Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate GFF2392 PGA1_c24230 acetylornithine aminotransferase ArgD
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__Phaeo:GFF2392 Length = 394 Score = 238 bits (608), Expect = 2e-67 Identities = 139/372 (37%), Positives = 205/372 (55%), Gaps = 22/372 (5%) Query: 1 MPLY-RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVA 59 +P Y R L V+GEG ++ + GRR+LDL AGI VN LGHAHP V ++ Q E + Sbjct: 6 LPTYNRAPLSFVKGEGAWLIEADGRRFLDLAAGIAVNALGHAHPALVKALTDQAETLWHV 65 Query: 60 GPMFEHDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARL------ATGRSEIVAM 113 ++ +++ + + L + V+ NSGTE+ E A+K AR R EI+ Sbjct: 66 SNLYHIPQQQALADRLVEHSFADTVFFTNSGTESCELAVKMARKYFHDKGQPERVEILTF 125 Query: 114 TNAFHGRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQG 173 + +FHGR+ +SA +K GFGP++PGFKH+ F +++ +AIT +TAA++ EP+QG Sbjct: 126 SGSFHGRSSAGISAAGSEKMTAGFGPMLPGFKHLMFGDLDGVTDAITDQTAAILIEPVQG 185 Query: 174 EGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGI 232 EGGI P + +K LR + ++ G LLI DEVQ G+ RTGK A E G+ PDI+ + KGI Sbjct: 186 EGGIRPVPDAELKALRQICDEHGLLLILDEVQCGVGRTGKLFAHEWAGITPDIMMVAKGI 245 Query: 233 GNGFPVSLTLTDLE----IPRGKHGSTFGGNPLACRAVATTL----------RILRRDRL 278 G GFP+ L E + G HGST+GGNPL C + + R+ L Sbjct: 246 GGGFPLGAVLATEEAASGMTAGTHGSTYGGNPLGCAVGCAVMDHVTDPEFLAEVSRKAGL 305 Query: 279 VEKAGEKFMEFSGERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLP 338 + + E + + RG GLM+G+ + V A E ++ A + V+RLLP Sbjct: 306 LRQKLEGLVASHPQVFEAVRGSGLMLGLKCVAANTDVVAAGYEAEVVTVPAADNVVRLLP 365 Query: 339 PLIIEGDTLEEA 350 PL + + + EA Sbjct: 366 PLTLTDEDIAEA 377 Lambda K H 0.320 0.140 0.410 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: 353 Number of extensions: 19 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: 362 Length of database: 394 Length adjustment: 30 Effective length of query: 332 Effective length of database: 364 Effective search space: 120848 Effective search space used: 120848 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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