Align trehalose-6-P hydrolase (TreA;BlTreA;BLi00797;BL03069) (EC 3.2.1.93) (characterized)
to candidate BPHYT_RS33775 BPHYT_RS33775 alpha-amylase
Query= CAZy::AAU39732.1 (562 letters) >FitnessBrowser__BFirm:BPHYT_RS33775 Length = 1154 Score = 226 bits (575), Expect = 5e-63 Identities = 150/524 (28%), Positives = 244/524 (46%), Gaps = 86/524 (16%) Query: 8 WWKKAVVYQIYPKSFKDTTGNGVGDIRGIIEKLDYIKELACDVIWLTPIYQSPQNDNGYD 67 W+K A++YQ++ KSF D +GVGD G+I KLDYI EL + IWL P Y SP+ D+GYD Sbjct: 42 WYKDAIIYQVHIKSFFDANNDGVGDFPGLIAKLDYIAELGVNAIWLLPFYPSPRRDDGYD 101 Query: 68 ISDYYSIHEEYGTMADFEELLEEAHKRGIKVIMDLVVNHTSTEHRWFKEAASGKE-NLYR 126 I+DY ++H +YG ++D + ++EAH RGI+VI +LV+NHTS +H WF+ A K + +R Sbjct: 102 IADYRNVHPDYGNLSDVKRFIQEAHARGIRVITELVINHTSDQHPWFQRARRAKPGSNHR 161 Query: 127 DFYIWKDMKPNGAPPTNWESKFGGSAWEFHAESGQYYLHLYDVTQADLNWENEAVRKKVY 186 ++Y+W D S W +G YY H + Q DLN++N AV K+V Sbjct: 162 NYYVWSDTDQKYQETRIIFIDSEPSNWTHDPVAGAYYWHRFYSHQPDLNFDNPAVLKEVL 221 Query: 187 EMMHFWFEKGIDGFRLDVINVISKDQRFPDDDEGDGRRFYTDGPRVHEFLNEMNREVFSK 246 ++M FW + GIDG RLD + + + EG + P H L ++ + ++ Sbjct: 222 QVMRFWLDMGIDGLRLDAVPYLV-------EREGTNNE---NLPETHAVLKKIRATIDAE 271 Query: 247 YDSMTVGEMSSTTIADCIRYTNPESRELDMVFNFHHLKADYPNGEKWALADFDFLKLKKI 306 Y + + ++ D Y E E M F+F + Y ++A D + I Sbjct: 272 YPNRMLLAEANQWPEDVKEYFGDED-ECHMAFHFPLMPRIY-----MSIASEDRFPITDI 325 Query: 307 LSEWQTEMNKGGGWNALFWCNHDQ-----------PRIVSRYGDDGKYR----------- 344 + + ++ W A+F NHD+ + + Y D + R Sbjct: 326 MRQ-TPDLAATNQW-AIFLRNHDELTLEMVTDSERDYLWNTYASDRRARLNLGIRRRLAP 383 Query: 345 -----KKSAKMLATAIHMLQGTPYIYQGEELGMTNPKFDDISLYRDVESLNMYRILKEAG 399 ++ +++ + + + GTP IY G+ELGM D+I L Sbjct: 384 LMERDRRRIELINSLLLSMPGTPVIYYGDELGMG----DNIHL----------------- 422 Query: 400 KPEAEIIEILKAKSRDNSRTPVQWNGEENAGFTAGTP-WIPVPD------NYKEINAEEA 452 RD RTP+QW+ + N GF+ P + +P + +N E Sbjct: 423 ------------GDRDGVRTPMQWSSDRNGGFSRADPEQLVLPPVMGSLYGFDAVNVEAQ 470 Query: 453 LNDPDSIFYHYKKLNELRKEFDIITTGDYQLILEDDQELYAYLR 496 DP S+ +++ R+ G + + +++++ AYLR Sbjct: 471 SRDPHSLLNWTRRMLATRRAKQTFGRGTIRFLKPENRKILAYLR 514 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: 1601 Number of extensions: 69 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 562 Length of database: 1154 Length adjustment: 41 Effective length of query: 521 Effective length of database: 1113 Effective search space: 579873 Effective search space used: 579873 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