Align trehalose-6-phosphate hydrolase (TreC) (EC 3.2.1.93) (characterized)
to candidate WP_086510096.1 BZY95_RS11675 alpha-glucosidase family protein
Query= CAZy::AAC77196.1 (551 letters) >NCBI__GCF_002151265.1:WP_086510096.1 Length = 536 Score = 296 bits (759), Expect = 1e-84 Identities = 191/565 (33%), Positives = 282/565 (49%), Gaps = 60/565 (10%) Query: 7 WWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQVDNGYD 66 WW+ GVIYQIYP+SF D+ G G GDL GV + LDY+ LGVD IWL+PF+ SP D GYD Sbjct: 7 WWRGGVIYQIYPRSFMDSNGDGVGDLPGVTERLDYVASLGVDGIWLSPFFTSPMRDFGYD 66 Query: 67 VANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREA-LNKESPYRQ 125 ++NY +DP +GTL DF L+ +A + G+++I+D V +HTS QH WF+E+ +N+++P Sbjct: 67 ISNYRDVDPLFGTLADFKALLERAHALGLKVIIDQVISHTSDQHPWFQESRMNRDNPRAD 126 Query: 126 FYIWRDGEPE-TPPNNWRSKFGGSAWRWHAESEQYYLHLFAPEQADLNWENPAVRAELKK 184 +Y+W D P+ T PNNW S FGG AW + + +QYYLH F Q DLN+ NP VRA Sbjct: 127 WYVWADPNPDGTAPNNWLSIFGGPAWTFDSRRQQYYLHNFLSSQPDLNFHNPEVRAAQLD 186 Query: 185 VCEFWADRGVDGLRLDVVNLISKDPRF----------------PEDLDGDGRRFYTD--G 226 FW + GVDG RLD VN D P++ +R D Sbjct: 187 NMRFWLELGVDGFRLDTVNFYFHDQHLRSNPALTIDATRTLGAPKENPYTWQRHIYDISR 246 Query: 227 PRAHEFLHEMNRDVFTPRGLMTVGEM-SSTSLEHCQRYAALTGSELSMTFNFHHLKVDYP 285 P EFL E+ + G TVGE+ T LE Y + G +L M + F L Sbjct: 247 PENVEFLRELRALMDEYPGTTTVGEIGDDTPLERMAEYTS-GGDKLHMAYTFDLLNAP-- 303 Query: 286 GGEKWTLAKPDFVALKTLFRHWQQGMHNVAWNALFWCNHDQPRIVSRFGDEGEYRVPAAK 345 PD++ + + +QQ AW NHD R +R+G E E + Sbjct: 304 -------RSPDYI--RGVLERFQQ-FAGDAWPCWALSNHDVVRSATRWGSE-ECAFAYPR 352 Query: 346 MLAMVLHGMQGTPYIYQGEEIGMTNPH--FTRITDYRDVESLNMFAELRNDGRDADELLA 403 + +L ++G+ +YQGEE+G+ F RI +D L ++ + Sbjct: 353 VALALLFSLRGSVCLYQGEELGLPEAEVPFERI---QDPYGLPLWPDF------------ 397 Query: 404 ILASKSRDNSRTPMQWSNGDNAGFTAGEPWIGLGDNYQQINVEAALADDSSVFYTYQKLI 463 K RD RTPM W + AGF+ EPW+ + + + ++V + S+ ++L+ Sbjct: 398 ----KGRDGCRTPMPWDDTPLAGFSDVEPWLPVAEPHLAMSVARQQDEPDSMLNATRRLL 453 Query: 464 ALRKQEAILTWGNYQDLLPNSPVLWCYRREWKGQTLLVIANLSREIQPWQAGQMRGNWQL 523 R Q L G+ LL L + R+ LL + NL+ + Q ++R Q Sbjct: 454 RFRHQHPALFDGD-MTLLDLGEALVAFTRQRGSDRLLCVFNLTGQPQSATLPEVREALQE 512 Query: 524 VMHNYEEASPQPCAMNLRPFEAVWW 548 YE + + ++L P++A ++ Sbjct: 513 HGFQYEVSGGR---LHLPPYQAAYF 534 Lambda K H 0.320 0.136 0.448 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: 1029 Number of extensions: 56 Number of successful extensions: 6 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: 536 Length adjustment: 35 Effective length of query: 516 Effective length of database: 501 Effective search space: 258516 Effective search space used: 258516 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 Apr 09 2024. 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