Align Alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate GFF2510 PS417_12800 alpha-amylase
Query= reanno::psRCH2:GFF856 (542 letters) >FitnessBrowser__WCS417:GFF2510 Length = 1115 Score = 249 bits (636), Expect = 4e-70 Identities = 181/560 (32%), Positives = 264/560 (47%), Gaps = 108/560 (19%) Query: 8 WWRGGVIYQVYPRSFFDSNGDGVGDLPGVLHKLDYIASLNVDAIWLSPFFTSPMKDFGYD 67 W++ VIYQV+ +S+FDSN DG+GD PG++ KLDYIA L V+ IWL PF+ SP +D GYD Sbjct: 16 WYKDAVIYQVHVKSYFDSNNDGIGDFPGLIAKLDYIADLGVNTIWLLPFYPSPRRDDGYD 75 Query: 68 VADYRGVDPLFGTLDDFVRLVEACHERGMRVLIDQVLNHSSDQHPWFAESRSSRDNDKA- 126 +A+YRGV +GT+ D R + H+RG+RV+ + V+NH+SDQHPWF +R ++ A Sbjct: 76 IAEYRGVHSDYGTMADAKRFIAEAHKRGLRVITELVINHTSDQHPWFQRARKAKPGSAAR 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 QDQLLDDMEFWLKLGVDGFRLDAANFYFHDAELRDNPPNTEIREGSIGVRIDNPYAYQRH 241 +L M +WL +G+DG RLDA + RD N + Sbjct: 191 MKAVLSVMRYWLDMGIDGLRLDAIPYLIE----RDGTNNENL------------------ 228 Query: 242 IYDKTRPENMDFLRRLRALLQ-RYPGASSVAEIGC---DESLRTMAAYTSGGDTLHMAYS 297 PE D L+++RA + YP +AE D L GD HMA+ Sbjct: 229 ------PETHDVLKQIRAEIDAHYPDRMLLAEANQWPEDTQLYFGDKKGDDGDECHMAFH 282 Query: 298 FDLLTE--QCSPGYIRHTVEGIERELAD-----GWSCWSMGNHDVVR------------- 337 F L+ R + I R+ + W+ + + NHD + Sbjct: 283 FPLMPRMYMALAQEDRFPITDILRQTPEIPANCQWAIF-LRNHDELTLEMVTDKERDYLW 341 Query: 338 --------------VMTRWALNGRPDPERGRLLMALLLSLRGSVCMYQGEELGLPEAELR 383 + R A D R LL +LLLS+ G+ +Y G+E+G+ + + Sbjct: 342 NYYAADRRARINLGIRRRLAPLMERDRRRVELLNSLLLSMPGTPTLYYGDEIGMGD-NIY 400 Query: 384 YEDLVDPYGITFWPEFKGRDGCRTPMPWESEAHHAGFTGSQP----WLPVDD---SHRSL 436 D RDG RTPM W + + GF+ + P P+ D + S+ Sbjct: 401 LGD---------------RDGVRTPMQWSID-RNGGFSRADPASLVLPPIMDPQYGYPSV 444 Query: 437 SVAAQDADPHSMLNCYRRFLGWRREQRLLIEGDIHMVYHDD-ALLVFERRL-----GDEA 490 +V Q DPHS+LN RR L R++ + G + M+ + +L + R +E Sbjct: 445 NVETQAQDPHSLLNWTRRMLAVRKQSKAFGRGSLKMLSPSNRRILAYTREFTGEDGRNEI 504 Query: 491 WLCLFNLGDLSRSYELPAQA 510 LC+ N+ +++ EL A Sbjct: 505 ILCVANVSRSAQAAELDLSA 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: 1693 Number of extensions: 95 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: 1115 Length adjustment: 41 Effective length of query: 501 Effective length of database: 1074 Effective search space: 538074 Effective search space used: 538074 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