Align trehalose-6-phosphate hydrolase (TreC;KP1_0530) (EC 3.2.1.93) (characterized)
to candidate SMc03064 SMc03064 alpha-glucosidase
Query= CAZy::BAG86620.1 (551 letters) >FitnessBrowser__Smeli:SMc03064 Length = 551 Score = 310 bits (793), Expect = 1e-88 Identities = 198/528 (37%), Positives = 267/528 (50%), Gaps = 60/528 (11%) Query: 7 WWQNGVIYQIYPKSFQDTTGSGTGDLRGVTARLDYLQKLGVDAIWLTPFYVSPQVDNGYD 66 WW+ VIYQIYP+SFQDT G G GDL+G+TARL ++ LG DAIW++PF+ SP D GYD Sbjct: 17 WWRGAVIYQIYPRSFQDTNGDGIGDLQGITARLPHIAGLGADAIWISPFFTSPMRDFGYD 76 Query: 67 VANYTAIDPSYGTMADFDALVAEAKARGIRIVLDMVLNHTSTEHEWFRQSLNKESPYR-Q 125 V+NY +DP +GT+ DFDAL+AEA G+R+++D+VL+HTS H WF +S + S + Sbjct: 77 VSNYVDVDPIFGTLEDFDALIAEAHRLGLRVMIDLVLSHTSDRHPWFVESRSSRSNAKAD 136 Query: 126 FYIWRDGEPDAL-PNNWRSKFGGNAWQWHADSGQYYLHLFAIEQADLNWENPAVRAELKK 184 +Y+W D +PD PNNW S FGG+AWQW QYYLH F Q DLN NP V+ L Sbjct: 137 WYVWADSKPDGTPPNNWLSIFGGSAWQWDPTRLQYYLHNFLTSQPDLNLHNPQVQEALLA 196 Query: 185 VCEFWADRGVDGLRLDVVNLISKDQTF---PCDLDGDGRRFYTDGPRVHEF-LQEMSRDV 240 V FW +RGVDG RLD +N D+ P + RR + P V+ + QE D Sbjct: 197 VERFWLERGVDGFRLDTINFYFHDRELRDNPALV--PERRNASTAPAVNPYNYQEHIYDK 254 Query: 241 FTPRNL----------------MTVGEM--SSTSLEHCQQYAALDGRELSMTFNFHHLKV 282 P NL VGE+ S LE +Y + G ++ M + F L Sbjct: 255 NRPENLEFLKRFRAVMDEFPAIAAVGEVGDSQRGLEIAGEYTS-GGDKVHMCYAFEFLAP 313 Query: 283 DYPGGEKWTLARPDYVA--LKALFRHWQQGMHNRAWNALFWCNHDQPRIVSRFGDEGEYR 340 D P VA L+ R +G W + NHD R VSR+ D Sbjct: 314 D--------RLTPQRVAEVLRDFHRAAPEG-----WACWAFSNHDVVRHVSRWADGVTDH 360 Query: 341 VTAAKMLAMVLHGMQGTPYIYQGEEIGMTNPHFSSISDYRDVESHNMFIERAAQGQSPDE 400 AK+LA +L ++GT IYQGEE+ + DY D+ Q P Sbjct: 361 DAHAKLLASLLMSLRGTVCIYQGEELALAEAEL----DYEDL-------------QDPYG 403 Query: 401 LLAILASKSRDNSRTPMPWHAGENGGFSDGEPWIGLGDNYQEINVEAALADPDSVFYTYQ 460 + K RD RTPM W + +GGFS PW+ + ++ V DP SV + Y+ Sbjct: 404 IQFWPDFKGRDGCRTPMVWESLPDGGFSSATPWLPISQSHIPRAVAVQEGDPASVLHHYR 463 Query: 461 QLITLRKTLPLLTWGDYEDLLPEHPSLWCYRRQWQGQTLVVAANLSRE 508 + + RK P L G+ E + SL + R + + N+S E Sbjct: 464 RFLAFRKANPALAKGEIE-FVETRGSLLGFLRSHGNEKVFCLFNMSDE 510 Lambda K H 0.320 0.136 0.446 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: 997 Number of extensions: 44 Number of successful extensions: 5 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: 551 Length of database: 551 Length adjustment: 36 Effective length of query: 515 Effective length of database: 515 Effective search space: 265225 Effective search space used: 265225 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