Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate H281DRAFT_02777 H281DRAFT_02777 alpha-glucosidase
Query= uniprot:A8LLL3 (552 letters) >FitnessBrowser__Burk376:H281DRAFT_02777 Length = 524 Score = 435 bits (1118), Expect = e-126 Identities = 223/492 (45%), Positives = 300/492 (60%), Gaps = 15/492 (3%) Query: 19 WWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKDFGYD 78 WW+ VIYQ+YPRSFQDSNGDGIGDL GI R+PY+A LG+DA+W+SP + SPM DFGYD Sbjct: 6 WWQRGVIYQVYPRSFQDSNGDGIGDLAGITSRLPYLAGLGIDAVWLSPIYPSPMADFGYD 65 Query: 79 ISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDNPKAD 138 ++DY D+DPMFG+L DF + AH GL+V++D V +H+SD+HPWFEESRSSR+NPK D Sbjct: 66 VADYCDIDPMFGTLGDFKQFADRAHELGLKVLLDFVPNHSSDRHPWFEESRSSRENPKRD 125 Query: 139 WYVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLTSQPDLNFHCADVQDALLG 198 WY+W D PDG PPNNWLS GGS W WD R QYY H FL QPDLN+ V+ A+ Sbjct: 126 WYLWRDPAPDGGPPNNWLSRMGGSAWEWDERTGQYYYHAFLREQPDLNWRNPQVRRAMDD 185 Query: 199 VGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPEERNSNIAPEVNPYNHQRHLYSKNQ 258 V RFWLDRGVDGFR+D + + D++ RDNPP P E P ++ Q Y+++Q Sbjct: 186 VLRFWLDRGVDGFRVDVLWLLIKDSQFRDNPPNPAYE------PGQPEHHRQLQTYTEDQ 239 Query: 259 PENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILGQYTRGETGVHMCYAFEFLAQEKL 318 PE E + RA ++EY +GE+ +++ Y G M + F+ L Sbjct: 240 PEVHEIVRSMRATLDEYGERVLIGEI--YLPVPQLVRYYGANGDGADMPFNFQLL-NAAW 296 Query: 319 TAKRVAEVLNKVDE-VASDGWACWAFSNHDVMRHVSRWDLTPGAQRGMLTLLMCLRGSVC 377 A +A ++ D + W W NHD R SR + R LL+ LRG+ Sbjct: 297 NAGEIARMIRDYDSALPVHAWPNWVLGNHDNPRVASR--VGAAQARVAAVLLLTLRGTPT 354 Query: 378 LYQGEELGLPEAEVAFDDLQDPYGIEFWPEYKGRDGCRTPMVWQSDNMSGGFSIHRPWLP 437 LY G+E+G+ + E++ D +QDP I +GRD RTPM W + GF+ R WLP Sbjct: 355 LYYGDEIGMTDGEISPDRVQDPAEIRQPDIGQGRDPERTPMQWDAALPGAGFTNGRSWLP 414 Query: 438 VSTEHLGLAVAVQEEAPDALLHHYRRALAFRRAHPALVKGDISDVTVVGDVISFLRKDPE 497 +ST+ +V Q+ P ++L YRR L RR++ ALV+G I +V GDV++F R Sbjct: 415 ISTD---TSVRAQDGDPSSMLSLYRRLLELRRSNAALVQGAIENVAASGDVLTFERHYRG 471 Query: 498 ETVFVAINMSDA 509 + +F+A+NM A Sbjct: 472 QRLFIALNMGAA 483 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: 1015 Number of extensions: 58 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: 524 Length adjustment: 35 Effective length of query: 517 Effective length of database: 489 Effective search space: 252813 Effective search space used: 252813 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