Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_010961322.1 MCA_RS10180 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000008325.1:WP_010961322.1 Length = 391 Score = 186 bits (471), Expect = 1e-51 Identities = 130/411 (31%), Positives = 208/411 (50%), Gaps = 59/411 (14%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 P+ GEG ++D +G + D SGV V ++GH+HP V +A+ QA + H S Y Sbjct: 13 PVTFTHGEGAWLFDTEGKRYLDAVSGVAVCSLGHAHPAVAKALCDQAGRLVHCSN---LY 69 Query: 97 ENAII--LAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVK-YGTGR----KQFLAFYH 149 + LA++L +L+ D + NSGAEANEAA+K+ + YG R + + Sbjct: 70 RIGLQEDLAKQLCDLSGMD---NAFFCNSGAEANEAALKIARRYGHHRGIDTPKIVVMEG 126 Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209 +FHGRT A LS T + VQ+ GF P + G +PY + + ++PD Sbjct: 127 SFHGRTLATLSATGNPKVQE-GFAPLVGGFVRLPYGDAE----AVAAVDDPD-------- 173 Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269 + A+ EP+QGEGG +PP + LK + G LL DEVQ G+ Sbjct: 174 --------------VVAVLVEPVQGEGGVRIPPDDYLARLKSLCERRGWLLMLDEVQTGM 219 Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHR-ADITFDKPGRHATTFGGNPVAI 328 GRTG+ + +H GV PD++ KA+G G+P+ + R G+H +TFGGNP+A Sbjct: 220 GRTGRMFGHQHTGVTPDVMALAKALGNGVPIGACLARGVAAEMLTAGKHGSTFGGNPLAC 279 Query: 329 AAGIEVVEIV--KELLPHVQEVGDYLHKYLEEFKEKYE---VIGDARGLGLAQAVEIVKS 383 AA + V++ + + L + +G L L+ F+ + + + RGLGL +E+ + Sbjct: 280 AAALAVIDTLTRQSLAQRAEILGQRL---LDGFRTRLSGRPGVIEIRGLGLMIGLELERP 336 Query: 384 KETKEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAME 434 R+V + ++GL++ + ++R +PPLI+T + D +E Sbjct: 337 ----------CTRLVGMALEQGLLINVTAERTVRLLPPLILTDAQADDLVE 377 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: 414 Number of extensions: 19 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: 391 Length adjustment: 31 Effective length of query: 414 Effective length of database: 360 Effective search space: 149040 Effective search space used: 149040 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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