Align Alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate WP_086508167.1 BZY95_RS01125 DUF3459 domain-containing protein
Query= reanno::psRCH2:GFF856 (542 letters) >NCBI__GCF_002151265.1:WP_086508167.1 Length = 558 Score = 683 bits (1763), Expect = 0.0 Identities = 329/544 (60%), Positives = 393/544 (72%), Gaps = 14/544 (2%) Query: 4 QLQNWWRGGVIYQVYPRSFFDSNGDGVGDLPGVLHKLDYIASLNVDAIWLSPFFTSPMKD 63 Q Q+WWRG VIYQ+YPRSF DSNGDG+GDLPG++ KLDYIASLNVDAIW+SPFFTSPMKD Sbjct: 10 QGQDWWRGAVIYQIYPRSFMDSNGDGIGDLPGIIDKLDYIASLNVDAIWISPFFTSPMKD 69 Query: 64 FGYDVADYRGVDPLFGTLDDFVRLVEACHERGMRVLIDQVLNHSSDQHPWFAESRSSRDN 123 FGYDVADYR VDP+FGTLDDF RLVEA H RG++V IDQVL+H+SD+HPWF+ESR SRDN Sbjct: 70 FGYDVADYRSVDPIFGTLDDFDRLVEAAHARGLKVTIDQVLSHTSDRHPWFSESRGSRDN 129 Query: 124 DKADWYVWADPKPDGTVPNNWLSVFGGPAWSWDSRRRQYYLHNFLSSQPDLNFHCPAVQD 183 KADWYVWA+ K DG+ P NW SVFGG AW WD+RR QYYLHNFL SQPDLNF PAV + Sbjct: 130 PKADWYVWAEAKADGSPPTNWQSVFGGSAWQWDTRRCQYYLHNFLDSQPDLNFRNPAVVE 189 Query: 184 QLLDDMEFWLKLGVDGFRLDAANFYFHDAELRDNPPNTEIREGSIGVRIDNPYAYQRHIY 243 +LD++ FWL GVDGFRLDA NF H EL DNPP ++ EG +GVR DNPY YQ H++ Sbjct: 190 AVLDEVRFWLDRGVDGFRLDAVNFCTH-GELVDNPPRSDAAEGFLGVRPDNPYGYQLHLH 248 Query: 244 DKTRPENMDFLRRLRALLQRYPGASSVAEIGCDESLRTMAAYTSGGDTLHMAYSFDLLTE 303 DKT+PEN+ FL +LRALL YPG +SV E+G D+SL MAAYT G LHMAYSFDLL E Sbjct: 249 DKTQPENLAFLEKLRALLDEYPGTTSVGEVGDDDSLNVMAAYTQGNKRLHMAYSFDLLGE 308 Query: 304 QCSPGYIRHTVEGIERELADGWSCWSMGNHDVVRVMTRWALNGRPDPERGRLLMALLLSL 363 + P ++ T+ +E ++ DGW CW++GNHDV R+ TRW + DP+R RL +A LL+ Sbjct: 309 RHDPDFLHRTMTAMEAKIGDGWPCWALGNHDVPRLATRW--KAQDDPDRLRLYLAFLLTQ 366 Query: 364 RGSVCMYQGEELGLPEAELRYEDLVDPYGITFWPEFKGRDGCRTPMPWESEAHHAGFTGS 423 RGSVC+YQGEELGLPEAEL E LVDP GITFWP +KGRDGCRTP PW + H F+ Sbjct: 367 RGSVCLYQGEELGLPEAELTLEQLVDPAGITFWPAYKGRDGCRTPHPWCGDTRHGDFSQG 426 Query: 424 QPWLPVDDSHRSLSVAAQDADPHSMLNCYRRFLGWRREQRLLIEGDIHMVYHDDALLVFE 483 +PWLPV ++H L++ QD P S+LN YR FL +RRE L +G++ D +L E Sbjct: 427 EPWLPVPEAHLELAMRHQDEAPDSLLNAYRAFLAFRREHVALKKGEVRYHPVRDEVLCLE 486 Query: 484 R----RLGDEAWLCLFNLGDLSRSYELPAQAVPLVDVPASFAEYDGHWA----RLPAHGF 535 R R +E L N D R+ P QA PL D PA +G WA +LP G Sbjct: 487 RHHPARAPNERLLVALNFSDAPRTLPAPRQARPLDDAPAL---VNGVWANGEVQLPPCGI 543 Query: 536 GYVR 539 R Sbjct: 544 AIAR 547 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: 1138 Number of extensions: 54 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: 542 Length of database: 558 Length adjustment: 36 Effective length of query: 506 Effective length of database: 522 Effective search space: 264132 Effective search space used: 264132 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: 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