Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate GFF856 Psest_0870 Glycosidases
Query= uniprot:H3K096 (538 letters) >FitnessBrowser__psRCH2:GFF856 Length = 542 Score = 664 bits (1714), Expect = 0.0 Identities = 309/534 (57%), Positives = 384/534 (71%), Gaps = 2/534 (0%) Query: 7 WWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGYD 66 WWRGGVIYQ+YPRSF DS GDGVGDL G+ KLDY+ASLNVD IWLSPFFTSPM DFGYD Sbjct: 8 WWRGGVIYQVYPRSFFDSNGDGVGDLPGVLHKLDYIASLNVDAIWLSPFFTSPMKDFGYD 67 Query: 67 VSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKAD 126 V+DYR VDP+FGTL+DF L+E H G++V+IDQV++H+SDQHPWF ESR +R N KAD Sbjct: 68 VADYRGVDPLFGTLDDFVRLVEACHERGMRVLIDQVLNHSSDQHPWFAESRSSRDNDKAD 127 Query: 127 WFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQLD 186 W+VWADPKPDGT PNNWLS+FGG AW++DSRR+QYYLHNFL+SQPD+NFH P + LD Sbjct: 128 WYVWADPKPDGTVPNNWLSVFGGPAWSWDSRRRQYYLHNFLSSQPDLNFHCPAVQDQLLD 187 Query: 187 NMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDLSR 246 +M FWL LGVDGFRLD NFYFHDAELRDNPP + ++G NPY +QRH+YD +R Sbjct: 188 DMEFWLKLGVDGFRLDAANFYFHDAELRDNPPNTEIREGSIGVRIDNPYAYQRHIYDKTR 247 Query: 247 PENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMPHSA 306 PEN+DFL+ LRAL+ YPG ++V EIG D L MA YT+GGD LHMAY+FDLL S Sbjct: 248 PENMDFLRRLRALLQRYPGASSVAEIGCDESLRTMAAYTSGGDTLHMAYSFDLLTEQCSP 307 Query: 307 SYLREVIERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPH-AYPKVMLAVLFSLRGSV 365 Y+R +E +R D W CW+ NHDVVR TRW + P ++++A+L SLRGSV Sbjct: 308 GYIRHTVEGIERELADGWSCWSMGNHDVVRVMTRWALNGRPDPERGRLLMALLLSLRGSV 367 Query: 366 CLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPW-TDGEQGGFSPVEPWL 424 C+YQGEELGLPEA++ +E + DPYG WPEFKGRDGCRTPMPW ++ GF+ +PWL Sbjct: 368 CMYQGEELGLPEAELRYEDLVDPYGITFWPEFKGRDGCRTPMPWESEAHHAGFTGSQPWL 427 Query: 425 PMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTRQKG 484 P++ H L+V+ Q DP++ LN R L +RR L +GD+ +V D LL F R+ G Sbjct: 428 PVDDSHRSLSVAAQDADPHSMLNCYRRFLGWRREQRLLIEGDIHMVYHDDALLVFERRLG 487 Query: 485 DETLLCVFNLTGQEQQTTLPVEVASDLPVAHFTATRDGSTLTLPAYQAAFMQVA 538 DE LC+FNL + LP + + V A DG LPA+ ++++A Sbjct: 488 DEAWLCLFNLGDLSRSYELPAQAVPLVDVPASFAEYDGHWARLPAHGFGYVRLA 541 Lambda K H 0.320 0.138 0.443 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: 1090 Number of extensions: 40 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: 538 Length of database: 542 Length adjustment: 35 Effective length of query: 503 Effective length of database: 507 Effective search space: 255021 Effective search space used: 255021 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