Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate WP_037455934.1 N825_RS19885 maltose alpha-D-glucosyltransferase
Query= CAZy::AAS80455.1 (528 letters) >NCBI__GCF_000576635.1:WP_037455934.1 Length = 1104 Score = 246 bits (628), Expect = 3e-69 Identities = 175/548 (31%), Positives = 264/548 (48%), Gaps = 103/548 (18%) Query: 1 MWWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGY 60 +W+K+AVIYQ++ ++F D + DG+GD G+ ++L YL+ LGV ALWL PFY SP++D GY Sbjct: 8 LWYKDAVIYQLHVKAFFDADNDGIGDFAGLSQKLDYLQELGVTALWLLPFYPSPLRDDGY 67 Query: 61 DVADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASR-NSPK 119 D+ADY +V+P +G ++DF + + E H+ G++V+ +LV NHTS +HPWF +R ++ S Sbjct: 68 DIADYRNVNPSYGFMKDFRQFVRECHSRGMRVITELVINHTSDQHPWFQRARTAKPGSNH 127 Query: 120 RDWYIWKDPAPDGGPPNNWQSFFGGPAWTLDEATGQYYLHQFLPEQPDLNWRNPEVREAI 179 R++Y+W D WT D Y+ H+F QPDLN+ NP V + Sbjct: 128 RNFYVWSDSDQKYQGTRIIFLDTEKSNWTWDPVAKSYFWHRFYSHQPDLNFDNPAVLREV 187 Query: 180 YEVMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPETY 239 V+RFWL GVDG R+D + L E R+ N E+ ET+ Sbjct: 188 LSVLRFWLDMGVDGLRLDAVPYLIE----REGTNN------------------ENLSETH 225 Query: 240 AYVREMRQVLDEFSEPGRERVMVGEI------YLPYPQLVRYYQAGCHLPFNFHL---IF 290 ++++R +D E +R+++ E LPY + CH+ F+F L ++ Sbjct: 226 DILKQIRAAVD---EGYADRMLLAEANQWPEDVLPYFGDLSKGGDECHMAFHFPLMPRMY 282 Query: 291 RGLPDWRPENLARIVEEYESLLTRWDWPNWVLGNHDQ----------------------- 327 + + I+ + + W + L NHD+ Sbjct: 283 MAIAQEDRHPVTDIMRQTPEIPETCQWAVF-LRNHDELTLEMVTDKERDYLWNFYAKDRR 341 Query: 328 --------PRLASRLGEAQARVAAM--LLFTLRGTPTWYYGDEIGMKNGEIPPEKVQDPA 377 RLA+ + + ++ + LLF++ GTP YYGDEIGM Sbjct: 342 MRINLGIRRRLATLMDNDRRKIELLNSLLFSMPGTPVVYYGDEIGM-------------- 387 Query: 378 ALRQKDRLGEHNLPPGRDPERTPMQWDDTPFAGFSTVEP---WLPVNPD----YKTRNVA 430 G++ RD RTPMQW GFS +P +LP D + NV Sbjct: 388 --------GDNVYLGDRDGVRTPMQWSPDRNGGFSRSDPARLYLPAVADPIYGFDAVNVE 439 Query: 431 AQEQDPRSMLHLVRRLIALRKDPDLL-YGAYR-TYRAREGVYAYLR---GEGWLVALNLT 485 AQE+ P S+L+ ++RLIA+R+ GA R Y V AYLR GE L NL+ Sbjct: 440 AQERSPSSLLNWMKRLIAVRQQQKSFGRGALRFLYPGNRKVLAYLREHEGEVILCVANLS 499 Query: 486 EKEKALEL 493 +A+EL Sbjct: 500 RSAQAVEL 507 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: 1781 Number of extensions: 91 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: 528 Length of database: 1104 Length adjustment: 40 Effective length of query: 488 Effective length of database: 1064 Effective search space: 519232 Effective search space used: 519232 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 Sep 24 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