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) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4677 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:
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