Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate SMc03064 SMc03064 alpha-glucosidase
Query= uniprot:A8LLL3 (552 letters) >FitnessBrowser__Smeli:SMc03064 Length = 551 Score = 744 bits (1921), Expect = 0.0 Identities = 354/508 (69%), Positives = 403/508 (79%), Gaps = 5/508 (0%) Query: 13 LAADPDWWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPM 72 L D DWWRGAVIYQIYPRSFQD+NGDGIGDL GI R+P+IA LG DAIWISPFFTSPM Sbjct: 11 LEPDRDWWRGAVIYQIYPRSFQDTNGDGIGDLQGITARLPHIAGLGADAIWISPFFTSPM 70 Query: 73 KDFGYDISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSR 132 +DFGYD+S+Y DVDP+FG+L DFDALI AH GLRVMIDLVLSHTSD+HPWF ESRSSR Sbjct: 71 RDFGYDVSNYVDVDPIFGTLEDFDALIAEAHRLGLRVMIDLVLSHTSDRHPWFVESRSSR 130 Query: 133 DNPKADWYVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLTSQPDLNFHCADV 192 N KADWYVWAD+KPDGTPPNNWLSIFGGS W WD R QYYLHNFLTSQPDLN H V Sbjct: 131 SNAKADWYVWADSKPDGTPPNNWLSIFGGSAWQWDPTRLQYYLHNFLTSQPDLNLHNPQV 190 Query: 193 QDALLGVGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPEERNSNIAPEVNPYNHQRH 252 Q+ALL V RFWL+RGVDGFRLDTINFY HD ELRDNP L PE RN++ AP VNPYN+Q H Sbjct: 191 QEALLAVERFWLERGVDGFRLDTINFYFHDRELRDNPALVPERRNASTAPAVNPYNYQEH 250 Query: 253 LYSKNQPENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILGQYTRGETGVHMCYAFEF 312 +Y KN+PENLEFL +FRA+M+E+PAIAAVGEVGD+Q GLEI G+YT G VHMCYAFEF Sbjct: 251 IYDKNRPENLEFLKRFRAVMDEFPAIAAVGEVGDSQRGLEIAGEYTSGGDKVHMCYAFEF 310 Query: 313 LAQEKLTAKRVAEVLNKVDEVASDGWACWAFSNHDVMRHVSRW--DLTPGAQRGML--TL 368 LA ++LT +RVAEVL A +GWACWAFSNHDV+RHVSRW +T L +L Sbjct: 311 LAPDRLTPQRVAEVLRDFHRAAPEGWACWAFSNHDVVRHVSRWADGVTDHDAHAKLLASL 370 Query: 369 LMCLRGSVCLYQGEELGLPEAEVAFDDLQDPYGIEFWPEYKGRDGCRTPMVWQSDNMSGG 428 LM LRG+VC+YQGEEL L EAE+ ++DLQDPYGI+FWP++KGRDGCRTPMVW+S GG Sbjct: 371 LMSLRGTVCIYQGEELALAEAELDYEDLQDPYGIQFWPDFKGRDGCRTPMVWES-LPDGG 429 Query: 429 FSIHRPWLPVSTEHLGLAVAVQEEAPDALLHHYRRALAFRRAHPALVKGDISDVTVVGDV 488 FS PWLP+S H+ AVAVQE P ++LHHYRR LAFR+A+PAL KG+I V G + Sbjct: 430 FSSATPWLPISQSHIPRAVAVQEGDPASVLHHYRRFLAFRKANPALAKGEIEFVETRGSL 489 Query: 489 ISFLRKDPEETVFVAINMSDAPGAVDLP 516 + FLR E VF NMSD +LP Sbjct: 490 LGFLRSHGNEKVFCLFNMSDEAATKELP 517 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: 1083 Number of extensions: 41 Number of successful extensions: 3 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: 551 Length adjustment: 36 Effective length of query: 516 Effective length of database: 515 Effective search space: 265740 Effective search space used: 265740 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