Align Probable alpha-glucosidase; EC 3.2.1.20 (uncharacterized)
to candidate PP_4059 PP_4059 fused trehalose synthase B/maltokinase
Query= curated2:Q9Z3R8 (551 letters) >FitnessBrowser__Putida:PP_4059 Length = 1106 Score = 246 bits (627), Expect = 4e-69 Identities = 193/560 (34%), Positives = 267/560 (47%), Gaps = 110/560 (19%) Query: 17 WWRGAVIYQIYPRSFQDTNGDGIGDLQGITARLPHIAGLGADAIWISPFFTSPMRDFGYD 76 W++ AVIYQ++ +SF D+N DGIGD G+ ++L +IA LG + +W+ PF+ SP RD GYD Sbjct: 16 WYKDAVIYQLHIKSFFDSNNDGIGDFAGLISKLDYIAELGVNTLWLLPFYPSPRRDDGYD 75 Query: 77 VSNYVDVDPIFGTLEDFDALIAEAHRLGLRVMIDLVLSHTSDRHPWFVESRSSRSNAKA- 135 ++ Y V P +G++ D IAEAH+ GLRV+ +LV++HTSD+HPWF +R ++ +KA Sbjct: 76 IAEYKAVHPDYGSMADARRFIAEAHKRGLRVITELVINHTSDQHPWFQRARHAKRGSKAR 135 Query: 136 DWYVWA--DSKPDGTPPNNWLSIF---GGSAWQWDPTRLQYYLHNFLTSQPDLNLHNPQV 190 ++YVW+ D K DGT IF S W WDP QY+ H F + QPDLN NPQV Sbjct: 136 EFYVWSDDDQKYDGT-----RIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDNPQV 190 Query: 191 QEALLAVERFWLERGVDGFRLDTINFYFHDRELRDNPALVPERRNASTAPAVNPYNYQEH 250 +A++ V RFWL+ GVDG RLD I Y +R+ +N Sbjct: 191 LKAVIGVMRFWLDLGVDGLRLDAIP-YLIERDGTNN------------------------ 225 Query: 251 IYDKNRPENLEFLKRFRAVMD-EFPAIAAVGEVGD-SQRGLEIAGEYTSGGDKVHMCYAF 308 +N E + LK RA +D +P + E + GE GD+ HM AF Sbjct: 226 ---ENLAETHDVLKAIRAEIDANYPDRMLLAEANQWPEDTRPYFGE--GDGDECHM--AF 278 Query: 309 EFLAPDRLTPQRVAE---VLRDFHRAAPE-----GWACWAFSNHD-----VVRHVSR--- 352 F R+ E + D R PE WA + NHD +V R Sbjct: 279 HFPLMPRMYMALAMEDRFPITDILRQTPEIPANCQWAIF-LRNHDELTLEMVTDRERDYL 337 Query: 353 WADGVTDHDA-------------------HAKLLASLLMSLRGTVCIYQGEELALAEAEL 393 W D A +LL SLL+S+ GT +Y G+EL + Sbjct: 338 WNYYAEDRRARINLGIRRRLAPLLQRDRRRIELLTSLLLSMPGTPTLYYGDELGMG---- 393 Query: 394 DYEDLQDPYGIQFWPDFKGRDGCRTPMVWESLPDGGFSSATPWL----PISQ---SHIPR 446 D L D RDG RTPM W +GGFS A P PI + Sbjct: 394 DNIYLGD------------RDGVRTPMQWSPDRNGGFSRADPQRLVLPPIMDPLYGYQTV 441 Query: 447 AVAVQEGDPASVLHHYRRFLAFRKANPALAKGEIE-FVETRGSLLGFLRSH----GN-EK 500 V Q DP S+L+ RR LA RK A +G + + +L ++R + GN E Sbjct: 442 NVEAQSHDPHSLLNWTRRMLAVRKQQKAFGRGSLRTLTPSNRRILAYIREYTDADGNTEV 501 Query: 501 VFCLFNMSDEAATKELPMKR 520 + C+ N+S A EL + + Sbjct: 502 ILCVANVSRAAQAAELELSQ 521 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: 1640 Number of extensions: 84 Number of successful extensions: 4 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: 551 Length of database: 1106 Length adjustment: 41 Effective length of query: 510 Effective length of database: 1065 Effective search space: 543150 Effective search space used: 543150 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