Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate BWI76_RS24630 BWI76_RS24630 putrescine aminotransferase
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__Koxy:BWI76_RS24630 Length = 468 Score = 253 bits (647), Expect = 6e-72 Identities = 151/418 (36%), Positives = 234/418 (55%), Gaps = 37/418 (8%) Query: 1 MLDLYEHTDKYSSKNYSPLKLALAKG------RGAKVW---------DIEDNCYIDCISG 45 M L + +Y ++ +P LA K GA W D + +IDC+ G Sbjct: 40 MKSLNQEVREYFKEHVNPGFLAYRKSVTAGGDYGAVEWQAGGLNTLVDTQGQEFIDCLGG 99 Query: 46 FSVVNQGHCHPKIIKALQEQSQRITMVSRALYSDNLGKWEEKICKLANKENVLPM--NTG 103 F + N GH +P ++ A++ Q + + S+ L + + L + N+G Sbjct: 100 FGIFNVGHRNPVVVSAVENQLAKQPLHSQELLDPLRAMLAKTLAALTPGKLKYSFFSNSG 159 Query: 104 TEAVETAIKMARKWGADIKNIDESSSEIIAMNGNFHGRTLGSLSLSSQDSYKKGFGPLLN 163 TE+VE A+K+A+ + + +A +G FHG++LG+LS +++ +++K F PLL Sbjct: 160 TESVEAALKLAKAYQSP-----RGKFTFVATSGAFHGKSLGALSATAKSTFRKPFMPLLP 214 Query: 164 NIHYADFGDIEQLKKLIN------NQTTAIILEPIQGEGGVNIPPTHFIQEVRQLCNEYN 217 + FGDI ++ L++ + A+ILEPIQGEGGV +PP ++ VR+LC+E+ Sbjct: 215 GFRHVPFGDINAMRTLLSECKKTGDDVAAVILEPIQGEGGVILPPPGYLPAVRKLCDEFG 274 Query: 218 VLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLGGGLYPISAVLANQDVMSVL--T 275 LLI DE+Q G+GRTGKMFA E EN +PDI L K+LGGG+ PI A +A ++V SVL Sbjct: 275 ALLILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFDN 334 Query: 276 PGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDRLLKHLQQIESE---LIVEVR 332 P H +TFGGNPLACA ++A ++VL ++L A GD LL +Q+ E L+ EVR Sbjct: 335 PFLHTTTFGGNPLACAAALATINVLLTQNLPAQAEQKGDMLLDGFRQLAREYPDLVNEVR 394 Query: 333 GRGLFIGIEL--NVAAQDYCEQMINKGVLCKETQGN--IIRIAPPLVIDKDEIDEVIR 386 G+G+ + IE N D+ +M + VL T N IR+ PPL + ++ ++V++ Sbjct: 395 GKGMLMAIEFVDNEIGYDFASEMFRQRVLVAGTLNNARTIRVEPPLTLTLEQCEQVLK 452 Lambda K H 0.317 0.136 0.396 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: 409 Number of extensions: 23 Number of successful extensions: 7 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: 394 Length of database: 468 Length adjustment: 32 Effective length of query: 362 Effective length of database: 436 Effective search space: 157832 Effective search space used: 157832 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 (21.6 bits) S2: 51 (24.3 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