Align Ornithine aminotransferase; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_013835162.1 THICY_RS03115 diaminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P07991 (424 letters) >NCBI__GCF_000214825.1:WP_013835162.1 Length = 428 Score = 167 bits (424), Expect = 4e-46 Identities = 137/417 (32%), Positives = 207/417 (49%), Gaps = 48/417 (11%) Query: 27 PVVFHKAKGAHVWDPEGKLYLDFLSAYSAVNQGHCHPHIIKALTEQAQ------TLTLSS 80 P VF A A + D EGK Y+DF ++N GH HP I +AL Q L ++ Sbjct: 21 PAVFDTATSATIVDVEGKRYIDFFGGAGSLNYGHNHPLINQALITYIQRNGITNALDKAT 80 Query: 81 RAFHNDVYA-QFAKFVTEFFGFETVLPMNTGAEAVETALKLARRWGYMKKNIPQDKAIIL 139 A H+ + A Q ++ TGA VETALKLAR+ MKK ++ ++ Sbjct: 81 VAKHDFISAFQSIILKPRKMDYKIQFVGPTGANGVETALKLARK---MKK-----RSNVI 132 Query: 140 GAEGNFHGRTFGAISLSTDYEDSKLHFGPF--VPNVASGHSVHKIRYG----HAEDFVPI 193 +HG + GA++++ ++ + G + VP +V+K+ Y H D V + Sbjct: 133 AFTNAYHGHSLGALAVT----GNEFYHGDYYDVPR-----NVNKMPYDNYFDHDMDSVDM 183 Query: 194 LESPEGKNV------AAIILEPIQGEAGIVVPPADYFPKVSALCRKHNVLLIVDEIQTGI 247 L G AA+I+E IQGE GI V + K+SALC++ ++LLI+DEIQ G Sbjct: 184 LRHYLGDGSSGYELPAAVIVESIQGEGGINVASVGWLQKLSALCKEMDILLIMDEIQVGN 243 Query: 248 GRTGELLCYDHYKAEAKPDIVLLGKALSGGVLPVSCVLSSHDIMSCFTPGSHGSTFGGNP 307 GRTG+ ++ +A PDI+ L K++ G +P+S VL + ++PG H TF GN Sbjct: 244 GRTGDYFSFE--RAGIMPDIITLSKSIGTG-MPMSIVLMKPSV-DVWSPGEHTGTFRGNS 299 Query: 308 LASRVAIAALEVIRDEKLCQRAAQLGSSFIAQLKALQAKSNGIISEVRGMGL---LTAIV 364 A AALE+ R++ + G A K QA+ G I++VRG+G+ L ++V Sbjct: 300 YAFIAGAAALELWRNDDFSRSIRAKGKQVEAAFKDFQARFPGWITDVRGLGMIWGLESLV 359 Query: 365 IDPSKANGKTAWDLCLLMKDHGLLAKPTHDHIIRLAPPLVISEEDLQTGVETIAKCI 421 K A+ L+M+ G D +++ PLVISE +L G E + I Sbjct: 360 EGFCNEVSKQAFQRGLMMETAG-----ASDQVLKFLGPLVISETELNEGFEILTDAI 411 Lambda K H 0.319 0.136 0.407 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: 448 Number of extensions: 25 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: 424 Length of database: 428 Length adjustment: 32 Effective length of query: 392 Effective length of database: 396 Effective search space: 155232 Effective search space used: 155232 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: 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