Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate GFF4502 PS417_23045 trehalose-6-phosphate hydrolase
Query= uniprot:H3K096 (538 letters) >FitnessBrowser__WCS417:GFF4502 Length = 548 Score = 283 bits (723), Expect = 2e-80 Identities = 187/538 (34%), Positives = 270/538 (50%), Gaps = 63/538 (11%) Query: 5 MMWWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFG 64 M W+ VIYQIYP+SF G+ GDL GI +KLDY+ L VD +W++PF SP D G Sbjct: 1 MQDWQHSVIYQIYPKSFHSHAGNATGDLLGIVDKLDYLKWLGVDCLWITPFLRSPQRDNG 60 Query: 65 YDVSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPK 124 YD+SDY +DP +GT+ D L+ +A G+K+M+D V++HTS +H WFQ++R + NP Sbjct: 61 YDISDYYAIDPSYGTMADCDLLISEAAKRGIKLMLDIVVNHTSIEHEWFQQARSSLDNPY 120 Query: 125 ADWFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQ 184 D+++W D PNNW S FGGSAW ++++ QY+LH F +Q D+N+ +P+ R Sbjct: 121 RDFYIWRD------QPNNWESKFGGSAWEYEAQTGQYFLHLFDHTQADLNWDNPKVRAEV 174 Query: 185 LDNMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDL 244 MRFW D GV GFRLD +N A+ PE N T R Y Sbjct: 175 FKLMRFWRDKGVGGFRLDVINLISKPADF----------------PEDN--TDGRRFY-T 215 Query: 245 SRPENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDK-LHMAYTFDLLNMP 303 P ++L+++ + E VGE+ + LE Y+ K L M + F L + Sbjct: 216 DGPNVHEYLQEMHREVFEGHDLINVGEMSSTS-LEHCIRYSRPESKELSMTFNFHHLKVD 274 Query: 304 H-------SASY----LREVIERFQ--RLAGDAWPCWATSNHDVVRSATRWGADEDPHAY 350 + A + L+++ +Q AG W NHD R +R+G D + Sbjct: 275 YPNLQKWVKADFDFLQLKQIFTDWQLGMQAGGGWNALFWCNHDQPRVVSRFGNDGEHRVV 334 Query: 351 PKVMLA-VLFSLRGSVCLYQGEELGLPEADVPFERIQ------------------DPYGK 391 MLA L L+G+ +YQGEELG+ + F+RI+ +P Sbjct: 335 SAKMLATALHFLQGTPYVYQGEELGM--TNPGFDRIEQYRDVESLNIFRLKRDAGEPEAS 392 Query: 392 VLWPEF-KGRDGCRTPMPWTDGEQGGFSPVEPWLPMEARHLELAVSRQQDDPNATLNTVR 450 + K RD RTPM W GE GFS EPW+ + A ++ V Q DDP++ L+ R Sbjct: 393 SMAAIMQKSRDNGRTPMQWNAGENAGFSTGEPWIGIPANAAQINVESQLDDPDSVLHHYR 452 Query: 451 ALLAFRRSHPALFDGDL-SLVDVGDDLLGFTRQKGDETLLCVFNLTGQEQQTTLPVEV 507 AL+A RR P + +G L+ + + R+ E LL + N G + LP V Sbjct: 453 ALIALRRHEPLIQEGVYRPLLQDHLRVWAYLREGHGERLLVLNNFYGTPCEIQLPDNV 510 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: 934 Number of extensions: 48 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: 548 Length adjustment: 35 Effective length of query: 503 Effective length of database: 513 Effective search space: 258039 Effective search space used: 258039 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 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