Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate WP_086510096.1 BZY95_RS11675 DUF3459 domain-containing protein
Query= uniprot:A8LLL3 (552 letters) >NCBI__GCF_002151265.1:WP_086510096.1 Length = 536 Score = 610 bits (1572), Expect = e-179 Identities = 295/532 (55%), Positives = 371/532 (69%), Gaps = 14/532 (2%) Query: 19 WWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKDFGYD 78 WWRG VIYQIYPRSF DSNGDG+GDL G+ ER+ Y+ASLGVD IW+SPFFTSPM+DFGYD Sbjct: 7 WWRGGVIYQIYPRSFMDSNGDGVGDLPGVTERLDYVASLGVDGIWLSPFFTSPMRDFGYD 66 Query: 79 ISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDNPKAD 138 IS+Y DVDP+FG+LADF AL+E AH GL+V+ID V+SHTSDQHPWF+ESR +RDNP+AD Sbjct: 67 ISNYRDVDPLFGTLADFKALLERAHALGLKVIIDQVISHTSDQHPWFQESRMNRDNPRAD 126 Query: 139 WYVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLTSQPDLNFHCADVQDALLG 198 WYVWAD PDGT PNNWLSIFGG W +D+RR QYYLHNFL+SQPDLNFH +V+ A L Sbjct: 127 WYVWADPNPDGTAPNNWLSIFGGPAWTFDSRRQQYYLHNFLSSQPDLNFHNPEVRAAQLD 186 Query: 199 VGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPEERNSNIAPEVNPYNHQRHLYSKNQ 258 RFWL+ GVDGFRLDT+NFY HD LR NP L + + AP+ NPY QRH+Y ++ Sbjct: 187 NMRFWLELGVDGFRLDTVNFYFHDQHLRSNPALTIDATRTLGAPKENPYTWQRHIYDISR 246 Query: 259 PENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILGQYTRGETGVHMCYAFEFLAQEKL 318 PEN+EFL + RA+M+EYP VGE+GD LE + +YT G +HM Y F+ L + Sbjct: 247 PENVEFLRELRALMDEYPGTTTVGEIGD-DTPLERMAEYTSGGDKLHMAYTFDLLNAPR- 304 Query: 319 TAKRVAEVLNKVDEVASDGWACWAFSNHDVMRHVSRWDLTPGA---QRGMLTLLMCLRGS 375 + + VL + + A D W CWA SNHDV+R +RW A R L LL LRGS Sbjct: 305 SPDYIRGVLERFQQFAGDAWPCWALSNHDVVRSATRWGSEECAFAYPRVALALLFSLRGS 364 Query: 376 VCLYQGEELGLPEAEVAFDDLQDPYGIEFWPEYKGRDGCRTPMVWQSDNMSGGFSIHRPW 435 VCLYQGEELGLPEAEV F+ +QDPYG+ WP++KGRDGCRTPM W D GFS PW Sbjct: 365 VCLYQGEELGLPEAEVPFERIQDPYGLPLWPDFKGRDGCRTPMPW-DDTPLAGFSDVEPW 423 Query: 436 LPVSTEHLGLAVAVQEEAPDALLHHYRRALAFRRAHPALVKGDISDVTVVGDVISFLRKD 495 LPV+ HL ++VA Q++ PD++L+ RR L FR HPAL GD++ + + +++F R+ Sbjct: 424 LPVAEPHLAMSVARQQDEPDSMLNATRRLLRFRHQHPALFDGDMTLLDLGEALVAFTRQR 483 Query: 496 PEETVFVAINMSDAPGAVDLPPGNWMQIGAELNSGGTSPD---GRVHLGPWQ 544 + + N++ P + LP ++ L G + GR+HL P+Q Sbjct: 484 GSDRLLCVFNLTGQPQSATLP-----EVREALQEHGFQYEVSGGRLHLPPYQ 530 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: 1102 Number of extensions: 57 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: 536 Length adjustment: 35 Effective length of query: 517 Effective length of database: 501 Effective search space: 259017 Effective search space used: 259017 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 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