Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate WP_011840128.1 RSPH17029_RS00200 DUF3459 domain-containing protein
Query= uniprot:H3K096 (538 letters) >NCBI__GCF_000015985.1:WP_011840128.1 Length = 536 Score = 591 bits (1524), Expect = e-173 Identities = 297/533 (55%), Positives = 359/533 (67%), Gaps = 13/533 (2%) Query: 7 WWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGYD 66 WWRG V YQIYPRSF DS GDGVGDL GI E+LD+VA L D IWLSP F SPM D GYD Sbjct: 4 WWRGSVTYQIYPRSFQDSDGDGVGDLRGIIERLDHVAWLGADAIWLSPIFPSPMEDMGYD 63 Query: 67 VSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKAD 126 VSDY + P+FG++EDF ALL +AH LGLKV+IDQV+SH+S HP+F+ESR++R NPKAD Sbjct: 64 VSDYTAIHPLFGSMEDFDALLARAHELGLKVIIDQVLSHSSSAHPFFRESRRSRDNPKAD 123 Query: 127 WFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQLD 186 W+VWAD +PDG+PPNNWLS+FGGSAW +D++R+QYYLHNFL SQPD NFH+PE + LD Sbjct: 124 WYVWADAQPDGSPPNNWLSVFGGSAWEWDAQRRQYYLHNFLISQPDFNFHNPEVQDWLLD 183 Query: 187 NMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDLSR 246 MRFWLD GVDGFRLDTVNFYFHDAELR N P P+ P N Y Q H + SR Sbjct: 184 QMRFWLDRGVDGFRLDTVNFYFHDAELRSNRPNPQNGP----IPPVNAYDMQDHAFSKSR 239 Query: 247 PENLDFLKDLRALMDEYPGTTTVGEIGDD-NPLERMAEYTAGGDKLHMAYTFDLLNMPHS 305 EN+ FL +R L+D+YP VGE+ D L MAEYT+G D+LHMAYTF++L+ + Sbjct: 240 IENIAFLLRMRKLLDDYPDRAMVGEVADGLRGLAIMAEYTSGADRLHMAYTFEMLSRTFT 299 Query: 306 ASYLREVIERFQRLAGDAWPCWATSNHDVVRSATRW---GADEDPHAYPKVMLAVLFSLR 362 A + R IE F A WPCWA SNHDVVR ATRW GA++D ++ A+L S Sbjct: 300 AGHFRSRIEEFFATAPHGWPCWAFSNHDVVRHATRWAGHGAEDD---VARLAAAMLLSFE 356 Query: 363 GSVCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPWTDGEQGGFSPVEP 422 GSV LYQGEELG E ++ +E + DP G WPE KGRDGCRTPM W DG GGF+ P Sbjct: 357 GSVSLYQGEELGQTETELLYEELTDPPGLRFWPEEKGRDGCRTPMVWDDGPAGGFTTGTP 416 Query: 423 WLPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTRQ 482 WLP++ L V+ Q+ P + L T RALL FRR+ PAL G D+ + +LGFTR Sbjct: 417 WLPVKPPQLARNVASQKGIPGSVLETYRALLQFRRTQPALIRGRSRFFDLPEPMLGFTRT 476 Query: 483 KGDETLLCVFNLTGQEQQTTLPVEVASDLPVAHFTATRDGSTLTLPAYQAAFM 535 ++L C FNL + TLP P A +G LTL A AF+ Sbjct: 477 LDGQSLACFFNLGIEPVSATLPGHGGLIGPAQ--AAVLEGDRLTLGANGYAFL 527 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: 1027 Number of extensions: 52 Number of successful extensions: 3 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: 536 Length adjustment: 35 Effective length of query: 503 Effective length of database: 501 Effective search space: 252003 Effective search space used: 252003 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 Apr 10 2024. 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