Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate AZOBR_RS03635 AZOBR_RS03635 aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__azobra:AZOBR_RS03635 Length = 471 Score = 209 bits (533), Expect = 1e-58 Identities = 145/429 (33%), Positives = 230/429 (53%), Gaps = 29/429 (6%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKF-THYSLTDFF 95 P++IERGEG+RV+D G + + + + +++G R+VEA +Q K T++ Sbjct: 46 PLIIERGEGVRVFDDSGKEYIEGLASLWCVSLGWGEERLVEAATRQMRKLPTYHVFGHKS 105 Query: 96 YENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTG------RKQFLAFYH 149 +E I LAE+LI+LAP + KV + NSG+EAN+ A+KLV Y +K+ L+ Sbjct: 106 HEPGIDLAERLIKLAPVPMS-KVFFANSGSEANDTAVKLVWYYNNALGRPEKKKILSRVK 164 Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209 A+HG T A SLT +D P + + H P+ YR + E ++ R+ + Sbjct: 165 AYHGVTVATASLTGLVNNHRDFDLP-IARIQHTDCPHHYRFA---EPGESEEDFATRLAE 220 Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269 +E + P I A+F EP+ G GG +VPP +F ++ +Y ILL DEV G Sbjct: 221 SLEALILAE-GPETIAAMFAEPVMGAGGVIVPPATYFAKIQPILKKYDILLVADEVICGF 279 Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGV-----IHRADITFDK---PGRHATT 320 GRTG FW + G++PD++ K + G LP++ V ++RA + K H T Sbjct: 280 GRTGNFWGSQTMGMQPDILTCAKQLSSGYLPISAVMVSDAVYRACVEESKKIGTFGHGYT 339 Query: 321 FGGNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAV 378 + +PVA A IE ++I +E L+ HV+ V + L+ + + ++G+ARG+GL A+ Sbjct: 340 YSAHPVAAAVAIETLKIYEERDLVGHVRAVAPLFQRRLKALAD-HPLVGEARGVGLIGAL 398 Query: 379 EIVKSKETKEKY-PELRDRIVKE--SAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEI 435 E+V KETK + P R V S + GL++ GD S+ PPL++ +E+I+ + Sbjct: 399 ELVADKETKTPFDPVGRAGAVVNGLSQENGLIIRAMGD-SVAVCPPLVIGEEDINRMFDR 457 Query: 436 FEEALKAAL 444 AL AA+ Sbjct: 458 LTTALDAAI 466 Lambda K H 0.320 0.141 0.418 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: 544 Number of extensions: 32 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: 445 Length of database: 471 Length adjustment: 33 Effective length of query: 412 Effective length of database: 438 Effective search space: 180456 Effective search space used: 180456 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 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