Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 3609962 Dshi_3343 aminotransferase class-III (RefSeq)
Query= curated2:Q976K0 (387 letters) >FitnessBrowser__Dino:3609962 Length = 413 Score = 148 bits (374), Expect = 2e-40 Identities = 106/343 (30%), Positives = 172/343 (50%), Gaps = 29/343 (8%) Query: 4 IQLYGDRGLTIVKGEGQYVWDISGTKYLDLHTGIGVAFLGHRNRRVIEYLSRQMENIMTL 63 + + D L IV+GEG ++WD G +YLD + V +GH + RV++ ++RQ + T Sbjct: 16 VPTFYDPPLHIVRGEGVWLWDAGGRRYLDCYNN--VPHVGHCHPRVVDAIARQARVLNTH 73 Query: 64 STSFSTPIRDEMLKELDPLKPDKMDNIILLNSGTEAVEAALKTARKITGRKKIIAFKNSF 123 + + D ++ L + +D +L+ +G+EAV+ AL+ AR TG+ +IA N++ Sbjct: 74 TRYLHEGVLD-YIERLTGTMDNGLDQALLVCTGSEAVDVALRMARAATGKTGLIATDNTY 132 Query: 124 HGRTAGSLSVTWNK----------RYREPFEPLMSPVQFLTY--NNIDELKNIDEQTAAV 171 HG T ++ + R EP F + EL+ AA+ Sbjct: 133 HGNTTAVAQLSTRRPPIGGYSDHVRLVPAPEPGTDGAAFGAHVARAAAELETAGHGVAAL 192 Query: 172 IVEPIQGESGVIPANEDFMKALREQTQKVGALLVVDEVQTGFGRTGKV-WAYQHYGIIPD 230 IV PI G+ F++ + G LL+ DEVQ GFGR G V W YQ GI PD Sbjct: 193 IVCPIFANEGLPCLPRGFLEPAVAALRTRGGLLISDEVQPGFGRLGDVFWGYQALGIAPD 252 Query: 231 LLTAGKAIGGGFPVSALFLPDWIAEKLEEG-DHGSTYGGNPMAMAAVTAASKVLKEDNVV 289 ++T GK++G G+PV+ + I E + +T+GG+P+A AA A VL+++ +V Sbjct: 253 VVTLGKSMGNGYPVAGVVARTEIMGAFREAFGYFNTFGGSPVAAAAAMAVLDVLEDEGLV 312 Query: 290 EQASIKGEIFKKILREKLSDLKSVRE-----IRGKGLMIGIEI 327 E A K++ R L L+++R +RG GL +++ Sbjct: 313 ENA-------KRVGRYTLERLQALRHPAIDGVRGYGLAFALDL 348 Lambda K H 0.318 0.135 0.383 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: 350 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: 387 Length of database: 413 Length adjustment: 31 Effective length of query: 356 Effective length of database: 382 Effective search space: 135992 Effective search space used: 135992 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 Aug 03 2021. The underlying query database was built on Aug 03 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