Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate AO353_22940 AO353_22940 alpha-amylase
Query= uniprot:H3K096 (538 letters) >FitnessBrowser__pseudo3_N2E3:AO353_22940 Length = 1113 Score = 240 bits (613), Expect = 2e-67 Identities = 180/565 (31%), Positives = 275/565 (48%), Gaps = 105/565 (18%) Query: 6 MWWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGY 65 +W++ VIYQ++ +S+ DS DG+GD G+ KLDY+A L V+ IWL PF+ SP D GY Sbjct: 15 LWYKDAVIYQVHVKSYFDSNNDGIGDFPGLIAKLDYIAELGVNTIWLLPFYPSPRRDDGY 74 Query: 66 DVSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKA 125 D+++YR V +GTL D K + +AH+ GL+V+ + VI+HTSDQHPWFQ +R+ + A Sbjct: 75 DIAEYRGVHRDYGTLTDAKRFIAEAHNRGLRVITELVINHTSDQHPWFQRARKAKPGSAA 134 Query: 126 -DWFVWA--DPKPDGTPPNNWLSIF---GGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPE 179 D++VW+ D K DGT IF S WT+D QY+ H F + QPD+NF +P+ Sbjct: 135 RDFYVWSDDDQKYDGT-----RIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDNPQ 189 Query: 180 ARQAQLDNMRFWLDLGVDGFRLDTVNFYF-HDAELRDNPPVPKGEAKTLGAPEANPYTWQ 238 +A L MR+WLDLG+DG RLD + + D +N P K + Sbjct: 190 VMKAVLSVMRYWLDLGIDGLRLDAIPYLIERDGTNNENLPETHAVLKQI----------- 238 Query: 239 RHVYDLSRPENLDFLKDLRALMDEYPGTTTV--GEIGDDNPLERMAEYTAGGDKLHMAYT 296 R D P+ + L A +++P T + G++ DN GD+ HMA+ Sbjct: 239 RAEIDAHYPDRM-----LLAEANQWPEDTQLYFGDVHGDN-----------GDECHMAFH 282 Query: 297 FDLLNMPHSASY------LREVIERFQRLAGDAWPCWATSNHD-----VVRSATR----- 340 F L+ + A + +++ + + + NHD +V R Sbjct: 283 FPLMPRMYMALAQEDRFPITDILRQTPEIPANCQWAIFLRNHDELTLEMVTDKERDYLWN 342 Query: 341 -WGAD-----------------EDPHAYPKVMLAVLFSLRGSVCLYQGEELGLPEADVPF 382 + AD E +++ ++L S+ G+ LY G+E+G+ Sbjct: 343 YYAADRRARINLGIRRRLAPLMERDRRRVELLNSLLLSMPGTPTLYYGDEIGM------- 395 Query: 383 ERIQDPYGKVLWPEFKGRDGCRTPMPWTDGEQGGFSPVEP---WLP--MEA--RHLELAV 435 G ++ RDG RTPM W+ GGFS +P LP M+ +L + V Sbjct: 396 -------GDNIY--LGDRDGVRTPMQWSIDRNGGFSRADPASLVLPPIMDPLYGYLSVNV 446 Query: 436 SRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGD-DLLGFTRQ-KGD----ETLL 489 Q DP++ LN R +LA R+ A G L ++ + +L +TR+ GD E +L Sbjct: 447 ETQAGDPHSLLNWTRRMLAIRKQSKAFGRGSLKMLSPSNRRILAYTREYTGDDGKHEIIL 506 Query: 490 CVFNLTGQEQQTTLPVEV-ASDLPV 513 CV N++ Q L + A +PV Sbjct: 507 CVANVSRSAQAAELDLSAFAGMVPV 531 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: 1614 Number of extensions: 89 Number of successful extensions: 6 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: 538 Length of database: 1113 Length adjustment: 41 Effective length of query: 497 Effective length of database: 1072 Effective search space: 532784 Effective search space used: 532784 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: 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