Align trehalose-6-P hydrolase (TreA;BlTreA;BLi00797;BL03069) (EC 3.2.1.93) (characterized)
to candidate 3608245 Dshi_1649 alpha amylase catalytic region (RefSeq)
Query= CAZy::AAU39732.1 (562 letters) >FitnessBrowser__Dino:3608245 Length = 552 Score = 285 bits (728), Expect = 4e-81 Identities = 171/527 (32%), Positives = 269/527 (51%), Gaps = 44/527 (8%) Query: 8 WWKKAVVYQIYPKSFKDTTGNGVGDIRGIIEKLDYIKELACDVIWLTPIYQSPQNDNGYD 67 WW+ AV+YQIYP+SF+D+ G+G+GD+ GI+E++ YI L D IW++P + SP D GYD Sbjct: 19 WWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKDFGYD 78 Query: 68 ISDYYSIHEEYGTMADFEELLEEAHKRGIKVIMDLVVNHTSTEHRWFKEAASGKENLYRD 127 ISDY+ + +G++ADF+ L+E AH G++V++DLV++HTS +H WF+E+ S ++N D Sbjct: 79 ISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDNPKAD 138 Query: 128 FYIWKDMKPNGAPPTNWESKFGGSAWEFHAESGQYYLHLYDVTQADLNWENEAVRKKVYE 187 +Y+W D KP+G PP NW S FGGS W + A QYYLH + +Q DLN+ V+ + Sbjct: 139 WYVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLTSQPDLNFHCADVQDALLG 198 Query: 188 MMHFWFEKGIDGFRLDVINVISKDQRFPDDDE-GDGRRFYTDGPRVHEFLNEMNREVFSK 246 + FW ++G+DGFRLD IN D D+ R P V+ + ++ R ++SK Sbjct: 199 VGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPEERNSNIAPEVNPYNHQ--RHLYSK 256 Query: 247 YDSMTVGEMSSTTIADCIRYTNPESRELDMVFNFHH---LKADYPNGEKWA--LADFDFL 301 + E + A Y P + V + + + Y GE F+FL Sbjct: 257 NQPENL-EFLAKFRAMMEEY--PAIAAVGEVGDAQYGLEILGQYTRGETGVHMCYAFEFL 313 Query: 302 KLKKILSEWQTE-MNK-----GGGWNALFWCNHDQPRIVSRYGDDGKYRKKSAKMLATAI 355 +K+ ++ E +NK GW + NHD R VSR+ + + + T + Sbjct: 314 AQEKLTAKRVAEVLNKVDEVASDGWACWAFSNHDVMRHVSRW----DLTPGAQRGMLTLL 369 Query: 356 HMLQGTPYIYQGEELGMTNPK--FDDISLYRDVESLNMYRILKEAGKPEAEIIEILKAKS 413 L+G+ +YQGEELG+ + FDD+ +E Y K Sbjct: 370 MCLRGSVCLYQGEELGLPEAEVAFDDLQDPYGIEFWPEY-------------------KG 410 Query: 414 RDNSRTPVQWNGEE-NAGFTAGTPWIPVPDNYKEINAEEALNDPDSIFYHYKKLNELRKE 472 RD RTP+ W + + GF+ PW+PV + + PD++ +HY++ R+ Sbjct: 411 RDGCRTPMVWQSDNMSGGFSIHRPWLPVSTEHLGLAVAVQEEAPDALLHHYRRALAFRRA 470 Query: 473 FDIITTGDYQLILEDDQELYAYLRNGADEKLLVINNFYGKETEFQLP 519 + GD + ++ ++LR +E + V N LP Sbjct: 471 HPALVKGDISDVTVVG-DVISFLRKDPEETVFVAINMSDAPGAVDLP 516 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: 960 Number of extensions: 48 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: 552 Length adjustment: 36 Effective length of query: 526 Effective length of database: 516 Effective search space: 271416 Effective search space used: 271416 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: 53 (25.0 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