Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_053937056.1 WG78_RS06780 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_001294205.1:WP_053937056.1 Length = 400 Score = 204 bits (518), Expect = 5e-57 Identities = 132/411 (32%), Positives = 203/411 (49%), Gaps = 46/411 (11%) Query: 38 IVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYE 97 IV RG G RV+D G + DF G+ V ++GH HP +V A+ +Q K H S F E Sbjct: 21 IVPVRGAGSRVWDQAGKEYIDFGGGIAVNSLGHCHPELVAALTEQGNKLWHISNV-FTNE 79 Query: 98 NAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV------KYGTGRKQFLAFYHAF 151 A+ LA+ L+E +V + NSGAEANEAA+KL KYG + + L+ ++F Sbjct: 80 PALALAKTLVEHT---FAERVFFCNSGAEANEAALKLARRASIEKYGERKNKVLSALNSF 136 Query: 152 HGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFI 211 HGRT +S+ DGF P G+ H Y + L + Sbjct: 137 HGRTFFTVSVGGQP-KYSDGFGPKPAGIEHFKYND---------------------LASL 174 Query: 212 EEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGR 271 E + + + EPIQGEGG + F + ++ D++ LL DEVQ G GR Sbjct: 175 EALI-----DDDTACVIIEPIQGEGGVTPATQEFLQGVRALCDKFNALLIFDEVQSGNGR 229 Query: 272 TGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD-KPGRHATTFGGNPVAIAA 330 TG +A FGV PD++ K +GGG P+ ++ + G H TT+GGNP+A A Sbjct: 230 TGSLYAYMDFGVVPDILSTAKGLGGGFPIGAMLTTEKVAKHLVAGTHGTTYGGNPLATAV 289 Query: 331 GIEVVEIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKE 388 + I+ E L V+ + + L+ +KY V+ + RG+GL V++ K Sbjct: 290 AGTAISIITRPETLSGVKAKSERIRAGLQAIADKYPVVAEIRGMGLLIGVQL------KA 343 Query: 389 KYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEA 439 +Y ++ +A+ G+++L G + +RF P L+++ +EID + E+A Sbjct: 344 EYAGRSRDVLNAAAEEGVLVLAAGPDVVRFAPSLVISDDEIDAGLARVEKA 394 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: 439 Number of extensions: 25 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 445 Length of database: 400 Length adjustment: 32 Effective length of query: 413 Effective length of database: 368 Effective search space: 151984 Effective search space used: 151984 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