Align α-glucosidase (Gsj) (EC 3.2.1.20) (characterized)
to candidate AZOBR_RS04510 AZOBR_RS04510 trehalose synthase
Query= CAZy::BAE48285.1 (555 letters) >FitnessBrowser__azobra:AZOBR_RS04510 Length = 562 Score = 249 bits (635), Expect = 3e-70 Identities = 177/551 (32%), Positives = 261/551 (47%), Gaps = 98/551 (17%) Query: 1 MKKTWWKEGVAYQIYPRSFMDANGDGIGDLRGIIEKLDYLVELGVDIVWICPIYRSPNAD 60 +K W+K V Y + +FMDANGDGIGD +G+ +LDYL LGV +W+ P SP D Sbjct: 2 IKDLWYKNAVIYNLSVGTFMDANGDGIGDFQGLQRRLDYLQGLGVTCLWLGPFQPSPMRD 61 Query: 61 NGYDISDYYAIMDEFGTMDDFDELLAQAHRRGLKVILDLVINHTSDEHPWFIESRSSRDN 120 +GYD++DYY + +GT+ DF E +RG++VI+DLV+NHTSD+HPWF +R D+ Sbjct: 62 HGYDVADYYNVDPRYGTLGDFVEFSHACKQRGIRVIIDLVVNHTSDQHPWFQAARKDPDS 121 Query: 121 PKRDWYIWRDGKDGREPNNWESIFGG---SAWQYDERTGQYYLHIFDVKQPDLNWENSEV 177 P RDWY+W D K + + +F G + W +D+ YY H F QPDLN N EV Sbjct: 122 PYRDWYVWSDKKP--DDADQGVVFPGVQKTTWSWDKEARAYYFHRFYEFQPDLNTANPEV 179 Query: 178 RQALYEMVNWWLDKGIDGFRIDAISHIKKKPGLPDLPNPKGLKYVPSFAGHMNQPGIMEY 237 + L +++ +W++ G+ GFR+DA+ + G PD+ PK Q ++ Sbjct: 180 QAELLKVMGFWIELGVSGFRMDAVPFVIATKG-PDVKKPK------------QQFDMLRT 226 Query: 238 LRELKEQTFARYDIMTVGEANGV-TVDEAEQWVGEENGVFNMIFQFE-HLGLWERRADGS 295 RE + D + + EAN + TVD +++ G++ M+F F+ + L+ A + Sbjct: 227 FREFVQWRCG--DAVLLAEANVLPTVD--QEYFGDDGDRMQMVFNFQVNQNLFYALA--T 280 Query: 296 IDVRRLKRTLTKWQKGLENRGWNALFLENHD-----------LPRSVSTWGNDRDY---- 340 D R L + L + + LFL NHD R +G D+D Sbjct: 281 ADTRPLAKALDVTRVPRPSTNQWGLFLRNHDELDLGRLTEAQRKRVFDAFGPDKDMQLYD 340 Query: 341 ----------------WAESAKALGALYFFMQGTPFIYQGQEIGMTNVRFDDIRDYRDVS 384 W E A +L F + GTP + G EIGM DD Sbjct: 341 RGIRRRLAPMLRGDRRWLELAY---SLLFTLPGTPVLRYGDEIGMG----DD-------- 385 Query: 385 ALRLYELERAKGRTHEEAMTIIWKTGRDNSRTPMQWSGASNAGFTTGT----PWIKVNE- 439 L L E R+ +RTPMQWS GFT P I Sbjct: 386 -LSLPE--------------------RECARTPMQWSDEPQGGFTKADDPVHPVISGGAY 424 Query: 440 NYRTINVEAERRDPNSVWSFYRQMIQLRKANELFVYGTYDLLLENHPSIYAYTRTLGRDR 499 Y IN +RRDP+++ ++ ++I++RK +G + +L ++ A + Sbjct: 425 GYERINAAHQRRDPSALLNWTERIIRMRKECPEIGWGDFQVLPTGSNAVLAIRYDWRNNS 484 Query: 500 ALVVVNLSDRP 510 LVV NL DRP Sbjct: 485 VLVVHNLDDRP 495 Lambda K H 0.320 0.138 0.441 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: 1041 Number of extensions: 69 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: 555 Length of database: 562 Length adjustment: 36 Effective length of query: 519 Effective length of database: 526 Effective search space: 272994 Effective search space used: 272994 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 (21.8 bits) S2: 53 (25.0 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