Align Probable alpha-glucosidase; EC 3.2.1.20 (uncharacterized)
to candidate AZOBR_RS09450 AZOBR_RS09450 alpha-amylase
Query= curated2:Q9Z3R8 (551 letters) >FitnessBrowser__azobra:AZOBR_RS09450 Length = 1107 Score = 249 bits (637), Expect = 3e-70 Identities = 181/592 (30%), Positives = 282/592 (47%), Gaps = 98/592 (16%) Query: 14 DRDWWRGAVIYQIYPRSFQDTNGDGIGDLQGITARLPHIAGLGADAIWISPFFTSPMRDF 73 D W++ AVIYQ++ ++F D + DGIGD+ G+T +L +I LG +W+ PF+ SP+RD Sbjct: 13 DTLWYKDAVIYQLHVKAFFDADNDGIGDIAGLTQKLDYIQELGVTTLWLLPFYPSPLRDD 72 Query: 74 GYDVSNYVDVDPIFGTLEDFDALIAEAHRLGLRVMIDLVLSHTSDRHPWFVESRSSRSNA 133 GYD+++Y V+P +G L+DF + E H GLRV+ +LV++HTSD+HPWF +R ++ + Sbjct: 73 GYDIADYKAVNPSYGNLQDFKRFLRECHDRGLRVITELVINHTSDQHPWFQRARQAKPGS 132 Query: 134 K-ADWYVWADSKPDGTPPNNWLSIFGGSAWQWDPTRLQYYLHNFLTSQPDLNLHNPQVQE 192 ++YVW+D+ S W WD Y+ H F + QPDLN NP+V + Sbjct: 133 NHRNFYVWSDTDQKYQGTRIIFCDTEKSNWTWDSEAQAYFWHRFYSHQPDLNFDNPKVLQ 192 Query: 193 ALLAVERFWLERGVDGFRLDTINFYFHDRELRDNPALVPERRNASTAPAVNPYNYQEHIY 252 +L V RFWL+ GVDG RLD + Y +RE +N Sbjct: 193 EVLNVMRFWLDMGVDGLRLDAVP-YLKEREGTNN-------------------------- 225 Query: 253 DKNRPENLEFLKRFRAVMDE-FPAIAAVGEVGD-SQRGLEIAGEYTSGGDKVHMCYAFE- 309 +N PE + LK R +D+ + + E + L G+ GGD+ HM + F Sbjct: 226 -ENLPETHDVLKAIRTEIDKGYGDRMLLAEANQWPEDVLPYFGDLEKGGDECHMAFHFPL 284 Query: 310 ----FLAPDRLTPQRVAEVLRDFHRAAPE-GWA---------------------CWAFSN 343 ++A +A+++R E WA W F Sbjct: 285 MPRIYMAVAMEDRHPIADIMRQTPDIPDECQWAIFLRNHDELTLEMVTDRERDYLWDFYA 344 Query: 344 HDVVRHVS-----RWADGVTDHDAHAKLLASLLMSLRGTVCIYQGEELALAEAELDYEDL 398 D ++ R A + + +LL SLL+S+ GT +Y G+E+ + D L Sbjct: 345 ADRRMRINLGIRRRLAPLLQNDRRKIELLKSLLLSMPGTPVLYYGDEIGMG----DNIYL 400 Query: 399 QDPYGIQFWPDFKGRDGCRTPMVWESLPDGGFSSATP---WLPISQSHIPRAVAV----Q 451 D RDG RTPM W +GGFS A P +LP Q I A+ Q Sbjct: 401 GD------------RDGVRTPMQWSPDRNGGFSRADPARLYLPAIQDPIYGFQAINVEAQ 448 Query: 452 EGDPASVLHHYRRFLAFRKANPALAKGEIEFV-ETRGSLLGFLRSH----GNEKVFCLFN 506 + P+S+L+ +R +A R+ + A +G + + +L +LR H G+E + C+ N Sbjct: 449 QRSPSSLLNWMKRLIAVRQQHKAFGRGRFQLLYPGNRKVLAYLRCHSTEEGDEVILCVAN 508 Query: 507 MSDEAATKELPMKRLE---PLE--GHGFVSEI--LDHEVKLPAWGAFFARLA 551 +S A EL +K+ P+E G + L + + +PA+G ++ LA Sbjct: 509 LSRSAQAVELDLKQFRGRVPVEMLGRTVFPPVGDLPYLLTIPAYGFYWFALA 560 Lambda K H 0.321 0.138 0.443 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: 1680 Number of extensions: 86 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: 551 Length of database: 1107 Length adjustment: 41 Effective length of query: 510 Effective length of database: 1066 Effective search space: 543660 Effective search space used: 543660 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