Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate HSERO_RS11645 HSERO_RS11645 alpha-amylase
Query= CAZy::AAS80455.1 (528 letters) >FitnessBrowser__HerbieS:HSERO_RS11645 Length = 1121 Score = 237 bits (604), Expect = 2e-66 Identities = 174/551 (31%), Positives = 254/551 (46%), Gaps = 106/551 (19%) Query: 1 MWWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGY 60 +W+K+AVIYQ++ +S+ D N DG+GD G+ ++L Y+ LGV+ +WL PFY SP +D GY Sbjct: 8 LWYKDAVIYQIHVKSYFDANDDGIGDFAGLIQKLDYITGLGVNTIWLLPFYPSPRRDDGY 67 Query: 61 DVADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASR-NSPK 119 D+++Y +V P +G + D R + AH GL+V+ +LV NHTS +HPWF +R +R S Sbjct: 68 DISEYKNVHPDYGNMSDVRRFIAAAHEHGLRVITELVINHTSDQHPWFQRARRARPGSVA 127 Query: 120 RDWYIWKDPAPDGGPPNNWQSFFGGPAWTLDEATGQYYLHQFLPEQPDLNWRNPEVREAI 179 R++Y+W D WT D Y+ H+F QPDLN+ NP V +A+ Sbjct: 128 RNFYVWSDDDKSYADTRIIFVDTEKSNWTWDPVAKAYFWHRFYSHQPDLNFDNPHVLKAV 187 Query: 180 YEVMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPETY 239 VM FWL G+DG R+D + L E R+ N E+ PET+ Sbjct: 188 LNVMSFWLDLGIDGLRLDAVPYLIE----REGTSN------------------ENLPETH 225 Query: 240 AYVREMRQVLDEFSEPGRERVMVGEIYLPYPQLVRYY---QAGCHLPFNFHL-------- 288 A ++ +R +D +R+++ E + +P+ V+ Y CH+ F+F L Sbjct: 226 AILKRIRAEMD---SKYPDRMLLAEANM-WPEDVQQYFGDSDECHMAFHFPLMPRMYMAL 281 Query: 289 ----------IFRGLPDWRPE-NLARIVEEYESLLTRW--DWPNWVLGNHDQPRLASRLG 335 I R PD + A + ++ L D L NH P +R+ Sbjct: 282 ASQDRFPITDILRQTPDIPADCQWAIFLRNHDELTLEMVTDAERDYLWNHYAPDRRARIN 341 Query: 336 EAQARVAAML--------------LFTLRGTPTWYYGDEIGMKNGEIPPEKVQDPAALRQ 381 R A L L ++ GTP YYGDEIGM Sbjct: 342 LGIRRRLAPLVERDWRRIQLLNSFLLSMPGTPVIYYGDEIGM------------------ 383 Query: 382 KDRLGEHNLPPGRDPERTPMQWDDTPFAGFSTVEPWLPVNP-------DYKTRNVAAQEQ 434 G++ RD RTPMQW GFS V+P V P Y+T NV AQ Sbjct: 384 ----GDNIHLGDRDGVRTPMQWTPDRNGGFSRVDPARLVLPLLMDPQYGYQTINVEAQSA 439 Query: 435 DPRSMLHLVRRLIALRKDPDLL--YGAYRTYRAREGVYAYLR----------GEGWLVAL 482 D SML+ +RRL+ +RK Y + ++AYLR E L Sbjct: 440 DRHSMLNWMRRLLNVRKQHQAFGRGSLALVYPSNRKIFAYLREFTDPRPGGATETILCVA 499 Query: 483 NLTEKEKALEL 493 N+++ +A+EL Sbjct: 500 NVSQSAQAVEL 510 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: 1802 Number of extensions: 101 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: 1121 Length adjustment: 41 Effective length of query: 487 Effective length of database: 1080 Effective search space: 525960 Effective search space used: 525960 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