Align α-glucosidase (EC 3.2.1.20) (characterized)
to candidate AO353_15985 AO353_15985 trehalose-6-phosphate hydrolase
Query= CAZy::AAF71997.1 (562 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15985 Length = 549 Score = 699 bits (1804), Expect = 0.0 Identities = 324/555 (58%), Positives = 415/555 (74%), Gaps = 11/555 (1%) Query: 6 WKKAVVYQIYPKSFNDTNGDGIGDLAGIIEKLDYLKQLGVDVIKLKPIYKSPQRDNGYDI 65 W+++V+YQIYPKSF+ G+ GDL G++ KLDYL+ LGVD + + P +SPQRDNGYDI Sbjct: 4 WQRSVIYQIYPKSFHSHAGNPTGDLLGVVAKLDYLQWLGVDCLWITPFLRSPQRDNGYDI 63 Query: 66 SDYFQIHDEYGTMEDFDRLLEEVHRRGMKLIMDMVVNHTSTEHEWFKQARTSKDNPYRHF 125 SDY+ I YGTM D + L+ E +RG+KL++D+VVNHTS EH WF+QAR+S DNPYR F Sbjct: 64 SDYYAIDPSYGTMADCELLIAEAGKRGIKLMLDIVVNHTSIEHSWFQQARSSLDNPYRDF 123 Query: 126 YIWRDPKPDGSAPTNWQSKFGGSAWEYDEKTGQYYLHLFDVTQADLNWENEELRRRIYDM 185 YIWRD P NW+SKFGGSAWEY+ +TGQY+LHLFD TQADLNW+N ++R ++ + Sbjct: 124 YIWRDQ------PNNWESKFGGSAWEYEAQTGQYFLHLFDHTQADLNWDNPQVRAEVFKL 177 Query: 186 MHFWFQKGVDGFRLDVVNLLSKDQRFLDDDGSMPPGDGRKFYTDGPRIHEFLHEMNREVF 245 M FW KGV GFRLDV+NL+SK F +D DGR+FYTDGP +HE+L EM+REVF Sbjct: 178 MRFWRDKGVGGFRLDVINLISKPADFPEDHT-----DGRRFYTDGPNVHEYLQEMHREVF 232 Query: 246 SKYDVMTVGEMSSTTIDHCIKYTNPERRELNMVFNFHHLKVDYPNGEKWAVADFDFLALK 305 +D++ VGEMSST+++HCI+Y+ P+ +EL+M FNFHHLKVDYPN +KW ADFDFL LK Sbjct: 233 EGHDLINVGEMSSTSLEHCIRYSRPDSKELSMTFNFHHLKVDYPNMQKWVRADFDFLELK 292 Query: 306 RILSEWQVEMHKGGGWNALFWCNHDQPRIVSRYGDDGKYHKESAKMLATVIHMMQGTPYI 365 RILS+WQ M GGGWNALFWCNHDQPR+VSR+GDDG++ SAKML T +H +QGTP+I Sbjct: 293 RILSDWQTGMQAGGGWNALFWCNHDQPRVVSRFGDDGEHRVVSAKMLGTALHFLQGTPFI 352 Query: 366 YQGEEIGMTDPKFERIDDYRDVESLNMYHILREQGKSEQEVLEILKRKSRDNSRTPMQWD 425 YQGEE+GMT+P FERI+ YRDVE+LN+Y + RE G+SE + + +KSRDNSRTPMQW Sbjct: 353 YQGEELGMTNPGFERIEQYRDVETLNIYRLKREAGESEASSMAAIMQKSRDNSRTPMQWS 412 Query: 426 DSENAGFTTGKPWIRVAPNYQQINVKKALEDPTSVFYHYQRLIQLRKQYDIITTGDYQLL 485 NAGF++ +PWI V N QINV+ L+D TSV +HY++LI LR+ +I G Y+ L Sbjct: 413 ALPNAGFSSSEPWIGVPANAMQINVENQLDDTTSVLHHYRQLIALRRSEPLIQDGVYRQL 472 Query: 486 LEDHPDIFAYLRNGENEKLLVVNNFYGRETTFILPDDVDVNGYASEILISNYDDSPSDFR 545 L H ++ YLR GE E+LLVVNNFYG LP+ V + ++ISNY DS + Sbjct: 473 LPTHKQVWVYLREGEGERLLVVNNFYGTACEVELPERVITDCMLQRLVISNYPDSEVRKQ 532 Query: 546 KITLRPYESIVYYLT 560 ++ LRPYES V +LT Sbjct: 533 QLFLRPYESFVLHLT 547 Lambda K H 0.320 0.138 0.433 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: 1184 Number of extensions: 56 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: 562 Length of database: 549 Length adjustment: 36 Effective length of query: 526 Effective length of database: 513 Effective search space: 269838 Effective search space used: 269838 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: 53 (25.0 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