Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate GFF2510 PS417_12800 alpha-amylase
Query= CAZy::AAS80455.1 (528 letters) >FitnessBrowser__WCS417:GFF2510 Length = 1115 Score = 246 bits (628), Expect = 3e-69 Identities = 168/506 (33%), Positives = 244/506 (48%), Gaps = 107/506 (21%) Query: 1 MWWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGY 60 +W+K+AVIYQV+ +S+ D+N DG+GD G+ +L Y+ LGV+ +WL PFY SP +D GY Sbjct: 15 LWYKDAVIYQVHVKSYFDSNNDGIGDFPGLIAKLDYIADLGVNTIWLLPFYPSPRRDDGY 74 Query: 61 DVADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESR-ASRNSPK 119 D+A+Y V +GT+ D R + EAH GL+V+ +LV NHTS +HPWF +R A S Sbjct: 75 DIAEYRGVHSDYGTMADAKRFIAEAHKRGLRVITELVINHTSDQHPWFQRARKAKPGSAA 134 Query: 120 RDWYIWKDPAPDGGPPNNWQSFF---GGPAWTLDEATGQYYLHQFLPEQPDLNWRNPEVR 176 RD+Y+W D D + + F WT D GQY+ H+F QPDLN+ NP+V Sbjct: 135 RDFYVWSD---DDQKYDGTRIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDNPQVM 191 Query: 177 EAIYEVMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQP 236 +A+ VMR+WL G+DG R+D + L E RD N E+ P Sbjct: 192 KAVLSVMRYWLDMGIDGLRLDAIPYLIE----RDGTNN------------------ENLP 229 Query: 237 ETYAYVREMRQVLDEFSEPGRERVMVGEIYLPYPQLVRYYQAG--------CHLPFNFHL 288 ET+ ++++R +D +R+++ E +P+ + Y CH+ F+F L Sbjct: 230 ETHDVLKQIRAEIDAHYP---DRMLLAEAN-QWPEDTQLYFGDKKGDDGDECHMAFHFPL 285 Query: 289 IFRGLPDWRPEN---LARIVEEYESLLTRWDWPNWVLGNHDQ------------------ 327 + R E+ + I+ + + W + L NHD+ Sbjct: 286 MPRMYMALAQEDRFPITDILRQTPEIPANCQWAIF-LRNHDELTLEMVTDKERDYLWNYY 344 Query: 328 -------------PRLASRLGEAQARVAAM--LLFTLRGTPTWYYGDEIGMKNGEIPPEK 372 RLA + + RV + LL ++ GTPT YYGDEIGM Sbjct: 345 AADRRARINLGIRRRLAPLMERDRRRVELLNSLLLSMPGTPTLYYGDEIGM--------- 395 Query: 373 VQDPAALRQKDRLGEHNLPPGRDPERTPMQWDDTPFAGFSTVEPWLPVNP-------DYK 425 G++ RD RTPMQW GFS +P V P Y Sbjct: 396 -------------GDNIYLGDRDGVRTPMQWSIDRNGGFSRADPASLVLPPIMDPQYGYP 442 Query: 426 TRNVAAQEQDPRSMLHLVRRLIALRK 451 + NV Q QDP S+L+ RR++A+RK Sbjct: 443 SVNVETQAQDPHSLLNWTRRMLAVRK 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: 1659 Number of extensions: 94 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 528 Length of database: 1115 Length adjustment: 40 Effective length of query: 488 Effective length of database: 1075 Effective search space: 524600 Effective search space used: 524600 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 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