Align Alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate BPHYT_RS33775 BPHYT_RS33775 alpha-amylase
Query= reanno::psRCH2:GFF856 (542 letters) >FitnessBrowser__BFirm:BPHYT_RS33775 Length = 1154 Score = 252 bits (644), Expect = 5e-71 Identities = 179/546 (32%), Positives = 264/546 (48%), Gaps = 97/546 (17%) Query: 8 WWRGGVIYQVYPRSFFDSNGDGVGDLPGVLHKLDYIASLNVDAIWLSPFFTSPMKDFGYD 67 W++ +IYQV+ +SFFD+N DGVGD PG++ KLDYIA L V+AIWL PF+ SP +D GYD Sbjct: 42 WYKDAIIYQVHIKSFFDANNDGVGDFPGLIAKLDYIAELGVNAIWLLPFYPSPRRDDGYD 101 Query: 68 VADYRGVDPLFGTLDDFVRLVEACHERGMRVLIDQVLNHSSDQHPWFAESRSSR-DNDKA 126 +ADYR V P +G L D R ++ H RG+RV+ + V+NH+SDQHPWF +R ++ ++ Sbjct: 102 IADYRNVHPDYGNLSDVKRFIQEAHARGIRVITELVINHTSDQHPWFQRARRAKPGSNHR 161 Query: 127 DWYVWADPKPDGTVPNNWLSVFGGPA-WSWDSRRRQYYLHNFLSSQPDLNFHCPAVQDQL 185 ++YVW+D + + P+ W+ D YY H F S QPDLNF PAV ++ Sbjct: 162 NYYVWSD-TDQKYQETRIIFIDSEPSNWTHDPVAGAYYWHRFYSHQPDLNFDNPAVLKEV 220 Query: 186 LDDMEFWLKLGVDGFRLDAANFYFHDAELRDNPPNTEIREGSIGVRIDNPYAYQRH-IYD 244 L M FWL +G+DG RLDA PY +R + Sbjct: 221 LQVMRFWLDMGIDGLRLDAV-----------------------------PYLVEREGTNN 251 Query: 245 KTRPENMDFLRRLRALLQ-RYPGASSVAEIGCDESLRTMAAYTSGGDTLHMAYSFDLLTE 303 + PE L+++RA + YP +AE ++ + Y D HMA+ F L+ Sbjct: 252 ENLPETHAVLKKIRATIDAEYPNRMLLAE--ANQWPEDVKEYFGDEDECHMAFHFPLMPR 309 Query: 304 --QCSPGYIRHTVEGIERELAD-----GWSCWSMGNHDVVR------------------- 337 R + I R+ D W+ + + NHD + Sbjct: 310 IYMSIASEDRFPITDIMRQTPDLAATNQWAIF-LRNHDELTLEMVTDSERDYLWNTYASD 368 Query: 338 --------VMTRWALNGRPDPERGRLLMALLLSLRGSVCMYQGEELGLPEAELRYEDLVD 389 + R A D R L+ +LLLS+ G+ +Y G+ELG+ + + D Sbjct: 369 RRARLNLGIRRRLAPLMERDRRRIELINSLLLSMPGTPVIYYGDELGMGD-NIHLGD--- 424 Query: 390 PYGITFWPEFKGRDGCRTPMPWESEAHHAGFTGSQP----WLPVDDS---HRSLSVAAQD 442 RDG RTPM W S+ + GF+ + P PV S +++V AQ Sbjct: 425 ------------RDGVRTPMQWSSD-RNGGFSRADPEQLVLPPVMGSLYGFDAVNVEAQS 471 Query: 443 ADPHSMLNCYRRFLGWRREQRLLIEGDIHMVYHDD-ALLVFERRL-GDEAWLCLFNLGDL 500 DPHS+LN RR L RR ++ G I + ++ +L + R + G+ LC+ NL Sbjct: 472 RDPHSLLNWTRRMLATRRAKQTFGRGTIRFLKPENRKILAYLREMPGEPPILCVANLSRA 531 Query: 501 SRSYEL 506 ++ EL Sbjct: 532 PQAVEL 537 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: 1770 Number of extensions: 93 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 542 Length of database: 1154 Length adjustment: 41 Effective length of query: 501 Effective length of database: 1113 Effective search space: 557613 Effective search space used: 557613 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