Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate PfGW456L13_3254 Trehalose synthase (EC 5.4.99.16)
Query= uniprot:A8LLL3 (552 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3254 Length = 1113 Score = 223 bits (567), Expect = 4e-62 Identities = 164/530 (30%), Positives = 248/530 (46%), Gaps = 106/530 (20%) Query: 5 AQMREVKSLAADPDWWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWI 64 A+ + + DP W++ AVIYQ++ +S+ DSN DGIGD G++ ++ YIA LGV+ IW+ Sbjct: 2 AKKPKAATFIKDPLWYKDAVIYQVHVKSYFDSNNDGIGDFPGLIAKLDYIADLGVNTIWL 61 Query: 65 SPFFTSPMKDFGYDISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPW 124 PF+ SP +D GYDI++Y V +G++AD I AH GLRV+ +LV++HTSDQHPW Sbjct: 62 LPFYPSPRRDDGYDIAEYRGVHSDYGTMADARRFIAEAHKRGLRVITELVINHTSDQHPW 121 Query: 125 FEESRSSRDNPKA-DWYVWA--DAKPDGTPPNNWLSIF---GGSGWHWDARRCQYYLHNF 178 F+ +R ++ A D+YVW+ D K DGT IF S W WD QY+ H F Sbjct: 122 FQRARKAKPGSAARDFYVWSDDDQKYDGT-----RIIFLDTEKSNWTWDPVAGQYFWHRF 176 Query: 179 LTSQPDLNFHCADVQDALLGVGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPEERNS 238 + QPDLNF V A+L V R+WLD G+DG RLD I + + E + Sbjct: 177 YSHQPDLNFDNPQVMKAVLSVMRYWLDMGIDGLRLDAIPYLI-------------ERDGT 223 Query: 239 NIAPEVNPYNHQRHLYSKNQPENLEFLAKFRAMME-EYPAIAAVGEVGDAQYGLEILGQY 297 N ++N PE + L K RA ++ YP + E ++ Sbjct: 224 N---------------NENLPETHDVLKKIRAEIDANYPDRMLLAEANQWPEDTQLYFGD 268 Query: 298 T--RGETG--VHMCYAFEFLAQEKLTAKR-----VAEVLNKVDEV-ASDGWACWAFSNHD 347 T +G G HM + F + + + + + ++L + ++ A+ WA + NHD Sbjct: 269 TDKKGLNGDECHMAFHFPLMPRMYMALAQEDRFPITDILRQTPDIPANCQWAIF-LRNHD 327 Query: 348 VM--------RHVSRWDLTPGAQRGML-----------------------TLLMCLRGSV 376 + W+ +R + +LL+ + G+ Sbjct: 328 ELTLEMVTDKERDYLWNYYAADRRARINLGIRRRLAPLMERDRRRVELLNSLLLSMPGTP 387 Query: 377 CLYQGEELGLPEAEVAFDDLQDPYGIEFWPEYKGRDGCRTPMVWQSDNMSGGFS------ 430 LY G+E+G+ + D RDG RTPM W D +GGFS Sbjct: 388 TLYYGDEIGMGDNIYLGD----------------RDGVRTPMQWSIDR-NGGFSRADPAS 430 Query: 431 -IHRPWLPVSTEHLGLAVAVQEEAPDALLHHYRRALAFRRAHPALVKGDI 479 + P + +L + V Q P +LL+ RR LA R+ A +G + Sbjct: 431 LVLPPIMDPQYGYLSVNVETQAGDPHSLLNWTRRMLAVRKHSKAFGRGTL 480 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: 1593 Number of extensions: 88 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