Align trehalose-6-P hydrolase (TreA;BlTreA;BLi00797;BL03069) (EC 3.2.1.93) (characterized)
to candidate SMc01532 SMc01532 alpha-glycosylase
Query= CAZy::AAU39732.1 (562 letters) >FitnessBrowser__Smeli:SMc01532 Length = 547 Score = 312 bits (799), Expect = 2e-89 Identities = 184/537 (34%), Positives = 277/537 (51%), Gaps = 60/537 (11%) Query: 8 WWKKAVVYQIYPKSFKDTTGNGVGDIRGIIEKLDYIKELACDVIWLTPIYQSPQNDNGYD 67 WW+ AV+YQ+YP+SF+DT G+G+GD+RG+ +L +I L D IWL+P + SPQ D GYD Sbjct: 11 WWRGAVIYQVYPRSFQDTDGDGMGDLRGVTRRLPHIASLGVDAIWLSPFFTSPQADMGYD 70 Query: 68 ISDYYSIHEEYGTMADFEELLEEAHKRGIKVIMDLVVNHTSTEHRWFKEAASGKENLYRD 127 +SDY + +GT+ADF+E+L EAH+ G+KVI+D V++HTS H WF E+ S + N D Sbjct: 71 VSDYCDVDPMFGTLADFDEMLAEAHRLGLKVIIDQVISHTSDRHPWFVESRSSRTNAKAD 130 Query: 128 FYIWKDMKPNGAPPTNWESKFGGSAWEFHAESGQYYLHLYDVTQADLNWENEAVRKKVYE 187 +Y+W D KP+G P NW S FGG WE+ QYYLH + +Q DLN+ N V++ V Sbjct: 131 WYVWADPKPDGTAPNNWLSIFGGPGWEWDGVRRQYYLHNFLSSQPDLNFHNPEVQEAVLA 190 Query: 188 MMHFWFEKGIDGFRLDVINVISKDQRFPDDDE--GDGRRFYTDGPRVH------------ 233 + FW ++G+DGFRLD N D+ D+ D D P V+ Sbjct: 191 TVRFWLDRGVDGFRLDTANFYFHDRLLRDNPPLVPDPDATSRDAPEVNPYGMQDHLYDKT 250 Query: 234 -----EFLNEMNREVFSKYDS-MTVGEM--SSTTIADCIRYTNPESRELDMVFNFHHLKA 285 +FL R V +Y TVGE+ S ++ YT+ + L M + F L Sbjct: 251 QPENLDFLRRF-RAVLDEYGGRATVGEVGDGSRSLQTVAAYTSGGDK-LHMCYTFDLLG- 307 Query: 286 DYPNGEKWALADFDFLKLKKILSEWQTEMNKGGGWNALFWCNHDQPRIVSRYGDDGKYRK 345 +F ++ + +Q+ + GW + NHD R VSR+ R+ Sbjct: 308 ----------PEFTARHFRRCVENFQSTVT--DGWVCWAFSNHDVMRHVSRFALREADRE 355 Query: 346 KSAKMLATAIHMLQGTPYIYQGEELGMTNPK--FDDISLYRDVESLNMYRILKEAGKPEA 403 + AK+ + + L+GT +YQGEELG+ + F+++ RD + + Sbjct: 356 RVAKLAISLLASLRGTICLYQGEELGLPEAELAFEEL---RDPYGIRFWPAF-------- 404 Query: 404 EIIEILKAKSRDNSRTPVQWNGE-ENAGFTAGTPWIPVPDNYKEINAEEALNDPDSIFYH 462 RD RTP+ W E NAGF+AGTPW+PV D ++ + + ++ H Sbjct: 405 --------AGRDGCRTPMVWERELSNAGFSAGTPWLPVRDGHRMLAVDAQEGVEGAVLEH 456 Query: 463 YKKLNELRKEFDIITTGDYQLILEDDQELYAYLRNGADEKLLVINNFYGKETEFQLP 519 Y++ R+ + GD + L +Q+L + R DE+LL + N + F LP Sbjct: 457 YRQTLGFRRAQSALVDGD-MVFLGTNQDLLVFTREKDDERLLFVFNLTQEPQTFHLP 512 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: 930 Number of extensions: 42 Number of successful extensions: 4 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: 562 Length of database: 547 Length adjustment: 36 Effective length of query: 526 Effective length of database: 511 Effective search space: 268786 Effective search space used: 268786 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