Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate RR42_RS21370 RR42_RS21370 4-aminobutyrate aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__Cup4G11:RR42_RS21370 Length = 420 Score = 264 bits (675), Expect = 4e-75 Identities = 154/406 (37%), Positives = 230/406 (56%), Gaps = 20/406 (4%) Query: 41 ERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAI 100 ER E ++DV+G + DFA+G+ V+N GH HPR+VEA+++Q E+FTH + Y + I Sbjct: 27 ERAENSEIWDVEGKRYIDFAAGIAVLNTGHRHPRLVEAMQRQLERFTHTAYQIVPYASYI 86 Query: 101 ILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLS 160 LAE++ + APG +K + +GAEA E A+K+ + TGR +AF FHGRT ++ Sbjct: 87 ELAERINQRAPGRGAKKTAFFTTGAEAVENAIKIARAATGRPGVIAFSGGFHGRTMMGMA 146 Query: 161 LTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFR-HV 219 LT + GF P V H PYP + G D L E++F+ V Sbjct: 147 LTGKVVPYKVGFGPFPGEVFHAPYP------CALHGVSVEDALK------AMEHLFKADV 194 Query: 220 PPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIE 279 P + AI FEP+QGEGG+ V P F KAL+ DE+GILL DEVQ G GRTGK +A+E Sbjct: 195 DPKRVAAIIFEPVQGEGGFNVAPPAFVKALRAICDEHGILLVADEVQTGFGRTGKLFAME 254 Query: 280 HFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVVEIV 338 H+ V PDL K++ GG+PL+ V RA++ PG T+ GNP+A+A+ + V++++ Sbjct: 255 HYDVAPDLTTMAKSLAGGMPLSAVCGRAEVMDAPAPGGLGGTYAGNPLAVASALAVLDVL 314 Query: 339 --KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDR 396 ++L+P +G L LE K + I + RGLG AVE ++ + E Sbjct: 315 EGEQLIPRGAALGQRLVARLEALKARVPQIAEIRGLGAMVAVEFRRADGAPD--AEFTRE 372 Query: 397 IVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEAL 440 + + ++GL+LL CG N IRF+ PL ++ ++ ++I + L Sbjct: 373 VQNRALEQGLLLLSCGVYGNVIRFLFPLTISDAVMNEGLDILADVL 418 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: 501 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: 420 Length adjustment: 32 Effective length of query: 413 Effective length of database: 388 Effective search space: 160244 Effective search space used: 160244 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