Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate GFF2831 PGA1_c28770 taurine--pyruvate aminotransferase Tpa
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__Phaeo:GFF2831 Length = 465 Score = 188 bits (478), Expect = 3e-52 Identities = 133/434 (30%), Positives = 216/434 (49%), Gaps = 33/434 (7%) Query: 34 ENLPIVIERGEGIRVYDVDGNVFYDFASG-VGVINVGHSHPRVVEAIKKQAEKFTHYSLT 92 EN P +I G+G+RV+D +G + D SG V +NVG+ + +A+ Q K +++ + Sbjct: 33 ENDPRIIVEGKGMRVWDQNGKEWLDAVSGGVWTVNVGYGREEIAKAVYDQLMKLCYFAQS 92 Query: 93 DFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV------KYGTGRKQFLA 146 A+ AEKLIE PG +V Y NSG+EANE A K+V KYG + + L Sbjct: 93 AGSIPGALF-AEKLIEKMPG--MSRVYYNNSGSEANEKAFKMVRQIAHKKYGGKKTKILY 149 Query: 147 FYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYR-NTWGIDGYEEPDELTN 205 +HG T A +S + + P P +P+ YR + G++ + E Sbjct: 150 RDRDYHGSTLAAMSAGGQEERNMQ-YGPFAPDFVKVPHCMEYRKHELGLE-HLSGKEFGI 207 Query: 206 RVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEV 265 + IEE + R P +GA+ EP+ GG + P+G++ +++ +Y ILL DEV Sbjct: 208 AAANQIEEIILRE-GPDTVGALCLEPVTAGGGVIEAPEGYWPRVQEICKQYDILLHIDEV 266 Query: 266 QMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD----------KPG 315 G+GRTG ++ +H+G++PD + K + G + + FD Sbjct: 267 VCGVGRTGTWFGYQHYGIQPDFVTMAKGVASGYAAIACLVTTEAVFDMFKDDASDPMNYF 326 Query: 316 RHATTFGGNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLG 373 R +TFGG AA + ++I+++ LL + +G + LE EK++VIGD RG G Sbjct: 327 RDISTFGGCTAGPAAALVNMQIIEDENLLDNCTAMGARMKSNLEALMEKHQVIGDVRGKG 386 Query: 374 LAQAVEIVKSKETKEKYPE-LRDRIVKESAKRGLVL------LGCGDNSIRFIPPLIVTK 426 L E+V ++TKE E L +V E + +++ + +N++ F P LIVT Sbjct: 387 LFIGAELVADRDTKEPVDEKLAQAVVAECGNQNVIIGVTNRSIPGKNNTLCFSPALIVTP 446 Query: 427 EEIDVAMEIFEEAL 440 E++D + + AL Sbjct: 447 EDVDKITDAVDVAL 460 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: 500 Number of extensions: 34 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: 465 Length adjustment: 33 Effective length of query: 412 Effective length of database: 432 Effective search space: 177984 Effective search space used: 177984 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