Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate SMc01532 SMc01532 alpha-glycosylase
Query= uniprot:A8LLL3 (552 letters) >FitnessBrowser__Smeli:SMc01532 Length = 547 Score = 648 bits (1672), Expect = 0.0 Identities = 305/507 (60%), Positives = 367/507 (72%), Gaps = 6/507 (1%) Query: 15 ADPDWWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKD 74 +D +WWRGAVIYQ+YPRSFQD++GDG+GDL G+ R+P+IASLGVDAIW+SPFFTSP D Sbjct: 7 SDENWWRGAVIYQVYPRSFQDTDGDGMGDLRGVTRRLPHIASLGVDAIWLSPFFTSPQAD 66 Query: 75 FGYDISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDN 134 GYD+SDY DVDPMFG+LADFD ++ AH GL+V+ID V+SHTSD+HPWF ESRSSR N Sbjct: 67 MGYDVSDYCDVDPMFGTLADFDEMLAEAHRLGLKVIIDQVISHTSDRHPWFVESRSSRTN 126 Query: 135 PKADWYVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLTSQPDLNFHCADVQD 194 KADWYVWAD KPDGT PNNWLSIFGG GW WD R QYYLHNFL+SQPDLNFH +VQ+ Sbjct: 127 AKADWYVWADPKPDGTAPNNWLSIFGGPGWEWDGVRRQYYLHNFLSSQPDLNFHNPEVQE 186 Query: 195 ALLGVGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPE-ERNSNIAPEVNPYNHQRHL 253 A+L RFWLDRGVDGFRLDT NFY HD LRDNPPL P+ + S APEVNPY Q HL Sbjct: 187 AVLATVRFWLDRGVDGFRLDTANFYFHDRLLRDNPPLVPDPDATSRDAPEVNPYGMQDHL 246 Query: 254 YSKNQPENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILGQYTRGETGVHMCYAFEFL 313 Y K QPENL+FL +FRA+++EY A VGEVGD L+ + YT G +HMCY F+ L Sbjct: 247 YDKTQPENLDFLRRFRAVLDEYGGRATVGEVGDGSRSLQTVAAYTSGGDKLHMCYTFDLL 306 Query: 314 AQEKLTAKRVAEVLNKVDEVASDGWACWAFSNHDVMRHVSRWDLTPGAQRGM----LTLL 369 E TA+ + +DGW CWAFSNHDVMRHVSR+ L + + ++LL Sbjct: 307 GPE-FTARHFRRCVENFQSTVTDGWVCWAFSNHDVMRHVSRFALREADRERVAKLAISLL 365 Query: 370 MCLRGSVCLYQGEELGLPEAEVAFDDLQDPYGIEFWPEYKGRDGCRTPMVWQSDNMSGGF 429 LRG++CLYQGEELGLPEAE+AF++L+DPYGI FWP + GRDGCRTPMVW+ + + GF Sbjct: 366 ASLRGTICLYQGEELGLPEAELAFEELRDPYGIRFWPAFAGRDGCRTPMVWERELSNAGF 425 Query: 430 SIHRPWLPVSTEHLGLAVAVQEEAPDALLHHYRRALAFRRAHPALVKGDISDVTVVGDVI 489 S PWLPV H LAV QE A+L HYR+ L FRRA ALV GD+ + D++ Sbjct: 426 SAGTPWLPVRDGHRMLAVDAQEGVEGAVLEHYRQTLGFRRAQSALVDGDMVFLGTNQDLL 485 Query: 490 SFLRKDPEETVFVAINMSDAPGAVDLP 516 F R+ +E + N++ P LP Sbjct: 486 VFTREKDDERLLFVFNLTQEPQTFHLP 512 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: 1046 Number of extensions: 37 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 552 Length of database: 547 Length adjustment: 36 Effective length of query: 516 Effective length of database: 511 Effective search space: 263676 Effective search space used: 263676 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: 53 (25.0 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