Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate RR42_RS26850 RR42_RS26850 hypothetical protein
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__Cup4G11:RR42_RS26850 Length = 447 Score = 192 bits (488), Expect = 2e-53 Identities = 144/438 (32%), Positives = 222/438 (50%), Gaps = 31/438 (7%) Query: 32 DPNEYFLVIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAG 91 +P + V +G+ +D +G +D S G V +G +P+VIEAIK+Q D + +A Sbjct: 8 NPRQTLAVAVAGKGIELVDSNGKHYIDASGGAAVSCLGHGHPRVIEAIKQQADSLAYAHT 67 Query: 92 TDYYNPYQVELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIAKW------STNRKMFI 145 + + ELA+ L + APGD+ F+S G+EA EAALK+A+ T R+ FI Sbjct: 68 SFFTTEVSEELARTLAQAAPGDLNHVYFVSG-GSEAVEAALKLARQYFVEIGQTQRRHFI 126 Query: 146 AFIGAFHGRTHGTMSLTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELIN 205 A ++HG T G +++ +R P + HV YR+ + E + Sbjct: 127 ARRQSYHGNTLGALAI-GGNAWRREPFLPLLVPAHHVAPCYAYRDQ---EAGETDQQYAQ 182 Query: 206 RVIDYIEEYLFEHYVPAEEVAGIFFEPIQGEGGYVVPP-KNFFKELKKLADKHGILLIDD 264 R+ D +E + E + VA E + G VPP ++ + ++ + DK+G+LLI D Sbjct: 183 RLADELEAKILE--LGPHSVAAFVAETVVGATAGAVPPVADYLRRVRAVCDKYGVLLILD 240 Query: 265 EVQMGMGRTGRMWAIEHFDIVPDIVTVAKALGGGI-PIGATIFRA---DLDFGVSGV--H 318 E+ GMGRTG ++A E +VPDIVT+AK L G PIGA I + D G SG H Sbjct: 241 EIMSGMGRTGYLFACEEDGVVPDIVTIAKGLAAGYQPIGAMISSSRIYDAVVGGSGFFQH 300 Query: 319 SNTFGGNTVAAAAALAVIEEL-QNGLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLA 377 +T+ G+ A AAALAV + ++ L+EN R RL E + +GD+RG GL Sbjct: 301 GHTYIGHATACAAALAVQRTIAEDCLLENVLARGGQLRARLRETLGDHPNVGDIRGRGLF 360 Query: 378 WGVEFVKDRKTK---EYATKERGEIVVEALKRGLALLGCGKSA-------IRLIPPLIIS 427 GVEFV +R+TK + A K + A++ GL + G + + PP I S Sbjct: 361 VGVEFVAERETKATLDPALKMHARLKSTAMQNGLLIYPMGGTVDGMRGDHVLFAPPFICS 420 Query: 428 EEEAKMGLDIFEEAIKVV 445 ++ ++ F +++ V Sbjct: 421 AQDIDRIVERFAASVQAV 438 Lambda K H 0.319 0.139 0.410 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: 498 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: 454 Length of database: 447 Length adjustment: 33 Effective length of query: 421 Effective length of database: 414 Effective search space: 174294 Effective search space used: 174294 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 (21.7 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