGGNPLACAVSIASLEVLEDEKLADRS 315 GGG+ PI + +I V H STFGGN A A IA++EVL EKL + Sbjct: 280 GGGIMPIGAFITNDDIWQKAYGSVEKATLHTSTFGGNTWAAAAGIAAIEVLVKEKLPAAA 339 Query: 316 LELGEYFKSELESIDS--PVIKEVRGRGLFIGVELTEAARPYCERLKEEGLLCKETHD-- 371 E G YF S L + P+++EVRG+GL IG+EL + GL K +H+ Sbjct: 340 AEKGTYFISGLRDLQKKYPLLQEVRGQGLLIGIELAQPGG--LTNKATMGLASKLSHEYL 397 Query: 372 -----------------------TVIRFAPPLIISKEDLDWAIEKIKHVLR 399 VIR PPL ++ E+LD+ + + VL+ Sbjct: 398 GSMVAGELLNRHRIITAYTLNNPNVIRMEPPLTVTGEELDYVLNALDDVLK 448 Lambda K H 0.318 0.136 0.401 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: 467 Number of extensions: 26 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 401 Length of database: 471 Length adjustment: 32 Effective length of query: 369 Effective length of database: 439 Effective search space: 161991 Effective search space used: 161991 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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