Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate WP_086508167.1 BZY95_RS01125 DUF3459 domain-containing protein
Query= uniprot:H3K096 (538 letters) >NCBI__GCF_002151265.1:WP_086508167.1 Length = 558 Score = 615 bits (1586), Expect = e-180 Identities = 298/503 (59%), Positives = 358/503 (71%), Gaps = 9/503 (1%) Query: 7 WWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGYD 66 WWRG VIYQIYPRSF+DS GDG+GDL GI +KLDY+ASLNVD IW+SPFFTSPM DFGYD Sbjct: 14 WWRGAVIYQIYPRSFMDSNGDGIGDLPGIIDKLDYIASLNVDAIWISPFFTSPMKDFGYD 73 Query: 67 VSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKAD 126 V+DYR VDP+FGTL+DF L+E AH+ GLKV IDQV+SHTSD+HPWF ESR +R NPKAD Sbjct: 74 VADYRSVDPIFGTLDDFDRLVEAAHARGLKVTIDQVLSHTSDRHPWFSESRGSRDNPKAD 133 Query: 127 WFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQLD 186 W+VWA+ K DG+PP NW S+FGGSAW +D+RR QYYLHNFL SQPD+NF +P +A LD Sbjct: 134 WYVWAEAKADGSPPTNWQSVFGGSAWQWDTRRCQYYLHNFLDSQPDLNFRNPAVVEAVLD 193 Query: 187 NMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDLSR 246 +RFWLD GVDGFRLD VNF H EL DNPP LG NPY +Q H++D ++ Sbjct: 194 EVRFWLDRGVDGFRLDAVNFCTH-GELVDNPPRSDAAEGFLGVRPDNPYGYQLHLHDKTQ 252 Query: 247 PENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMPHSA 306 PENL FL+ LRAL+DEYPGTT+VGE+GDD+ L MA YT G +LHMAY+FDLL H Sbjct: 253 PENLAFLEKLRALLDEYPGTTSVGEVGDDDSLNVMAAYTQGNKRLHMAYSFDLLGERHDP 312 Query: 307 SYLREVIERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLFSLRGSVC 366 +L + + GD WPCWA NHDV R ATRW A +DP ++ LA L + RGSVC Sbjct: 313 DFLHRTMTAMEAKIGDGWPCWALGNHDVPRLATRWKAQDDPDRL-RLYLAFLLTQRGSVC 371 Query: 367 LYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPWT-DGEQGGFSPVEPWLP 425 LYQGEELGLPEA++ E++ DP G WP +KGRDGCRTP PW D G FS EPWLP Sbjct: 372 LYQGEELGLPEAELTLEQLVDPAGITFWPAYKGRDGCRTPHPWCGDTRHGDFSQGEPWLP 431 Query: 426 MEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTR---- 481 + HLELA+ Q + P++ LN RA LAFRR H AL G++ V D++L R Sbjct: 432 VPEAHLELAMRHQDEAPDSLLNAYRAFLAFRREHVALKKGEVRYHPVRDEVLCLERHHPA 491 Query: 482 QKGDETLLCVFNLTGQEQQTTLP 504 + +E LL N + + TLP Sbjct: 492 RAPNERLLVALNFS--DAPRTLP 512 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: 1096 Number of extensions: 53 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: 538 Length of database: 558 Length adjustment: 36 Effective length of query: 502 Effective length of database: 522 Effective search space: 262044 Effective search space used: 262044 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: 53 (25.0 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