Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate GFF2392 PGA1_c24230 acetylornithine aminotransferase ArgD
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__Phaeo:GFF2392 Length = 394 Score = 186 bits (472), Expect = 1e-51 Identities = 133/413 (32%), Positives = 204/413 (49%), Gaps = 51/413 (12%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 P+ +GEG + + DG F D A+G+ V +GH+HP +V+A+ QAE H S + Sbjct: 13 PLSFVKGEGAWLIEADGRRFLDLAAGIAVNALGHAHPALVKALTDQAETLWHVSNL-YHI 71 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVK---YGTG---RKQFLAFYHA 150 LA++L+E + D V + NSG E+ E A+K+ + + G R + L F + Sbjct: 72 PQQQALADRLVEHSFADT---VFFTNSGTESCELAVKMARKYFHDKGQPERVEILTFSGS 128 Query: 151 FHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDF 210 FHGR+ A +S S+ + GF P +PG H+ + + +DG +T+ + D Sbjct: 129 FHGRSSAGISAAGSEKMTA-GFGPMLPGFKHLMFGD-------LDG------VTDAITD- 173 Query: 211 IEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIG 270 + AI EP+QGEGG P KAL++ DE+G+LL DEVQ G+G Sbjct: 174 ------------QTAAILIEPVQGEGGIRPVPDAELKALRQICDEHGLLLILDEVQCGVG 221 Query: 271 RTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD-KPGRHATTFGGNPVAIA 329 RTGK +A E G+ PD++ K IGGG PL V+ + G H +T+GGNP+ A Sbjct: 222 RTGKLFAHEWAGITPDIMMVAKGIGGGFPLGAVLATEEAASGMTAGTHGSTYGGNPLGCA 281 Query: 330 AGIEVVEIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDA-RGLGLAQAVEIVKSKET 386 G V++ V E L V L + LE + + +A RG GL ++ V + Sbjct: 282 VGCAVMDHVTDPEFLAEVSRKAGLLRQKLEGLVASHPQVFEAVRGSGLMLGLKCVAANTD 341 Query: 387 KEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEA 439 +V + +V + DN +R +PPL +T E+I A ++A Sbjct: 342 ----------VVAAGYEAEVVTVPAADNVVRLLPPLTLTDEDIAEAFARLDQA 384 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: 408 Number of extensions: 21 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: 394 Length adjustment: 32 Effective length of query: 413 Effective length of database: 362 Effective search space: 149506 Effective search space used: 149506 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: 50 (23.9 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