Align α-1,4-glucosidase (MalA) (EC 3.2.1.20) (characterized)
to candidate Pf6N2E2_2118 Trehalose synthase (EC 5.4.99.16)
Query= CAZy::CAA55409.1 (549 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2118 Length = 1114 Score = 265 bits (676), Expect = 9e-75 Identities = 169/542 (31%), Positives = 275/542 (50%), Gaps = 60/542 (11%) Query: 5 WWKEAVAYQVYPRSFNDSNNDGIGDLPGVIEKLDYLNELGIDVIWLSPMYKSPNDDNGYD 64 W+K+AV YQV+ +S+ DSNNDGIGD PG+IEKLDY+ +LG++ IWL P Y SP D+GYD Sbjct: 16 WYKDAVIYQVHVKSYFDSNNDGIGDFPGLIEKLDYIADLGVNTIWLLPFYPSPRRDDGYD 75 Query: 65 ISDYTDIMDEFGTMDDFNLLLESVHQRGMKLILDLVVNHTSDEHPWFIESKSSKDNPK-R 123 I++Y + ++GTM D + H+R +++I +LV+NHTSD+HPWF ++ +K K R Sbjct: 76 IAEYRGVSADYGTMADARRFIAEAHKRNLRVITELVINHTSDQHPWFQRARKAKPGSKAR 135 Query: 124 DWYIWQEPKPDGSEPNNWESIF---NGSTWEYDDTTGEYYFHLFSKKQPDLNWGNKEVRH 180 D+Y+W + D + + IF S W +D G+Y++H F QPDLN+ N +V Sbjct: 136 DFYVWSD---DDHKYDGTRIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDNPQVIK 192 Query: 181 AIFEMMNWWFEKGIDGFRVDAITHIKKSFEAGDLPVPEGKTYAPAF--DVDMNQPGIQSW 238 A+ +M +W + GIDG R+DAI ++ + + +PE ++D N P Sbjct: 193 AVLSVMRYWLDMGIDGLRLDAIPYLIERDGTNNENLPETHDVLKLIRAEIDANYP----- 247 Query: 239 LQEMKEKSLSQYDIMTVGEANGVNPENA------VEWVGENEGKFNMIFQFEHLGLWNTG 292 D M + EAN PE+ V+ G N + +M F F + Sbjct: 248 ------------DRMLLAEANQW-PEDTQLYFGDVDAQGMNGDECHMAFHFPLMPRMYMA 294 Query: 293 DSKFDVKAYKDVLNRWQKQLENIGWNALFIENHDQPRRVSTWGDDQNY-W-YESATSHAI 350 ++ D D+L + + N W A+F+ NHD+ +++Y W Y +A A Sbjct: 295 LAQEDRFPITDILRQTPEIPANCQW-AIFLRNHDELTLEMVTDKERDYLWNYYAADRRAR 353 Query: 351 VY--FLQQGTPFIYQGQEIGMTNYPFESVETFNDVAVVNEYNIVKSQNGDVSALLEKHKM 408 + ++ P + + + VE N + +++ GD + + + Sbjct: 354 INLGIRRRLAPLVERDR---------RRVELLNSL-LLSMPGTPTLYYGDEIGMGDNIYL 403 Query: 409 ENRDNSRTPMQWNNQTNSGFSEHSPWFPVNP-------NYKTINVADQQQDPNSILNFYK 461 +RD RTPMQW+ N GFS P V P Y+++NV Q DP+S+LN+ + Sbjct: 404 GDRDGVRTPMQWSIDRNGGFSRADPASLVLPPIMDPQYGYQSVNVETQAGDPHSLLNWTR 463 Query: 462 SLITLKKSDDIYTYGTFDLVDKNNEQVFAYTRTL-----NNKKVLIVANLTNQTATFKYD 516 ++ ++K + GT ++ +N ++ AYTR ++ +L VAN++ + D Sbjct: 464 RMLAVRKQSKAFGRGTLKMLSPSNRRILAYTREYTGPDGKHEIILCVANVSRSAQAAELD 523 Query: 517 NS 518 S Sbjct: 524 LS 525 Lambda K H 0.315 0.133 0.417 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: 1583 Number of extensions: 91 Number of successful extensions: 5 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: 549 Length of database: 1114 Length adjustment: 41 Effective length of query: 508 Effective length of database: 1073 Effective search space: 545084 Effective search space used: 545084 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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