Align trehalose-6-phosphate hydrolase (TreC) (EC 3.2.1.93) (characterized)
to candidate H281DRAFT_02776 H281DRAFT_02776 maltose alpha-D-glucosyltransferase/ alpha-amylase
Query= CAZy::AAC77196.1 (551 letters) >FitnessBrowser__Burk376:H281DRAFT_02776 Length = 554 Score = 228 bits (581), Expect = 5e-64 Identities = 164/541 (30%), Positives = 242/541 (44%), Gaps = 92/541 (17%) Query: 7 WWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQVDNGYD 66 W++N ++Y + +F D G G GD +G+++ LDYL LGV IWL PF SP DNGYD Sbjct: 6 WYKNAIVYCLSVGTFMDANGDGVGDFQGLLRRLDYLQGLGVTTIWLMPFQPSPGRDNGYD 65 Query: 67 VANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREA-LNKESPYRQ 125 +++Y +DP YGTL DF E + RG+R+++D+V NHTS QH WFREA + +S YR Sbjct: 66 ISDYYNVDPKYGTLGDFSEFTHACRERGLRVMIDLVVNHTSDQHPWFREARSDPDSQYRD 125 Query: 126 FYIWRDGEPETPPNNWRSKFGG---SAWRWHAESEQYYLHLFAPEQADLNWENPAVRAEL 182 +Y+W D +P + F G S W + +++++Y H F Q DLN NP VRAEL Sbjct: 126 WYVWSDKQPPNAKDG--VVFPGVQKSTWTFDKQAKRWYFHRFYEFQPDLNTANPYVRAEL 183 Query: 183 KKVCEFWADRGVDGLRLDVVNLI--SKDPRFPEDLDGDGRRFYTDGPRAHEFLHEMNRDV 240 K+ FW GV G R+D V + +K P+ E ++ Y EFL D Sbjct: 184 LKIMGFWIQLGVSGFRMDAVPFVIATKGPKVREPVEQ-----YDMLREFREFLQWRQGDA 238 Query: 241 FTPRGLMTVGEMSSTSLEHCQRYAALTGSELSMTFNFHHLKVDYPGGEKWTLAKPDFVAL 300 L + T LE Y G L M FNF + + + LA D L Sbjct: 239 II---LAEANVLPDTDLE----YFGDEGERLQMMFNFQLNQNTF-----YALATGDTAPL 286 Query: 301 KTLFRHWQQGMHNVAWNALFWCNHDQ-----------PRIVSRFGDEGE---YRVPAAKM 346 K + W +F NHD+ + + F E + Y + Sbjct: 287 KKALTATRPRPATAQW-GVFLRNHDELDLGRLTPEQREAVFAAFAPEPDMQLYERGIRRR 345 Query: 347 LAMVLHG--------------MQGTPYIYQGEEIGMTNPHFTRITDYRDVESLNMFAELR 392 LA +L G + GTP G+EIGM Sbjct: 346 LAPMLAGDRRRLELAYSLMLTLPGTPVFRYGDEIGM------------------------ 381 Query: 393 NDGRDADELLAILASKSRDNSRTPMQWSNGDNAGFT--AGEPW---IGLGDNYQQINVEA 447 G D L R+ +RTPMQWS GFT A P G ++++NV + Sbjct: 382 --GDD-------LRLPERECARTPMQWSTEPEGGFTKHAKPPCRVITGGAYGFERVNVAS 432 Query: 448 ALADDSSVFYTYQKLIALRKQEAILTWGNYQDLLPNSPVLWCYRREWKGQTLLVIANLSR 507 D +S +++I +R++ ++WG++ L + + R +W+ ++L + N Sbjct: 433 QRRDPNSFLNWMERMIRMRREVPEISWGDFDVLRTSRSDVLALRFDWRNNSVLCLHNFGA 492 Query: 508 E 508 E Sbjct: 493 E 493 Lambda K H 0.320 0.136 0.448 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: 988 Number of extensions: 48 Number of successful extensions: 6 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: 551 Length of database: 554 Length adjustment: 36 Effective length of query: 515 Effective length of database: 518 Effective search space: 266770 Effective search space used: 266770 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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