Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__HerbieS:HSERO_RS05420 Length = 426 Score = 259 bits (662), Expect = 1e-73 Identities = 148/408 (36%), Positives = 229/408 (56%), Gaps = 17/408 (4%) Query: 41 ERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAI 100 ER ++DV+G F DFA+G+ V+N GH HP++++A++ Q +KFTH + Y + + Sbjct: 31 ERAANAELWDVEGRRFIDFAAGIAVLNTGHRHPKLLDAMRAQMDKFTHTAYQIVPYASYV 90 Query: 101 ILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLS 160 LAE++ L PG+ +K + ++GAEA E A+K+ + TGR +AF FHGRT ++ Sbjct: 91 ELAERINRLTPGNYPKKTAFFSTGAEAVENAIKIARAHTGRPGVIAFAGGFHGRTMMGMA 150 Query: 161 LTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVP 220 LT + GF P V H PYP+ + G D L+ ++ + Sbjct: 151 LTGKVAPYKLGFGPFPGDVFHAPYPS------ALHGITSED-----ALEAVKGLFKSDIE 199 Query: 221 PHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIEH 280 + AI EP+QGEGG+ P F + L+ DE+GILL DEVQ G GRTGK +A+EH Sbjct: 200 AKRVAAIILEPVQGEGGFYAAPADFMRGLRALCDEHGILLIADEVQSGYGRTGKLFAMEH 259 Query: 281 FGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVVEIVK 339 + V PDL+ K++ GG+PL+ V RA+I PG T+ GNP+AIA+ + V+++++ Sbjct: 260 YDVLPDLMTMAKSLAGGMPLSAVNGRAEIMDAPAPGGLGGTYAGNPLAIASALAVLDVME 319 Query: 340 E--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDRI 397 E L+ Q +GD L ++L+E + I + RG+G AVE T + E ++ Sbjct: 320 EEQLVTRGQRLGDKLQEHLKELRSSVPQIAEVRGVGAMVAVEFA-DPATGKPDAEYTKKV 378 Query: 398 VKESAKRGLVLLGCGD--NSIRFIPPLIVTKEEIDVAMEIFEEALKAA 443 + + GL+LL CG N IRF+ PL + +D A+ I +A++ A Sbjct: 379 QQHALNNGLLLLTCGSYGNVIRFLFPLTIPDTVMDEALGILAKAIRLA 426 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: 538 Number of extensions: 28 Number of successful extensions: 4 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: 426 Length adjustment: 32 Effective length of query: 413 Effective length of database: 394 Effective search space: 162722 Effective search space used: 162722 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 09 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