Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_015929538.1 MNOD_RS13870 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000022085.1:WP_015929538.1 Length = 457 Score = 167 bits (422), Expect = 8e-46 Identities = 130/428 (30%), Positives = 197/428 (46%), Gaps = 31/428 (7%) Query: 39 VIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFF--- 95 V+ +G V D G D +G+ +N G+ H +VEA +Q + + T +F Sbjct: 31 VLRSAKGATVTDAAGRELLDGFAGLWCVNAGYGHDSIVEAAARQMRELPY--ATAYFGLG 88 Query: 96 YENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVK-YGTGR-----KQFLAFYH 149 E AI LA L E APGD+ V + G++A + ++L++ Y T R QF++ Sbjct: 89 SEPAIRLAAALAERAPGDLNH-VYFTLGGSDAVDTTVRLIRNYQTVRGKPEKDQFISLEQ 147 Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209 +HG + LTA + P IP P PYRN G D + + L Sbjct: 148 GYHGSSTVGAGLTALPAFHANFGLP-FAWQHKIPSPYPYRNPAGSD----LEAIIAASLA 202 Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269 + V + P + A + EPIQG GG +VPP+G+ KA++ E IL DEV G Sbjct: 203 ALRAKV-EELGPERVAAFYAEPIQGSGGVIVPPRGWMKAMRDLCAELDILFVADEVITGF 261 Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKPG--------RHATTF 321 GRTG +A V PDL+ K + G G + ++ +D H T+ Sbjct: 262 GRTGPLFACTEDEVVPDLMTTAKGLTSGYVPMGAVFLSNRIYDTIADGAGEAAIGHGYTY 321 Query: 322 GGNPVAIAAGIEVVEIVKE-LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEI 380 +PV+ A G+EV+ + + LL + + G L L+ + + ++GD RG GL A+E+ Sbjct: 322 SAHPVSAAVGLEVLRLYENGLLENGRRAGTRLQAGLQSLAD-HPLVGDVRGRGLLAALEL 380 Query: 381 VKSKETKEKYPELRD---RIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFE 437 V K K P D RI + GLV+ G+ + + PPL T+ EID +E Sbjct: 381 VVDKARKAPLPAAADPARRIFDRAWNNGLVIRAFGNGILGYAPPLCCTEAEIDAIVERTR 440 Query: 438 EALKAALK 445 L L+ Sbjct: 441 RILDQTLE 448 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: 505 Number of extensions: 29 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: 457 Length adjustment: 33 Effective length of query: 412 Effective length of database: 424 Effective search space: 174688 Effective search space used: 174688 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