Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate AO353_11510 AO353_11510 4-aminobutyrate aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__pseudo3_N2E3:AO353_11510 Length = 425 Score = 260 bits (664), Expect = 7e-74 Identities = 155/408 (37%), Positives = 221/408 (54%), Gaps = 18/408 (4%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 PI + + V DV+G F DFA G+ V+N GH HP+V+ A+ +Q K TH Y Sbjct: 25 PIFADHAKNSTVTDVEGREFIDFAGGIAVLNTGHLHPKVIAAVTEQLNKLTHTCFQVLAY 84 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156 E + L EK+ PGD +K + +G+EA E ++K+ + TGR +AF A+HGRT Sbjct: 85 EPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENSIKIARAATGRAGVIAFTGAYHGRTM 144 Query: 157 AVLSLTASKWVQQDGFFPTMP-GVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYV 215 L LT K V MP G+ YPN + G D + + IE Sbjct: 145 MTLGLT-GKVVPYSAGMGLMPGGIFRALYPNE------LHGVSIDDSIAS-----IERIF 192 Query: 216 FRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKF 275 P +I AI EP+QGEGG+ V PK F K L+ D++GILL DEVQ G GRTG F Sbjct: 193 KNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTF 252 Query: 276 WAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRAD-ITFDKPGRHATTFGGNPVAIAAGIEV 334 +A+E GV DL F K+I GG PLAGV +A+ + PG T+ G+P+A AA + V Sbjct: 253 FAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAV 312 Query: 335 VEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPE 392 +E+ +E LL + VG+ L L+ + KY VIG+ R LG AVE+ ++ ++ + Sbjct: 313 MEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHKPNAA 372 Query: 393 LRDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEE 438 ++V ++ +GL+LL CG N +R + PL E++D + I EE Sbjct: 373 AVAKVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAIMEE 420 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: 483 Number of extensions: 30 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: 425 Length adjustment: 32 Effective length of query: 413 Effective length of database: 393 Effective search space: 162309 Effective search space used: 162309 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 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