Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate N515DRAFT_1751 N515DRAFT_1751 adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= SwissProt::P38021 (401 letters) >FitnessBrowser__Dyella79:N515DRAFT_1751 Length = 467 Score = 169 bits (427), Expect = 2e-46 Identities = 127/422 (30%), Positives = 198/422 (46%), Gaps = 50/422 (11%) Query: 16 HYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKDQADKI 75 H A LPIV E G W+ D +G Y+D +S++ GH +P+I ALK Q D + Sbjct: 39 HDHAGTVPMLPIVRGE--GPWLVDADGRRYLDGISSWWTNLFGHANPRIGAALKQQLDTL 96 Query: 76 T-LTSRAFHNDQLGPFYEKTAKLT--GKEMILPMNTGAEAVESAVKAARRWAYEVKGVAD 132 + F ++ E+ A++T G E + + G+ A+E A+K + + Y + A Sbjct: 97 EHVIFAGFTHEPAIELAERLAQITPAGLERVFLADNGSAAIEVALKMS--FHYWLNQGAG 154 Query: 133 NQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIP----------------- 175 + IA G++HG T+ A+S+S Y++ + P+L L P Sbjct: 155 QKTRFIALTGSYHGETLGALSVSDVALYRKTYAPLLLTPVLAPSPDAYEAEPGESAEACA 214 Query: 176 ---YGDVEALRQAITPNTAAFLFEP-IQGEAGIVIPPEGFLQEAAAICKEENVLFIADEI 231 G++ L + T A + EP +Q G+ + +L A+C E V FIADEI Sbjct: 215 ARRLGELRVLLEQHAHETCAVIVEPLVQCAGGMRMYHPSYLTGLRALCDEFGVHFIADEI 274 Query: 232 QTGLGRTGKTFACDWDGIVPDMYILGKALGGGVFPISCIAADREILGVF----NPGS--- 284 G GRTG FAC+ G+ PD L K L GG P+S + + F N G Sbjct: 275 AVGFGRTGTLFACEQAGVSPDFMCLSKGLTGGFLPLSAVLTTTPVYEAFYAEYNAGKAFL 334 Query: 285 HGSTFGGNPLACAVSIASLEVLEDEKLADRSLELGEYFKSELESI-DSPVIKEVRGRGLF 343 H ++ GNPLAC ++A+L++ DE + +R+ EL + L + + P + +VR G+ Sbjct: 335 HSHSYTGNPLACRAALATLDIFRDEPVLERNRELAAHLARRLAPLREHPQVADVRQTGMI 394 Query: 344 IGVEL-----TEAARPYCERL--------KEEGLLCKETHDTVIRFAPPLIISKEDLDWA 390 VEL T A P ER E G L + V+ F PP ++S ++LD Sbjct: 395 AAVELVRDKATRAPYPSEERRGLRVYLHGLEHGALLRPL-GNVVYFMPPYVVSTDELDHL 453 Query: 391 IE 392 ++ Sbjct: 454 VD 455 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: 456 Number of extensions: 26 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: 401 Length of database: 467 Length adjustment: 32 Effective length of query: 369 Effective length of database: 435 Effective search space: 160515 Effective search space used: 160515 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 Sep 17 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