Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate HSERO_RS19685 HSERO_RS19685 4-aminobutyrate aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__HerbieS:HSERO_RS19685 Length = 456 Score = 243 bits (619), Expect = 1e-68 Identities = 149/444 (33%), Positives = 238/444 (53%), Gaps = 27/444 (6%) Query: 11 PGPKAKEVIERNFKYLAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGH 70 PGPK +E + + +M + +PI +++ G+ D DGN F D ++GVGV +VG Sbjct: 23 PGPKTAAALELSARTESMA-RGGGRMPIAMDQAFGVTFKDPDGNTFIDLSAGVGVSSVGR 81 Query: 71 SHPRVVEAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVV--YGNSGAEAN 128 +PRVVEAI+KQ+E H + LA K+ E+ P + + + G++A Sbjct: 82 CNPRVVEAIRKQSESLMHSMEVNSSKRTE--LAAKISEIMPDGLRGDCITFFTQGGSDAL 139 Query: 129 EAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPY 188 EAA+K K TGR Q +AF+ +HG A +LT + GF P M GV H PYP Y Sbjct: 140 EAAVKFAKRVTGRHQIIAFHGGYHGIWNASNALTTGT-AYRKGFGPFMGGVIHAPYPYAY 198 Query: 189 RNTWGIDGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKA 248 R + ++ +++ +D++ + ++ A+ EP+QGEGGYV P F + Sbjct: 199 RFPFDTS-HKSAEQIAGEYVDYLLNTPY--TAADDVAAVIVEPVQGEGGYVPPSPEFLQI 255 Query: 249 LKKFADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRAD 308 L+K D G LL DEVQ G GRTGK WA+EH GV+PD++ FGK IGG +P+AG++ R+D Sbjct: 256 LRKACDRSGALLIVDEVQAGAGRTGKMWAVEHSGVKPDMLTFGKGIGGDMPMAGLVMRSD 315 Query: 309 ITFDKP-GRHATTFGGNPVAIAAGIEVVEIVK----ELLPHVQEVGDYLHKYLEEFKEKY 363 + P G TF N ++ A + + I++ +L+ +G + + F + Sbjct: 316 LAAKIPDGSQPNTFAANSISAAVALTNISILQDPRLDLVNRAHTLGLEAQERIRSFNSPW 375 Query: 364 EVIGDARGLGLAQAVEIVKSKET-----KEKYPELRDRIVKESAKRGLVLLGCG--DNSI 416 +G+ RG GL +E+V+++ET +EK +L D +V G++++ CG N + Sbjct: 376 --VGEVRGRGLMIGIELVENRETREPLSREKLGKLMDYVV----GHGVLMIPCGRYTNVM 429 Query: 417 RFIPPLIVTKEEIDVAMEIFEEAL 440 R +P L + + + ++IF L Sbjct: 430 RVMPSLTIPRSLMFKGLDIFGAGL 453 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: 520 Number of extensions: 38 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: 456 Length adjustment: 33 Effective length of query: 412 Effective length of database: 423 Effective search space: 174276 Effective search space used: 174276 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