Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate WP_043828307.1 RSPH17029_RS13100 alpha-amylase family protein
Query= CAZy::AAS80455.1 (528 letters) >NCBI__GCF_000015985.1:WP_043828307.1 Length = 548 Score = 249 bits (637), Expect = 1e-70 Identities = 168/510 (32%), Positives = 240/510 (47%), Gaps = 100/510 (19%) Query: 1 MWWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGY 60 +WWK AV Y + +FQD+NGDG+GD G+ RRL +L LGV +WL PFY SP +D GY Sbjct: 9 VWWKNAVFYCLDVETFQDSNGDGIGDFAGLTRRLDHLDRLGVSCIWLMPFYPSPNQDDGY 68 Query: 61 DVADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASRNSPKR 120 D+ DY VDP GTL DF L AH G++V+ DLV NHTS EHPWF SRA +SP R Sbjct: 69 DITDYYSVDPRLGTLGDFVEFLRAAHDRGMRVIADLVVNHTSREHPWFQASRADPDSPYR 128 Query: 121 DWYIWKDPAPDGGPPNNWQSFFGGPAWTLDEATGQYYLHQFLPEQPDLNWRNPEVREAIY 180 DWY+W+D P+ + +WT D G+YYLH+F QPDLN N VR+ I Sbjct: 129 DWYVWRDEKPEEDAASLVFPGEENSSWTWDAKAGKYYLHRFYSHQPDLNVENRAVRDEIQ 188 Query: 181 EVMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPETYA 240 ++ FWL+ G+ GFRVD + L E + D P + Sbjct: 189 RIVGFWLQLGLSGFRVDAVPFLLEQMSTVDTGFAP-----------------------HR 225 Query: 241 YVREMRQVLDEFSEPGRERVMVGEIYLPYPQLVRYY--QAG--CHLPFNFHLIFRGLPDW 296 ++R++R ++ S + V++GE+ L YP + R++ + G H+ +F+L Sbjct: 226 WLRDLRAFINRRS---GDAVLLGEVNLDYPDVRRFFGDEDGDELHMCLDFNLNQAMALAL 282 Query: 297 RPENLARIVEEYESLLTRWDWPNWV--LGNHDQPRLASRLGEAQ---------------- 338 E+ IV + W L NHD+ L +L EA+ Sbjct: 283 AREDAGPIVHGLRHMPELAPDDGWAHFLRNHDEWSL-DKLTEAERQEVFASFGPDPSMQL 341 Query: 339 -------------------ARVAAMLLFTLRGTPTWYYGDEIGM-KNGEIPPEKVQDPAA 378 R+A L+ ++ G+P +YG+EIGM +N EI Sbjct: 342 FGRGLRRRMPTMLKGNPDRLRMAYALMASMPGSPVIFYGEEIGMAENLEI---------- 391 Query: 379 LRQKDRLGEHNLPPGRDPERTPMQWDDTPFAGFSTVEPW-----LPVNPDYKTRNVAA-- 431 PGR R PMQWD P GFS + +P + V A Sbjct: 392 -------------PGRLAVRAPMQWDAGPHGGFSNASTEALHRPMVSDPQWGPGKVNAID 438 Query: 432 QEQDPRSMLHLVRRLIALRKD-PDLLYGAY 460 Q+ P +M H + L+ R++ P++ +G + Sbjct: 439 QQDRPDTMFHFMEHLLRRRRECPEIAFGEH 468 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: 1057 Number of extensions: 62 Number of successful extensions: 5 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: 528 Length of database: 548 Length adjustment: 35 Effective length of query: 493 Effective length of database: 513 Effective search space: 252909 Effective search space used: 252909 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: 52 (24.6 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