Align Alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate AO353_22940 AO353_22940 alpha-amylase
Query= reanno::psRCH2:GFF856 (542 letters) >FitnessBrowser__pseudo3_N2E3:AO353_22940 Length = 1113 Score = 251 bits (640), Expect = 1e-70 Identities = 185/557 (33%), Positives = 263/557 (47%), Gaps = 102/557 (18%) Query: 8 WWRGGVIYQVYPRSFFDSNGDGVGDLPGVLHKLDYIASLNVDAIWLSPFFTSPMKDFGYD 67 W++ VIYQV+ +S+FDSN DG+GD PG++ KLDYIA L V+ IWL PF+ SP +D GYD Sbjct: 16 WYKDAVIYQVHVKSYFDSNNDGIGDFPGLIAKLDYIAELGVNTIWLLPFYPSPRRDDGYD 75 Query: 68 VADYRGVDPLFGTLDDFVRLVEACHERGMRVLIDQVLNHSSDQHPWFAESRSSRDNDKA- 126 +A+YRGV +GTL D R + H RG+RV+ + V+NH+SDQHPWF +R ++ A Sbjct: 76 IAEYRGVHRDYGTLTDAKRFIAEAHNRGLRVITELVINHTSDQHPWFQRARKAKPGSAAR 135 Query: 127 DWYVWA--DPKPDGTVPNNWLSVF---GGPAWSWDSRRRQYYLHNFLSSQPDLNFHCPAV 181 D+YVW+ D K DGT +F W+WD QY+ H F S QPDLNF P V Sbjct: 136 DFYVWSDDDQKYDGT-----RIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDNPQV 190 Query: 182 QDQLLDDMEFWLKLGVDGFRLDAANFYF-HDAELRDNPPNTEIREGSIGVRIDNPYAYQR 240 +L M +WL LG+DG RLDA + D +N P T I ID Y Sbjct: 191 MKAVLSVMRYWLDLGIDGLRLDAIPYLIERDGTNNENLPETHAVLKQIRAEIDAHY---- 246 Query: 241 HIYDKTRPENMDFLRRLRALLQRYPGASSVAEIGCDESLRTMAAYTSGGDTLHMAYSFDL 300 P+ M L A ++P D L + GD HMA+ F L Sbjct: 247 -------PDRM-----LLAEANQWPE---------DTQLYFGDVHGDNGDECHMAFHFPL 285 Query: 301 LTE--QCSPGYIRHTVEGIERELAD-----GWSCWSMGNHDVVR---------------- 337 + R + I R+ + W+ + + NHD + Sbjct: 286 MPRMYMALAQEDRFPITDILRQTPEIPANCQWAIF-LRNHDELTLEMVTDKERDYLWNYY 344 Query: 338 -----------VMTRWALNGRPDPERGRLLMALLLSLRGSVCMYQGEELGLPEAELRYED 386 + R A D R LL +LLLS+ G+ +Y G+E+G+ + + D Sbjct: 345 AADRRARINLGIRRRLAPLMERDRRRVELLNSLLLSMPGTPTLYYGDEIGMGD-NIYLGD 403 Query: 387 LVDPYGITFWPEFKGRDGCRTPMPWESEAHHAGFTGSQP----WLPVDD---SHRSLSVA 439 RDG RTPM W + + GF+ + P P+ D + S++V Sbjct: 404 ---------------RDGVRTPMQWSID-RNGGFSRADPASLVLPPIMDPLYGYLSVNVE 447 Query: 440 AQDADPHSMLNCYRRFLGWRREQRLLIEGDIHMVYHDD-ALLVFERR-LGD----EAWLC 493 Q DPHS+LN RR L R++ + G + M+ + +L + R GD E LC Sbjct: 448 TQAGDPHSLLNWTRRMLAIRKQSKAFGRGSLKMLSPSNRRILAYTREYTGDDGKHEIILC 507 Query: 494 LFNLGDLSRSYELPAQA 510 + N+ +++ EL A Sbjct: 508 VANVSRSAQAAELDLSA 524 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: 1678 Number of extensions: 93 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 542 Length of database: 1113 Length adjustment: 41 Effective length of query: 501 Effective length of database: 1072 Effective search space: 537072 Effective search space used: 537072 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: 55 (25.8 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