Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate 5209418 Shew_1889 alpha amylase, catalytic region (RefSeq)
Query= uniprot:H3K096 (538 letters) >FitnessBrowser__PV4:5209418 Length = 541 Score = 656 bits (1692), Expect = 0.0 Identities = 296/502 (58%), Positives = 374/502 (74%), Gaps = 1/502 (0%) Query: 3 DNMMWWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLD 62 + + WWRG VIYQIYPRS +DS GDGVGDL GI KLDY+ASLNVD IW+SPFF SPM D Sbjct: 2 NQLSWWRGAVIYQIYPRSLMDSNGDGVGDLQGIISKLDYIASLNVDAIWISPFFKSPMKD 61 Query: 63 FGYDVSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTN 122 FGYD+SDYR +DP+FGT+ DF L++KAH LG+KV+IDQV+SHTSDQH WF ESRQ+R N Sbjct: 62 FGYDISDYRAIDPLFGTMADFDELIDKAHGLGIKVIIDQVLSHTSDQHAWFSESRQSRDN 121 Query: 123 PKADWFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQ 182 K DW+VWADP PDGT PNNWL+IFGG AW ++ RRQQYYLHNFLTSQPD+NFH+P+ RQ Sbjct: 122 AKQDWYVWADPNPDGTAPNNWLAIFGGCAWEWEPRRQQYYLHNFLTSQPDLNFHNPDVRQ 181 Query: 183 AQLDNMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVY 242 A LDN++FWLD GVDGFRLD + F +HD +LRDNPP P+ + + G E NPY +Q H Y Sbjct: 182 AVLDNVKFWLDKGVDGFRLDAITFCYHDEQLRDNPPKPEDKRQGRGFSEDNPYAYQYHYY 241 Query: 243 DLSRPENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNM 302 + +RP+ + F+++LRAL+++YPG T+GE+ ++ L MAEYT G D+LHMAY+F+LL Sbjct: 242 NNTRPQTVGFIEELRALINQYPGVVTLGEVSSEDSLATMAEYTQGDDRLHMAYSFELLTD 301 Query: 303 PHSASYLREVIERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLFSLR 362 S +Y+R +E ++ GD WPCWA NHDV R ATRWG D K++ A+L SLR Sbjct: 302 DFSPAYIRHTVEALEQSIGDGWPCWAIGNHDVQRVATRWGRDAFNSDMAKMLNAMLCSLR 361 Query: 363 GSVCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPWT-DGEQGGFSPVE 421 GSVC YQGEELGL E ++ +E++QDP+G WP FKGRDGCRTPMPW D GFS Sbjct: 362 GSVCSYQGEELGLGEVEIAYEQLQDPFGITFWPMFKGRDGCRTPMPWRHDANHAGFSDNT 421 Query: 422 PWLPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTR 481 PWLP+ A H +AV Q+ +P + LN R +LA+R+ HP L GD+ ++ D LL F R Sbjct: 422 PWLPVPADHKAVAVDVQEANPESILNHYRHMLAWRKLHPILVTGDIKFIESTDALLVFER 481 Query: 482 QKGDETLLCVFNLTGQEQQTTL 503 + G++TLL FNL+GQ Q +L Sbjct: 482 RLGEQTLLVAFNLSGQPQSFSL 503 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: 1031 Number of extensions: 43 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: 541 Length adjustment: 35 Effective length of query: 503 Effective length of database: 506 Effective search space: 254518 Effective search space used: 254518 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