Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_086510079.1 BZY95_RS11580 hypothetical protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_002151265.1:WP_086510079.1 Length = 474 Score = 166 bits (420), Expect = 1e-45 Identities = 126/424 (29%), Positives = 202/424 (47%), Gaps = 26/424 (6%) Query: 39 VIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHY-SLTDFFYE 97 VI G+GI + D DG F D +G+ +N+G+ V EAI +QA + ++Y + E Sbjct: 35 VITGGKGIHIVDKDGREFIDGFAGLYCVNIGYGRTEVAEAIYQQALELSYYHTYVGHSNE 94 Query: 98 NAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTG------RKQFLAFYHAF 151 I L+EK+I LA G KV YG G++ANE +K+V+Y +K+ ++ + Sbjct: 95 PQIALSEKIIALA-GPGMSKVYYGLGGSDANETQLKIVRYYNNVLGRPQKKKVISRQRGY 153 Query: 152 HGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFI 211 HG A SLT K D F + G+ H P Y +G E E + + Sbjct: 154 HGSGLATGSLTGLK-AFHDQFDLPLAGILHTEAPYYYHRAAEQEGMSER-EFSQFCAQKL 211 Query: 212 EEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGR 271 EE + P + A EP+ G GG V PP+G+++A++ +Y +LL DEV G GR Sbjct: 212 EEMILAE-GPDTVAAFIGEPVLGTGGIVPPPEGYWEAIQAVLAKYDVLLIADEVVCGFGR 270 Query: 272 TGKFWAIEHFGVEPDLIQFGKAIGGGL-PLAGVI--HRADITFDK------PGRHATTFG 322 G + H+G++PDLI K + PL+GVI R ++ P H T+ Sbjct: 271 IGADFGSHHYGIKPDLITVAKGLTSAYQPLSGVIVGDRVWSVLEQGTGQYGPIGHGWTYS 330 Query: 323 GNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEI 380 G+ + AA + + I++ L + E G YL + ++ ++ ++G+ RG+G+ A+E Sbjct: 331 GHALGCAAALANLAIIEREGLTRNAAETGAYLQQRMQAAFGEHPIVGNVRGVGMLAALEF 390 Query: 381 VKSKETKEKYP---ELRDRIVKESAKRGLVLLGCGDNSI-RFIPPLIVTKEEIDVAMEIF 436 + + ++ RI + L+ I F PPL+ T EID + Sbjct: 391 SVDPARRAHFDAAHKVGPRIAAAALDENLIARAMPQGDILGFAPPLVATPAEIDEIVARA 450 Query: 437 EEAL 440 E A+ Sbjct: 451 ERAV 454 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: 579 Number of extensions: 29 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: 474 Length adjustment: 33 Effective length of query: 412 Effective length of database: 441 Effective search space: 181692 Effective search space used: 181692 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 Apr 10 2024. The underlying query database was built on Apr 09 2024.
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