Align trehalose-6-P hydrolase (TreA;BlTreA;BLi00797;BL03069) (EC 3.2.1.93) (characterized)
to candidate HSERO_RS11645 HSERO_RS11645 alpha-amylase
Query= CAZy::AAU39732.1 (562 letters) >FitnessBrowser__HerbieS:HSERO_RS11645 Length = 1121 Score = 223 bits (568), Expect = 3e-62 Identities = 158/548 (28%), Positives = 250/548 (45%), Gaps = 93/548 (16%) Query: 3 TKENPWWKKAVVYQIYPKSFKDTTGNGVGDIRGIIEKLDYIKELACDVIWLTPIYQSPQN 62 T++ W+K AV+YQI+ KS+ D +G+GD G+I+KLDYI L + IWL P Y SP+ Sbjct: 4 TRDPLWYKDAVIYQIHVKSYFDANDDGIGDFAGLIQKLDYITGLGVNTIWLLPFYPSPRR 63 Query: 63 DNGYDISDYYSIHEEYGTMADFEELLEEAHKRGIKVIMDLVVNHTSTEHRWFKEAASGKE 122 D+GYDIS+Y ++H +YG M+D + AH+ G++VI +LV+NHTS +H WF+ A + Sbjct: 64 DDGYDISEYKNVHPDYGNMSDVRRFIAAAHEHGLRVITELVINHTSDQHPWFQRARRARP 123 Query: 123 -NLYRDFYIWKDMKPNGAPPTNWESKFGGSAWEFHAESGQYYLHLYDVTQADLNWENEAV 181 ++ R+FY+W D + A S W + + Y+ H + Q DLN++N V Sbjct: 124 GSVARNFYVWSDDDKSYADTRIIFVDTEKSNWTWDPVAKAYFWHRFYSHQPDLNFDNPHV 183 Query: 182 RKKVYEMMHFWFEKGIDGFRLDVINVISKDQRFPDDDEGDGRRFYTDGPRVHEFLNEMNR 241 K V +M FW + GIDG RLD + + + + +++ P H L + Sbjct: 184 LKAVLNVMSFWLDLGIDGLRLDAVPYLIEREGTSNENL----------PETHAILKRIRA 233 Query: 242 EVFSKYDSMTVGEMSSTTIADCIRYTNPESRELDMVFNFHHLKADYPNGEKWALADFDFL 301 E+ SKY + ++ D +Y +S E M F+F + Y ALA D Sbjct: 234 EMDSKYPDRMLLAEANMWPEDVQQYFG-DSDECHMAFHFPLMPRMY-----MALASQDRF 287 Query: 302 KLKKILSEWQTEMNKGGGWNALFWCNHDQPRIV-----------SRYGDDGKYRK----- 345 + IL + ++ W A+F NHD+ + + Y D + R Sbjct: 288 PITDILRQ-TPDIPADCQW-AIFLRNHDELTLEMVTDAERDYLWNHYAPDRRARINLGIR 345 Query: 346 -----------KSAKMLATAIHMLQGTPYIYQGEELGMTNPKFDDISLYRDVESLNMYRI 394 + ++L + + + GTP IY G+E+GM D+I L Sbjct: 346 RRLAPLVERDWRRIQLLNSFLLSMPGTPVIYYGDEIGMG----DNIHL------------ 389 Query: 395 LKEAGKPEAEIIEILKAKSRDNSRTPVQWNGEENAGFTAGTP-------WIPVPDNYKEI 447 RD RTP+QW + N GF+ P + Y+ I Sbjct: 390 -----------------GDRDGVRTPMQWTPDRNGGFSRVDPARLVLPLLMDPQYGYQTI 432 Query: 448 NAEEALNDPDSIFYHYKKLNELRKEFDIITTGDYQLILEDDQELYAYLR-------NGAD 500 N E D S+ ++L +RK+ G L+ +++++AYLR GA Sbjct: 433 NVEAQSADRHSMLNWMRRLLNVRKQHQAFGRGSLALVYPSNRKIFAYLREFTDPRPGGAT 492 Query: 501 EKLLVINN 508 E +L + N Sbjct: 493 ETILCVAN 500 Lambda K H 0.317 0.137 0.424 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: 1531 Number of extensions: 73 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 562 Length of database: 1121 Length adjustment: 41 Effective length of query: 521 Effective length of database: 1080 Effective search space: 562680 Effective search space used: 562680 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 (21.6 bits) S2: 55 (25.8 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