Align Probable alpha-glucosidase; EC 3.2.1.20 (uncharacterized)
to candidate Pf1N1B4_4677 Trehalose synthase (EC 5.4.99.16)
Query= curated2:Q9Z3R8 (551 letters) >lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4677 Trehalose synthase (EC 5.4.99.16) Length = 1113 Score = 254 bits (648), Expect = 2e-71 Identities = 194/576 (33%), Positives = 275/576 (47%), Gaps = 113/576 (19%) Query: 17 WWRGAVIYQIYPRSFQDTNGDGIGDLQGITARLPHIAGLGADAIWISPFFTSPMRDFGYD 76 W++ AVIYQ++ +SF D+N DGIGD G+ A+L +I+ LG + IW+ PF+ SP RD GYD Sbjct: 16 WYKDAVIYQVHVKSFFDSNNDGIGDFPGLIAKLDYISDLGVNTIWLLPFYPSPRRDDGYD 75 Query: 77 VSNYVDVDPIFGTLEDFDALIAEAHRLGLRVMIDLVLSHTSDRHPWFVESRSSR-SNAKA 135 ++ Y V P +GT+ D IAEAH+ GLRV+ +LV++HTSD+H WF +R ++ +A Sbjct: 76 IAEYRGVHPDYGTMADAKRFIAEAHKRGLRVITELVINHTSDQHAWFQRARKAKPGSAAR 135 Query: 136 DWYVWADS--KPDGTPPNNWLSIF---GGSAWQWDPTRLQYYLHNFLTSQPDLNLHNPQV 190 D+YVW+D+ K DGT IF S W WDP QY+ H F + QPDLN NPQV Sbjct: 136 DFYVWSDNDQKYDGT-----RIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDNPQV 190 Query: 191 QEALLAVERFWLERGVDGFRLDTINFYFHDRELRDNPALVPERRNASTAPAVNPYNYQEH 250 +A+L+V R+WL+ G+DG RLD I Y +R+ +N Sbjct: 191 MKAVLSVMRYWLDMGIDGLRLDAIP-YLIERDGTNN------------------------ 225 Query: 251 IYDKNRPENLEFLKRFRAVMD-EFPAIAAVGEVG----DSQRGLEIAGEYTSGGDKVHMC 305 +N PE + LK+ RA +D +P + E D+Q GD+ HM Sbjct: 226 ---ENLPETHDVLKQIRAEIDANYPDRMLLAEANQWPEDTQLYFGNTDASGQKGDECHMA 282 Query: 306 YAFEFLAPDRLT-PQRVAEVLRDFHRAAPE-----GWACWAFSNHD-----VVRHVSR-- 352 + F + + Q + D R PE WA + NHD +V R Sbjct: 283 FHFPLMPRMYMALAQEDRFPITDILRQTPEIPANCQWAIF-LRNHDELTLEMVTDRERDY 341 Query: 353 -WADGVTDHDA-------------------HAKLLASLLMSLRGTVCIYQGEELALAEAE 392 W D A +LL SLL+S+ GT +Y G+E+ + Sbjct: 342 LWNYYAADRRARINLGIRRRLAPLMERDRRRVELLNSLLLSMPGTPTLYYGDEIGMG--- 398 Query: 393 LDYEDLQDPYGIQFWPDFKGRDGCRTPMVWESLPDGGFSSATP----WLPISQ---SHIP 445 D L D RDG RTPM W +GGFS A P PI ++ Sbjct: 399 -DNIYLGD------------RDGVRTPMQWSIDRNGGFSRADPASLVLPPIMDPLYGYLS 445 Query: 446 RAVAVQEGDPASVLHHYRRFLAFRKANPALAKGEIEFVE-TRGSLLGFLRSH-----GNE 499 V Q GDP S+L+ RR LA RK + A +G ++ + + +L + R +E Sbjct: 446 VNVETQAGDPHSLLNWNRRLLAVRKQSKAFGRGTLKMLSPSNRRILAYTREFTGPDGKHE 505 Query: 500 KVFCLFNMSDEAATKELP------MKRLEPLEGHGF 529 + C+ N+S A EL M +E L G+ F Sbjct: 506 IILCVANVSRSAQAAELDLSAYVGMVPVEMLGGNAF 541 Lambda K H 0.321 0.138 0.443 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: 1637 Number of extensions: 88 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: 551 Length of database: 1113 Length adjustment: 41 Effective length of query: 510 Effective length of database: 1072 Effective search space: 546720 Effective search space used: 546720 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 (21.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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