Align α-glucosidase (EC 3.2.1.20) (characterized)
to candidate GFF4502 PS417_23045 trehalose-6-phosphate hydrolase
Query= CAZy::AAF71997.1 (562 letters) >FitnessBrowser__WCS417:GFF4502 Length = 548 Score = 712 bits (1837), Expect = 0.0 Identities = 327/555 (58%), Positives = 419/555 (75%), Gaps = 11/555 (1%) Query: 6 WKKAVVYQIYPKSFNDTNGDGIGDLAGIIEKLDYLKQLGVDVIKLKPIYKSPQRDNGYDI 65 W+ +V+YQIYPKSF+ G+ GDL GI++KLDYLK LGVD + + P +SPQRDNGYDI Sbjct: 4 WQHSVIYQIYPKSFHSHAGNATGDLLGIVDKLDYLKWLGVDCLWITPFLRSPQRDNGYDI 63 Query: 66 SDYFQIHDEYGTMEDFDRLLEEVHRRGMKLIMDMVVNHTSTEHEWFKQARTSKDNPYRHF 125 SDY+ I YGTM D D L+ E +RG+KL++D+VVNHTS EHEWF+QAR+S DNPYR F Sbjct: 64 SDYYAIDPSYGTMADCDLLISEAAKRGIKLMLDIVVNHTSIEHEWFQQARSSLDNPYRDF 123 Query: 126 YIWRDPKPDGSAPTNWQSKFGGSAWEYDEKTGQYYLHLFDVTQADLNWENEELRRRIYDM 185 YIWRD P NW+SKFGGSAWEY+ +TGQY+LHLFD TQADLNW+N ++R ++ + Sbjct: 124 YIWRDQ------PNNWESKFGGSAWEYEAQTGQYFLHLFDHTQADLNWDNPKVRAEVFKL 177 Query: 186 MHFWFQKGVDGFRLDVVNLLSKDQRFLDDDGSMPPGDGRKFYTDGPRIHEFLHEMNREVF 245 M FW KGV GFRLDV+NL+SK F +D+ DGR+FYTDGP +HE+L EM+REVF Sbjct: 178 MRFWRDKGVGGFRLDVINLISKPADFPEDNT-----DGRRFYTDGPNVHEYLQEMHREVF 232 Query: 246 SKYDVMTVGEMSSTTIDHCIKYTNPERRELNMVFNFHHLKVDYPNGEKWAVADFDFLALK 305 +D++ VGEMSST+++HCI+Y+ PE +EL+M FNFHHLKVDYPN +KW ADFDFL LK Sbjct: 233 EGHDLINVGEMSSTSLEHCIRYSRPESKELSMTFNFHHLKVDYPNLQKWVKADFDFLQLK 292 Query: 306 RILSEWQVEMHKGGGWNALFWCNHDQPRIVSRYGDDGKYHKESAKMLATVIHMMQGTPYI 365 +I ++WQ+ M GGGWNALFWCNHDQPR+VSR+G+DG++ SAKMLAT +H +QGTPY+ Sbjct: 293 QIFTDWQLGMQAGGGWNALFWCNHDQPRVVSRFGNDGEHRVVSAKMLATALHFLQGTPYV 352 Query: 366 YQGEEIGMTDPKFERIDDYRDVESLNMYHILREQGKSEQEVLEILKRKSRDNSRTPMQWD 425 YQGEE+GMT+P F+RI+ YRDVESLN++ + R+ G+ E + + +KSRDN RTPMQW+ Sbjct: 353 YQGEELGMTNPGFDRIEQYRDVESLNIFRLKRDAGEPEASSMAAIMQKSRDNGRTPMQWN 412 Query: 426 DSENAGFTTGKPWIRVAPNYQQINVKKALEDPTSVFYHYQRLIQLRKQYDIITTGDYQLL 485 ENAGF+TG+PWI + N QINV+ L+DP SV +HY+ LI LR+ +I G Y+ L Sbjct: 413 AGENAGFSTGEPWIGIPANAAQINVESQLDDPDSVLHHYRALIALRRHEPLIQEGVYRPL 472 Query: 486 LEDHPDIFAYLRNGENEKLLVVNNFYGRETTFILPDDVDVNGYASEILISNYDDSPSDFR 545 L+DH ++AYLR G E+LLV+NNFYG LPD+V +LISNY D P Sbjct: 473 LQDHLRVWAYLREGHGERLLVLNNFYGTPCEIQLPDNVINPAREQRVLISNYPDCPQRTA 532 Query: 546 KITLRPYESIVYYLT 560 +TLRPYES V +LT Sbjct: 533 TVTLRPYESFVLHLT 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: 1181 Number of extensions: 55 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: 548 Length adjustment: 36 Effective length of query: 526 Effective length of database: 512 Effective search space: 269312 Effective search space used: 269312 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