Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate Pf1N1B4_4677 Trehalose synthase (EC 5.4.99.16)
Query= uniprot:A8LLL3 (552 letters) >lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4677 Trehalose synthase (EC 5.4.99.16) Length = 1113 Score = 223 bits (569), Expect = 2e-62 Identities = 173/581 (29%), Positives = 268/581 (46%), Gaps = 113/581 (19%) Query: 16 DPDWWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKDF 75 DP W++ AVIYQ++ +SF DSN DGIGD G++ ++ YI+ LGV+ IW+ PF+ SP +D Sbjct: 13 DPLWYKDAVIYQVHVKSFFDSNNDGIGDFPGLIAKLDYISDLGVNTIWLLPFYPSPRRDD 72 Query: 76 GYDISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDNP 135 GYDI++Y V P +G++AD I AH GLRV+ +LV++HTSDQH WF+ +R ++ Sbjct: 73 GYDIAEYRGVHPDYGTMADAKRFIAEAHKRGLRVITELVINHTSDQHAWFQRARKAKPGS 132 Query: 136 KA-DWYVWA--DAKPDGTPPNNWLSIF---GGSGWHWDARRCQYYLHNFLTSQPDLNFHC 189 A D+YVW+ D K DGT IF S W WD QY+ H F + QPDLNF Sbjct: 133 AARDFYVWSDNDQKYDGT-----RIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDN 187 Query: 190 ADVQDALLGVGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPEERNSNIAPEVNPYNH 249 V A+L V R+WLD G+DG RLD I + + E +N Sbjct: 188 PQVMKAVLSVMRYWLDMGIDGLRLDAIPYLI-------------ERDGTN---------- 224 Query: 250 QRHLYSKNQPENLEFLAKFRAMME-EYPAIAAVGEVGDAQYGLEILGQYT--RGETG--V 304 ++N PE + L + RA ++ YP + E ++ T G+ G Sbjct: 225 -----NENLPETHDVLKQIRAEIDANYPDRMLLAEANQWPEDTQLYFGNTDASGQKGDEC 279 Query: 305 HMCYAFEFLAQEKLTAKR-----VAEVLNKVDEV-ASDGWACWAFSNHDVM--------R 350 HM + F + + + + + ++L + E+ A+ WA + NHD + Sbjct: 280 HMAFHFPLMPRMYMALAQEDRFPITDILRQTPEIPANCQWAIF-LRNHDELTLEMVTDRE 338 Query: 351 HVSRWDLTPGAQRGML-----------------------TLLMCLRGSVCLYQGEELGLP 387 W+ +R + +LL+ + G+ LY G+E+G+ Sbjct: 339 RDYLWNYYAADRRARINLGIRRRLAPLMERDRRRVELLNSLLLSMPGTPTLYYGDEIGMG 398 Query: 388 EAEVAFDDLQDPYGIEFWPEYKGRDGCRTPMVWQSDNMSGGFS-------IHRPWLPVST 440 + D RDG RTPM W D +GGFS + P + Sbjct: 399 DNIYLGD----------------RDGVRTPMQWSIDR-NGGFSRADPASLVLPPIMDPLY 441 Query: 441 EHLGLAVAVQEEAPDALLHHYRRALAFRRAHPALVKGDI-----SDVTVVGDVISFLRKD 495 +L + V Q P +LL+ RR LA R+ A +G + S+ ++ F D Sbjct: 442 GYLSVNVETQAGDPHSLLNWNRRLLAVRKQSKAFGRGTLKMLSPSNRRILAYTREFTGPD 501 Query: 496 PEETVFVAI-NMSDAPGAVDLPPGNWM-QIGAELNSGGTSP 534 + + + + N+S + A +L ++ + E+ G P Sbjct: 502 GKHEIILCVANVSRSAQAAELDLSAYVGMVPVEMLGGNAFP 542 Lambda K H 0.321 0.138 0.451 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: 1626 Number of extensions: 90 Number of successful extensions: 4 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: 552 Length of database: 1113 Length adjustment: 41 Effective length of query: 511 Effective length of database: 1072 Effective search space: 547792 Effective search space used: 547792 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 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