Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate H281DRAFT_03179 H281DRAFT_03179 4-aminobutyrate aminotransferase apoenzyme
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__Burk376:H281DRAFT_03179 Length = 429 Score = 275 bits (702), Expect = 3e-78 Identities = 161/406 (39%), Positives = 229/406 (56%), Gaps = 17/406 (4%) Query: 41 ERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAI 100 ER + ++DV+G F DFA+G+ V N GH HP++V AI+ Q ++FTH + Y + + Sbjct: 29 ERAQNAELWDVEGRRFIDFAAGIAVCNTGHRHPKIVAAIRDQLDRFTHTAYQIVPYASYV 88 Query: 101 ILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLS 160 LAEKL E APGD +K + +GAEA E A+K+ + TGR +AF FHGRT ++ Sbjct: 89 ELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKIARAATGRPGVIAFTGGFHGRTLMGMA 148 Query: 161 LTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVP 220 LT + GF P V H P+PNP + G D L + ++F+ + + Sbjct: 149 LTGKVAPYKAGFGPFPSDVFHAPFPNP------LHGVSTADSL--KAIEFLFK---ADID 197 Query: 221 PHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIEH 280 P + AI FEP+QGEGG+ P F +AL+K +E+GILL DEVQ G RTGK +A+ H Sbjct: 198 PKRVAAIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEVQTGFARTGKLFAMHH 257 Query: 281 FGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVVEIVK 339 + V PDL+ K++ GG+PL+GVI RAD+ PG T+ GNP+A+AA + V++I+ Sbjct: 258 YDVVPDLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGNPLAVAAALAVLDIID 317 Query: 340 E--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDRI 397 E L +GD + L + + I D RG G AVE K T E E R+ Sbjct: 318 EEKLCERATILGDRVKAKLIALQNEAPQIADVRGPGGMVAVEFCKPGST-EPDAEFTKRV 376 Query: 398 VKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALK 441 + KRGL+LL CG N +RF+ PL + D A+ I E+ +K Sbjct: 377 QTRALKRGLLLLVCGVYSNVVRFLFPLTIEDTVFDEALAILEDVIK 422 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: 511 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: 445 Length of database: 429 Length adjustment: 32 Effective length of query: 413 Effective length of database: 397 Effective search space: 163961 Effective search space used: 163961 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