Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate GFF2114 Psest_2157 trehalose synthase
Query= uniprot:H3K096 (538 letters) >FitnessBrowser__psRCH2:GFF2114 Length = 1108 Score = 238 bits (608), Expect = 7e-67 Identities = 189/598 (31%), Positives = 278/598 (46%), Gaps = 115/598 (19%) Query: 6 MWWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGY 65 +W++ V+YQ++ +SF DS DGVGD G+ +KLDY+A L V+ IWL PF+ SP D GY Sbjct: 15 LWYKDAVVYQVHLKSFYDSNNDGVGDFAGLIDKLDYIADLGVNTIWLLPFYPSPRRDDGY 74 Query: 66 DVSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKA 125 D++DYR V P +GT+ D + + +AH GL+V+ + VI+HTSDQHPWFQ +R+ R A Sbjct: 75 DIADYRGVHPEYGTMADARRFIAEAHKRGLRVITELVINHTSDQHPWFQRARKARKGSAA 134 Query: 126 -DWFVWA--DPKPDGTPPNNWLSIF---GGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPE 179 +++VW+ D K DGT IF S WT+D +QY+ H F + QPD+NF +P+ Sbjct: 135 RNFYVWSDTDEKYDGT-----RIIFLDTEKSNWTWDPVAKQYFWHRFYSHQPDLNFDNPQ 189 Query: 180 ARQAQLDNMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQR 239 +A L MR+WLD+G+DG RLD + PY +R Sbjct: 190 VMKAVLAVMRYWLDMGIDGLRLDAI-----------------------------PYLVER 220 Query: 240 H-VYDLSRPENLDFLKDLRALMD-EYPGTTTVGEIG---DDNPLERMAEYTAGGDKLHMA 294 + + PE LK +RA +D YP + E +D L E GD+ HMA Sbjct: 221 DGTNNENLPETHAVLKAIRAEIDANYPDRMLLAEANQWPEDTQLYFGGEDGGPGDECHMA 280 Query: 295 YTFDLL-----------------------NMPHS---ASYLREVIERFQRLAGD-----A 323 + F L+ ++P + A +LR E + D Sbjct: 281 FHFPLMPRMYMAIAQEDRFPITDILRQTPDIPENCQWAIFLRNHDELTLEMVTDRERDYL 340 Query: 324 WPCWATSNHDVVRSATRWGAD---EDPHAYPKVMLAVLFSLRGSVCLYQGEELGLPEADV 380 W +A+ + R E +++ ++L S+ G+ +Y G+E+G+ D Sbjct: 341 WNYYASDKRARINLGIRRRLAPLLERDRRRIELLNSLLLSMPGTPVIYYGDEIGM--GDN 398 Query: 381 PFERIQDPYGKVLWPEFKGRDGCRTPMPWTDGEQGGFSPVEP---WLPMEARHL----EL 433 F RDG RTPM W+ GGFS +P LP L + Sbjct: 399 IF--------------LGDRDGVRTPMQWSVDRNGGFSRADPPNLVLPPVMDPLYGYYTI 444 Query: 434 AVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDD-----LLGFTRQKGD-ET 487 V QQ DP++ LN R +L R+ A G L ++ + L FT GD E Sbjct: 445 NVEAQQRDPHSLLNWTRRMLTIRKQFKAFGRGTLKMLAPSNRRILAYLREFTGANGDTEI 504 Query: 488 LLCVFNLTGQEQQTTLPV-EVASDLPV------AHFTATRDGSTLTLPAYQAAFMQVA 538 + CV N++ Q L + + A +PV A + LTLP Y + Q+A Sbjct: 505 IFCVANVSRSAQAAELEMSQYAGMVPVEMVGGSAFPPIGQLPYLLTLPPYGFYWFQLA 562 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: 1573 Number of extensions: 92 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 538 Length of database: 1108 Length adjustment: 41 Effective length of query: 497 Effective length of database: 1067 Effective search space: 530299 Effective search space used: 530299 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