Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate 5209418 Shew_1889 alpha amylase, catalytic region (RefSeq)
Query= uniprot:A8LLL3 (552 letters) >FitnessBrowser__PV4:5209418 Length = 541 Score = 596 bits (1536), Expect = e-175 Identities = 277/500 (55%), Positives = 351/500 (70%), Gaps = 5/500 (1%) Query: 19 WWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKDFGYD 78 WWRGAVIYQIYPRS DSNGDG+GDL GI+ ++ YIASL VDAIWISPFF SPMKDFGYD Sbjct: 6 WWRGAVIYQIYPRSLMDSNGDGVGDLQGIISKLDYIASLNVDAIWISPFFKSPMKDFGYD 65 Query: 79 ISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDNPKAD 138 ISDY +DP+FG++ADFD LI+ AH G++V+ID VLSHTSDQH WF ESR SRDN K D Sbjct: 66 ISDYRAIDPLFGTMADFDELIDKAHGLGIKVIIDQVLSHTSDQHAWFSESRQSRDNAKQD 125 Query: 139 WYVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLTSQPDLNFHCADVQDALLG 198 WYVWAD PDGT PNNWL+IFGG W W+ RR QYYLHNFLTSQPDLNFH DV+ A+L Sbjct: 126 WYVWADPNPDGTAPNNWLAIFGGCAWEWEPRRQQYYLHNFLTSQPDLNFHNPDVRQAVLD 185 Query: 199 VGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPEERNSNIAPEVNPYNHQRHLYSKNQ 258 +FWLD+GVDGFRLD I F HD +LRDNPP P ++R E NPY +Q H Y+ + Sbjct: 186 NVKFWLDKGVDGFRLDAITFCYHDEQLRDNPPKPEDKRQGRGFSEDNPYAYQYHYYNNTR 245 Query: 259 PENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILGQYTRGETGVHMCYAFEFLAQEKL 318 P+ + F+ + RA++ +YP + +GEV ++ L + +YT+G+ +HM Y+FE L + Sbjct: 246 PQTVGFIEELRALINQYPGVVTLGEV-SSEDSLATMAEYTQGDDRLHMAYSFELLTDD-F 303 Query: 319 TAKRVAEVLNKVDEVASDGWACWAFSNHDVMRHVSRW--DLTPGAQRGMLTLLMC-LRGS 375 + + + +++ DGW CWA NHDV R +RW D ML ++C LRGS Sbjct: 304 SPAYIRHTVEALEQSIGDGWPCWAIGNHDVQRVATRWGRDAFNSDMAKMLNAMLCSLRGS 363 Query: 376 VCLYQGEELGLPEAEVAFDDLQDPYGIEFWPEYKGRDGCRTPMVWQSDNMSGGFSIHRPW 435 VC YQGEELGL E E+A++ LQDP+GI FWP +KGRDGCRTPM W+ D GFS + PW Sbjct: 364 VCSYQGEELGLGEVEIAYEQLQDPFGITFWPMFKGRDGCRTPMPWRHDANHAGFSDNTPW 423 Query: 436 LPVSTEHLGLAVAVQEEAPDALLHHYRRALAFRRAHPALVKGDISDVTVVGDVISFLRKD 495 LPV +H +AV VQE P+++L+HYR LA+R+ HP LV GDI + ++ F R+ Sbjct: 424 LPVPADHKAVAVDVQEANPESILNHYRHMLAWRKLHPILVTGDIKFIESTDALLVFERRL 483 Query: 496 PEETVFVAINMSDAPGAVDL 515 E+T+ VA N+S P + L Sbjct: 484 GEQTLLVAFNLSGQPQSFSL 503 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: 1007 Number of extensions: 36 Number of successful extensions: 4 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: 541 Length adjustment: 36 Effective length of query: 516 Effective length of database: 505 Effective search space: 260580 Effective search space used: 260580 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: 52 (24.6 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