Align trehalose 6-P hydrolase (ECs5216) (EC 3.2.1.93) (characterized)
to candidate WP_057507037.1 ABB28_RS02135 alpha-glucosidase
Query= CAZy::BAB38639.1 (551 letters) >NCBI__GCF_001431535.1:WP_057507037.1 Length = 538 Score = 308 bits (789), Expect = 3e-88 Identities = 197/551 (35%), Positives = 287/551 (52%), Gaps = 70/551 (12%) Query: 1 MTNLPHWWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQRLDYLHKLGVDAIWLTPFYVSPQ 60 M+N P WW+ VIYQIYP+SF D G G GDL G+I RLDY+ LGVDAIW++PF+ SP Sbjct: 1 MSNTP-WWRGAVIYQIYPRSFLDANGDGVGDLPGIIDRLDYIAALGVDAIWISPFFRSPM 59 Query: 61 VDNGYDVANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREA-LNK 119 D GYD+A+Y +DP +G LDDFD L+ +A + G+++++D V +HTS +H WFRE+ ++ Sbjct: 60 ADFGYDIADYRDVDPLFGNLDDFDRLLAKAHALGLKVMIDQVLSHTSIEHDWFRESRQDR 119 Query: 120 ESPYRQFYIWRD-GEPETPPNNWRSKFGGSAWRWHAESEQYYLHLFAPEQADLNWENPAV 178 +P +Y+W D E T PNNW S FGG AW+W EQY+LH F +Q DLN+ NPAV Sbjct: 120 TNPKADWYVWADPREDGTAPNNWMSLFGGVAWQWEPRREQYFLHNFLADQPDLNFHNPAV 179 Query: 179 RAELKKVCEFWADRGVDGLRLDVVNLISKDPRFPDDLDGD-----GRRFYTDGPRAHE-- 231 + FW DRGVDG RLD +N D + D+ GR F D P A++ Sbjct: 180 QKATLDNVRFWLDRGVDGFRLDAINFCFHDRQLRDNPPKPADKRVGRGFSPDNPYAYQYH 239 Query: 232 -----------FLHEMNRDVFTPRGLMTVGEMSS-TSLEHCQRYAALTGSELSMTFNFHH 279 FL E+ + G +++GE+SS SL Y T L M ++F Sbjct: 240 YFNNTQPENLPFLEELRALLDQYPGAVSLGEISSEDSLATTAEYT--TAKRLHMGYSFEL 297 Query: 280 LKVDYPGGE-KWTLAKPDFVALKTLFRHWQQGMHNVALNALFWCNHDQPRIVSRFGDEGE 338 L DY + T+++ + + +G A++ NHD R V+R+G G Sbjct: 298 LVDDYSAAYIRDTVSRLETAMI--------EGWPCWAIS-----NHDVERAVTRWG--GH 342 Query: 339 YRVP-AAKMLAMVLHGMQGTPYIYQGEEIGM--TNPHFTRITDYRDVESLNMFAELRNDG 395 P A+ML +L ++G+ +YQGEE+G+ + F + D + F Sbjct: 343 PADPRLARMLVAMLCSLRGSICLYQGEELGLGEADVPFEALQDPYGITFWPNF------- 395 Query: 396 RDADELLAILASKSRDNSRTPMQWSNGDNAGFTAGEPWIGLGDNYQQINVEAALADESSV 455 K RD RTP+ W + AGFT GEPW+ + ++Q V A SV Sbjct: 396 ------------KGRDGCRTPLPWIDAPLAGFTTGEPWLPIPADHQSRAVAVQEAQPDSV 443 Query: 456 FYTYQKLIALRKQEAILTWGNYQDLLPNSPVLWCYRREWKGQTLLVIANLS----REIQP 511 +++ +A R+ + +L G+ + L PVL + R + +L+ NLS R++ P Sbjct: 444 LLAFRRFLAWRRTQPVLLHGDIRFLDSAEPVL-LFERTLGDEVMLLAFNLSSLPGRQLLP 502 Query: 512 ---WQPGQMRG 519 WQ + G Sbjct: 503 EGAWQAMDVPG 513 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: 1001 Number of extensions: 52 Number of successful extensions: 4 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: 538 Length adjustment: 35 Effective length of query: 516 Effective length of database: 503 Effective search space: 259548 Effective search space used: 259548 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 24 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