Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate WP_011840806.1 RSPH17029_RS05655 maltose alpha-D-glucosyltransferase
Query= CAZy::AAS80455.1 (528 letters) >NCBI__GCF_000015985.1:WP_011840806.1 Length = 1102 Score = 266 bits (680), Expect = 3e-75 Identities = 184/546 (33%), Positives = 269/546 (49%), Gaps = 105/546 (19%) Query: 2 WWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGYD 61 W+K+A+IYQ++ ++FQD NGDG+GD G+ +RL Y+++LGV A+WL PFY SP++D GYD Sbjct: 25 WYKDAIIYQLHIKAFQDANGDGIGDFAGLMQRLDYVQALGVTAIWLLPFYPSPLRDDGYD 84 Query: 62 VADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLES-RASRNSPKR 120 ++DY ++P +G ++DF ++EAH GL+V+ +LV NHTS +HPWF + RA + S R Sbjct: 85 ISDYRSINPSYGAMRDFKLFVQEAHKRGLRVITELVINHTSDQHPWFQRARRAKKGSAAR 144 Query: 121 DWYIWKDPAPDGGPPNNWQSFFGGPA--WTLDEATGQYYLHQFLPEQPDLNWRNPEVREA 178 DWY+W D D P F WT D G YY H+F QPDLN+ NP V E Sbjct: 145 DWYVWSD--TDQKFPETRIIFLDTEKSNWTWDPVAGAYYWHRFYSHQPDLNFDNPRVLEE 202 Query: 179 IYEVMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPET 238 + ++MR WL GVDG R+D + L E R+ N E+ PET Sbjct: 203 VLKIMRMWLEMGVDGLRLDAIPYLVE----REGTNN------------------ENLPET 240 Query: 239 YAYVREMRQVLDEFSEPGRERVMVGEIYLPYPQLVR-YYQAG--CHLPFNFHL---IFRG 292 + ++++R LD+ +R+++ E +P+ R Y+ G CH+ F+F L ++ Sbjct: 241 HDVLKKIRANLDQHFP---DRMLLAEAN-QWPEDTRPYFGEGDECHMGFHFPLMPRMYMA 296 Query: 293 LPDWRPENLARIVEEYESLLTRWDWPNWVLGNHDQ------------------------- 327 L + I+ + + W L NHD+ Sbjct: 297 LAQADRHPITDIIRQTPEIPEGCQW-GIFLRNHDELTLEMVTAEERDYMWRFYAEDSRAR 355 Query: 328 ------PRLASRLGEAQARVAAM--LLFTLRGTPTWYYGDEIGMKNGEIPPEKVQDPAAL 379 RLA + + ++ + +L ++ GTP YYGDEIGM Sbjct: 356 INLGIRRRLAPLMKNDRRKIELLNQMLMSMPGTPIVYYGDEIGM---------------- 399 Query: 380 RQKDRLGEHNLPPGRDPERTPMQWDDTPFAGFSTVEP---WLPVNPD----YKTRNVAAQ 432 G++ RD RTPMQW GFS P +LP D ++ NV AQ Sbjct: 400 ------GDNYYLGDRDGVRTPMQWSADRNGGFSRCNPQQLYLPTILDPVYGHQAINVEAQ 453 Query: 433 EQDPRSMLHLVRRLIALRKD-PDLLYGAYR-TYRAREGVYAYLR---GEGWLVALNLTEK 487 DP S+L+ RRLIA+RK P G+ Y V AY+R G L NL++ Sbjct: 454 AADPSSLLNWTRRLIAVRKQHPAFGRGSMSLLYPRNRKVLAYVRSHEGTDILCVANLSDT 513 Query: 488 EKALEL 493 +A+EL Sbjct: 514 AQAVEL 519 Lambda K H 0.321 0.141 0.466 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: 1791 Number of extensions: 95 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: 528 Length of database: 1102 Length adjustment: 40 Effective length of query: 488 Effective length of database: 1062 Effective search space: 518256 Effective search space used: 518256 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: 55 (25.8 bits)
This GapMind analysis is from Apr 10 2024. 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