Align Alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate WP_086510098.1 BZY95_RS11685 DUF3459 domain-containing protein
Query= reanno::psRCH2:GFF856 (542 letters) >NCBI__GCF_002151265.1:WP_086510098.1 Length = 550 Score = 675 bits (1741), Expect = 0.0 Identities = 321/537 (59%), Positives = 390/537 (72%), Gaps = 10/537 (1%) Query: 7 NWWRGGVIYQVYPRSFFDSNGDGVGDLPGVLHKLDYIASLNVDAIWLSPFFTSPMKDFGY 66 +WWRG VIYQ+YPRSF DS G G+GDL GV+ +LDYIASLNVDAIWL+PFFTSPMKDFGY Sbjct: 11 DWWRGAVIYQIYPRSFQDSRGAGIGDLQGVIDRLDYIASLNVDAIWLAPFFTSPMKDFGY 70 Query: 67 DVADYRGVDPLFGTLDDFVRLVEACHERGMRVLIDQVLNHSSDQHPWFAESRSSRDNDKA 126 DV+DYRGVDP FGTLDDF RLVEA H RG+RV IDQVL+HSSDQHPWFAESRSSRDN KA Sbjct: 71 DVSDYRGVDPTFGTLDDFDRLVEAAHARGLRVTIDQVLSHSSDQHPWFAESRSSRDNPKA 130 Query: 127 DWYVWADPKPDGTVPNNWLSVFGGPAWSWDSRRRQYYLHNFLSSQPDLNFHCPAVQDQLL 186 DWYVWAD + DG+ P NW ++FGG AW WD+RR QYYLHNFL QPDLNFH P V + +L Sbjct: 131 DWYVWADARSDGSPPTNWQAIFGGSAWQWDTRRCQYYLHNFLVEQPDLNFHNPEVVEAIL 190 Query: 187 DDMEFWLKLGVDGFRLDAANFYFHDAELRDNPPNTEIREGSIGVRIDNPYAYQRHIYDKT 246 +++ FWL+ GVDGFRLDA NF H L+DNPP +I EG IGVR DNPYA+QRH+YDKT Sbjct: 191 EEVRFWLERGVDGFRLDAVNFCTH-GPLKDNPPREKIVEGFIGVRPDNPYAFQRHLYDKT 249 Query: 247 RPENMDFLRRLRALLQRYPGASSVAEIGCDESLRTMAAYTSGGDTLHMAYSFDLLTEQCS 306 +PEN+ FL RLRALL YP +++ E+G D+SL M+ YT GG LHM YSF+LLT++ + Sbjct: 250 QPENLAFLERLRALLDEYPSTTTIGEVGDDDSLGVMSEYTQGGKRLHMCYSFNLLTDKAT 309 Query: 307 PGYIRHTVEGIERELADGWSCWSMGNHDVVRVMTRWALNGRPDPERGRLLMALLLSLRGS 366 P + + +E + DGW CW++GNHD+ RV TRW N D + RL +A LL+ RGS Sbjct: 310 PADLLAPLTEMEARIGDGWPCWAVGNHDITRVATRW--NVASDMAKLRLYLAFLLTQRGS 367 Query: 367 VCMYQGEELGLPEAELRYEDLVDPYGITFWPEFKGRDGCRTPMPWESEAHHAGFTGSQPW 426 +C+YQGEELGL EAEL +E LVDP GITFWP +KGRDGCRTPMPW ++A H GFT + PW Sbjct: 368 ICLYQGEELGLTEAELTFEQLVDPAGITFWPSYKGRDGCRTPMPWVADALHGGFTTATPW 427 Query: 427 LPVDDSHRSLSVAAQDADPHSMLNCYRRFLGWRREQRLLIEGDIHMVYHDDALLVFERRL 486 LPV ++H +L+V Q+ DP S+LN YR FL +RR Q L++GDIH ++ FER Sbjct: 428 LPVPEAHLALAVDRQERDPGSLLNAYRDFLLFRRNQPALVKGDIHYHPLQGDVICFERLH 487 Query: 487 GDEAWLCLFNLGDLSRSYELPAQAVPLVDVPASFAEYDGHWA----RLPAHGFGYVR 539 GD+ L N + + P A PL P+ +G W LPA G R Sbjct: 488 GDDRLLVALNFANDPCTLSAPLDARPLAGAPSL---VNGRWTAERLELPAFGIAIAR 541 Lambda K H 0.322 0.140 0.464 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: 1085 Number of extensions: 44 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: 542 Length of database: 550 Length adjustment: 35 Effective length of query: 507 Effective length of database: 515 Effective search space: 261105 Effective search space used: 261105 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 (21.9 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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