Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate BPHYT_RS22435 BPHYT_RS22435 4-aminobutyrate aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__BFirm:BPHYT_RS22435 Length = 427 Score = 270 bits (690), Expect = 7e-77 Identities = 161/406 (39%), Positives = 227/406 (55%), Gaps = 17/406 (4%) Query: 41 ERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAI 100 ER E ++DV+G F DFA+G+ V N GH HP+++ AI+ Q + FTH + Y + + Sbjct: 27 ERAENAELWDVEGRRFIDFAAGIAVCNTGHRHPKILAAIRDQLDHFTHTAYQIVPYASYV 86 Query: 101 ILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLS 160 LAEKL E APGD +K + +GAEA E A+K+ + TGR +AF FHGRT ++ Sbjct: 87 ELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKIARAATGRPGVIAFTGGFHGRTLMGMA 146 Query: 161 LTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVP 220 LT + GF P V H P+PNP + G D L + ++F+ + + Sbjct: 147 LTGKVAPYKIGFGPFPSDVFHAPFPNP------LHGVTTADSL--KAIEFLFK---ADID 195 Query: 221 PHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIEH 280 P + AI FEP+QGEGG+ P F +AL+K +E+GILL DEVQ G RTGK +A+ H Sbjct: 196 PKRVAAIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEVQTGFARTGKLFAMHH 255 Query: 281 FGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVVEIVK 339 + V PDL+ K++ GG+PL+GVI RAD+ PG T+ GNP+A+AA V++I+ Sbjct: 256 YDVVPDLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGNPLAVAAAHAVLDIID 315 Query: 340 E--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDRI 397 E L +GD + L + I D RG G AVE K+ T E E R+ Sbjct: 316 EEKLCERATLLGDRVKAKLIALQSDVPQIADVRGPGGMVAVEFCKAGGT-EPDAEFTKRV 374 Query: 398 VKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALK 441 + +RGL+LL CG N +RF+ PL + D AM I E+ +K Sbjct: 375 QTRALERGLLLLVCGVYSNVVRFLFPLTIQDAVFDEAMAILEDVIK 420 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: 509 Number of extensions: 27 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: 445 Length of database: 427 Length adjustment: 32 Effective length of query: 413 Effective length of database: 395 Effective search space: 163135 Effective search space used: 163135 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 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