Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_011307353.1 MBAR_RS12680 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000195895.1:WP_011307353.1 Length = 471 Score = 307 bits (787), Expect = 4e-88 Identities = 180/436 (41%), Positives = 263/436 (60%), Gaps = 18/436 (4%) Query: 12 GPKAKEVIERNFKYLAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHS 71 GP+A+E+IE++ K + T P P+V++ +G + DVDG + D +G+ V+N G+S Sbjct: 48 GPRAREIIEQDCKITSACTARP--YPLVVDSAKGSVIRDVDGREYIDLIAGIAVMNAGYS 105 Query: 72 HPRVVEAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAA 131 +P V AI Q EK TH DFF E + LA+KL +L+ KV Y NSG EA EAA Sbjct: 106 NPEVKAAISAQLEKMTHCGYGDFFAEPPVKLAKKLEDLSGYS---KVFYCNSGTEAVEAA 162 Query: 132 MKLVKYGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPN--PYR 189 +KL + T R+ ++FY++FHGRT LSLT SK Q++ F +H Y P++ Sbjct: 163 IKLAFWKTKRQGLISFYNSFHGRTLGSLSLTCSKARQKEHFPVLHTAHSHYAYCYRCPFK 222 Query: 190 NTWGIDGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKAL 249 + G E EL N + R + P + A+F EP+QGEGGY+VPP F K + Sbjct: 223 LEYPSCGIECAKELENLIFR-------RELSPTDTAAVFVEPVQGEGGYIVPPPEFHKEV 275 Query: 250 KKFADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI 309 ++ + +LL DEVQ G RTG F A+E+FGV ++ F KA+GGGLPL ++ ++ Sbjct: 276 RRICTDNDVLLVADEVQAGCFRTGPFLAMENFGVRAEISCFAKALGGGLPLGAMLADREL 335 Query: 310 TFDKPGRHATTFGGNPVAIAAGIEVVEIV-KELLPH-VQEVGDYLHKYLEEFKEKYEVIG 367 G H+ TFGGN +A AA + +E + KE + H V+E+G + + L E +E + IG Sbjct: 336 MDWPQGIHSNTFGGNLLASAASLASLEFLEKENIEHRVKELGSQMKQRLRELQENFPCIG 395 Query: 368 DARGLGLAQAVEIVKSKETKEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKE 427 D RGLGL VEIVK ++ + P RDRI++++ K G++LL CGD+ IRF PPL++T E Sbjct: 396 DVRGLGLMVGVEIVKPDKSID--PIQRDRILRKAFKEGILLLPCGDSVIRFSPPLVITDE 453 Query: 428 EIDVAMEIFEEALKAA 443 E+D +E F++AL+ A Sbjct: 454 ELDSGLEKFQKALEKA 469 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: 548 Number of extensions: 25 Number of successful extensions: 6 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 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