Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate 201365 SO2213 oligo-1,6-glucosidase (NCBI ptt file)
Query= uniprot:H3K096 (538 letters) >FitnessBrowser__MR1:201365 Length = 540 Score = 644 bits (1662), Expect = 0.0 Identities = 300/537 (55%), Positives = 379/537 (70%), Gaps = 3/537 (0%) Query: 5 MMWWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFG 64 + WWRG VIYQIYPRS LD+ GDGVGDL GI KLDY+ASLNVD IW+SPFF SPM DFG Sbjct: 4 LTWWRGAVIYQIYPRSLLDTNGDGVGDLRGIITKLDYIASLNVDAIWISPFFKSPMADFG 63 Query: 65 YDVSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPK 124 YD+SDYR++DP+FG+++DF L+EKAH G+KV+IDQV+SHTSDQH WF ESR++RTNPK Sbjct: 64 YDISDYREIDPLFGSMQDFDELIEKAHQRGIKVIIDQVLSHTSDQHAWFIESRESRTNPK 123 Query: 125 ADWFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQ 184 ADW+VWADP+ DGTPPNNWL+IFGG AW ++ RRQQYYLHNFL SQPD+NFH+P+ RQA Sbjct: 124 ADWYVWADPREDGTPPNNWLAIFGGCAWEWEPRRQQYYLHNFLRSQPDINFHNPDVRQAV 183 Query: 185 LDNMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDL 244 LDN+ FWL GVDGFRLD + F FHD LRDNP PK + + G E NPY +Q H Y+ Sbjct: 184 LDNVEFWLKKGVDGFRLDAITFCFHDELLRDNPAKPKEKRQGRGFSEDNPYAYQYHYYNN 243 Query: 245 SRPENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMPH 304 RP+ + F++ LR L++ YPGT T+GE+ ++ L MA YT G D+LHMAY+F+LL + Sbjct: 244 DRPQTIQFIEALRQLINRYPGTVTLGEVSAEDSLAVMAAYTKGDDRLHMAYSFELLTDDY 303 Query: 305 SASYLREVIERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLFSLRGS 364 SA+Y+R+ +E + GD WPCWA NHDV R A+RWG + K++ A+L SLRGS Sbjct: 304 SAAYIRQTVEALENSIGDGWPCWAIGNHDVQRVASRWGRGKQTSDMAKMLNAMLCSLRGS 363 Query: 365 VCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPWTD-GEQGGFSPVEPW 423 VC YQGEELGL E + F +QDP+GK WP FKGRDGCRTPMPW + GFS V PW Sbjct: 364 VCSYQGEELGLTEVPIEFHELQDPFGKTFWPMFKGRDGCRTPMPWEQYADFSGFSQVSPW 423 Query: 424 LPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTRQK 483 LP+ A H LAV Q+ D ++ L+ R LA+R+ +PAL ++ +D + LL F R+ Sbjct: 424 LPIAAAHRALAVDLQEADCHSVLHGYRQFLAWRKCYPALITSEIEFLDAPEPLLVFVRKL 483 Query: 484 GDETLLCVFNLTGQEQQTTLPVEVASDLPVAH--FTATRDGSTLTLPAYQAAFMQVA 538 G++ LL FNL E Q +L H TA R G +L AY + + +A Sbjct: 484 GEQKLLVCFNLLDAETQLSLTGLKLQQELAGHGLKTAHRQGDSLIFSAYASFYALLA 540 Lambda K H 0.320 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: 953 Number of extensions: 36 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 538 Length of database: 540 Length adjustment: 35 Effective length of query: 503 Effective length of database: 505 Effective search space: 254015 Effective search space used: 254015 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: 52 (24.6 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