Align α-glucosidase (PalZ) (EC 3.2.1.20) (characterized)
to candidate GFF3717 Psest_3786 Glycosidases
Query= CAZy::AAK28739.1 (552 letters) >FitnessBrowser__psRCH2:GFF3717 Length = 539 Score = 209 bits (531), Expect = 3e-58 Identities = 165/546 (30%), Positives = 250/546 (45%), Gaps = 89/546 (16%) Query: 4 WWKEAVAYQIYPRSFNDSNNDGIGDLNGITEKLDYLEDLGIDLIWICPMYQSPNDDNGYD 63 W++ A YQI P F DSN DG GDL GITE+LDY+ LG +W+ P YQSP +D GYD Sbjct: 5 WYRNAAIYQIDPTLFRDSNGDGCGDLRGITERLDYIRGLGCTAVWLMPFYQSPFEDAGYD 64 Query: 64 ISDYQKIMAEFGTMDDFDRLLEQVHARGMRLIIDLVVNHTSDEHPWFLASSASRDNPKRD 123 ISD+ ++ FG + D LLE+ G+ +II+LVV HTS +H WF + R++P RD Sbjct: 65 ISDHLQVDERFGDLADIVALLEKAEELGLHVIIELVVQHTSIQHKWFQEARRDRNSPYRD 124 Query: 124 WYIWRDGKAGAEPNNW-ESIF---NGSAWKYSAATGQYFLHLFSEKQPDLNWENPEVRSA 179 +YIW D EP+++ E IF S W + GQY+ HLF + +PDL+ NP V Sbjct: 125 YYIWAD-----EPDDFMEPIFPTVEDSIWTWDEEAGQYYRHLFYKHEPDLDLTNPRVIHE 179 Query: 180 VYAMMRWWLDKGVDGFRIDAICHMKKEPTFSDMPNPLALPYVPSFERHLNYDGLLDYVDD 239 + +M +WL GV GFRIDA HM ++ ++ LL+++ D Sbjct: 180 IERIMSFWLRLGVSGFRIDAAVHMVRQAGGGELEKGY---------------WLLEHMRD 224 Query: 240 MCEQVFSHYDIVTIGEMNGASAEQGEEWVGEQRGRLNMIFQF---EHVKL-WQDGQKDTL 295 + V +GE++ ++ E+ G++ R+ ++ F H+ L Q + L Sbjct: 225 FV--TMRRPETVLLGEID-TDPDKYVEYFGDEADRVTLLLDFWTNNHLFLSLARQQAEPL 281 Query: 296 EASLDLPGLKEIFTRWQTLLENKGWNAL-YVENHDLPRVVSGWGDDKN---YQR------ 345 +L+ L +++ + N +L +E + V+ + D+N Y R Sbjct: 282 VRALNSQPLPPSHSQYALWIRNHDELSLDRLEEDERNEVMDTFAPDENMRAYNRGIRRRL 341 Query: 346 --------ESATAIAAMFFLMKGTPFIYQGQELGMTNTHFASLEDFDDVAAKKLAVEMRR 397 A A+ F + GTP I G+E+GM DD+ Sbjct: 342 APMLDGDERRIAATHALLFSLPGTPIIRYGEEIGMG----------DDL----------- 380 Query: 398 QGREEPEILAFLSRTGRENSRTPMQSDQSAHGGFS-----NATPWFPANS-NYPVINVAD 451 + PE LA RTPMQ + GFS A P Y INV Sbjct: 381 ---DRPERLAV---------RTPMQWSNEPNAGFSCTKGELAAPVIDEGPFTYEKINVFA 428 Query: 452 QRADSGSVLNFYRALIRLRRQMPVLIEGAYQLLLPTHPQIYAYTRRLNEQQVLVIVNFSA 511 Q S S++ +IR R + + G + P ++A R N VL++VN + Sbjct: 429 QTLRSDSLMARTGNMIRTRIGLREIGIGKRTTVEVNDPAVFA-IRHDNGSTVLMLVNLAD 487 Query: 512 HQQEID 517 + ++ Sbjct: 488 QETTVE 493 Lambda K H 0.319 0.136 0.427 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: 836 Number of extensions: 36 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: 539 Length adjustment: 35 Effective length of query: 517 Effective length of database: 504 Effective search space: 260568 Effective search space used: 260568 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