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) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4677 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:
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