Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate 5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq)
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__PV4:5210744 Length = 426 Score = 268 bits (686), Expect = 2e-76 Identities = 148/397 (37%), Positives = 224/397 (56%), Gaps = 17/397 (4%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 P+ +ER ++DV+G + DF +G+ V N GHSHP+VV A+K Q + F+H + Y Sbjct: 23 PVYVERALNAELWDVEGKRYIDFGTGIAVCNTGHSHPKVVAAVKAQLDNFSHTCVMVNPY 82 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156 E+A+ LAE+L +APG ++K ++ +GAEA E +K+ + TGR+ +AF FHGRT Sbjct: 83 ESAVALAEQLNRIAPGGSDKKAIFVTTGAEAVENCVKIARAHTGRRGVIAFNGGFHGRTN 142 Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216 ++LT + F P + H PYP + D L IE Sbjct: 143 LTMALTGKITPYKHQFGPFAGDIFHAPYPVAFHGVSVKDS-----------LKAIEHLFK 191 Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276 + P ++ AI EP+QGEGG+ P F +AL+ D++GI+L DE+Q G GRTGK + Sbjct: 192 VDIAPCDVAAIVVEPVQGEGGFYAAPPEFLQALRALCDQHGIVLVMDEIQTGFGRTGKMF 251 Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVV 335 + EH GVEPDL+ K I GG PLA V+ +++I PG T+GG+PV A + V+ Sbjct: 252 SCEHAGVEPDLMTMAKGIAGGFPLAAVVGKSEIMDAPLPGGLGGTYGGSPVGCVAALAVL 311 Query: 336 EIVKE--LLPHVQEVGDYLHKYLEEFKEKY-EVIGDARGLGLAQAVEIVKSKETKEKYPE 392 E+++E L+ ++GD ++ L KE+Y ++IG+ R G A+E+V + ++ Sbjct: 312 EVMQEEQLVERAVKIGDSFNQALSALKEQYPQLIGEVRNQGAMIAMELVIDGDIEQPNTA 371 Query: 393 LRDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKE 427 L I+ +A GLVLL CG N IRF+P L ++ E Sbjct: 372 LTQAIIANAAAHGLVLLACGFYGNVIRFLPALTISDE 408 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: 515 Number of extensions: 25 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 Sep 17 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