Align trehalose-6-phosphate hydrolase (TreC) (EC 3.2.1.93) (characterized)
to candidate GFF856 Psest_0870 Glycosidases
Query= CAZy::AAC77196.1 (551 letters) >FitnessBrowser__psRCH2:GFF856 Length = 542 Score = 293 bits (750), Expect = 1e-83 Identities = 178/528 (33%), Positives = 263/528 (49%), Gaps = 61/528 (11%) Query: 4 LPHWWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQVDN 63 L +WW+ GVIYQ+YP+SF D+ G G GDL GV+ LDY+ L VDAIWL+PF+ SP D Sbjct: 5 LQNWWRGGVIYQVYPRSFFDSNGDGVGDLPGVLHKLDYIASLNVDAIWLSPFFTSPMKDF 64 Query: 64 GYDVANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREA-LNKESP 122 GYDVA+Y +DP +GTLDDF LV RG+R+++D V NH+S QH WF E+ ++++ Sbjct: 65 GYDVADYRGVDPLFGTLDDFVRLVEACHERGMRVLIDQVLNHSSDQHPWFAESRSSRDND 124 Query: 123 YRQFYIWRDGEPE-TPPNNWRSKFGGSAWRWHAESEQYYLHLFAPEQADLNWENPAVRAE 181 +Y+W D +P+ T PNNW S FGG AW W + QYYLH F Q DLN+ PAV+ + Sbjct: 125 KADWYVWADPKPDGTVPNNWLSVFGGPAWSWDSRRRQYYLHNFLSSQPDLNFHCPAVQDQ 184 Query: 182 LKKVCEFWADRGVDGLRLDVVNLISKDPRFPEDLDGDGRR-----FYTDGPRAH------ 230 L EFW GVDG RLD N D ++ R D P A+ Sbjct: 185 LLDDMEFWLKLGVDGFRLDAANFYFHDAELRDNPPNTEIREGSIGVRIDNPYAYQRHIYD 244 Query: 231 -------EFLHEMNRDVFTPRGLMTVGEMSSTSLEHCQRYAALT--GSELSMTFNFHHLK 281 +FL + + G +V E+ E + AA T G L M ++F L Sbjct: 245 KTRPENMDFLRRLRALLQRYPGASSVAEIGCD--ESLRTMAAYTSGGDTLHMAYSFDLLT 302 Query: 282 VDYPGGEKWTLAKPDFVALKTLFRHWQQGMHNV---AWNALFWCNHDQPRIVSRFGDEGE 338 P ++ RH +G+ W+ NHD R+++R+ G Sbjct: 303 EQ---------CSPGYI------RHTVEGIERELADGWSCWSMGNHDVVRVMTRWALNGR 347 Query: 339 YRVPAAKMLAMVLHGMQGTPYIYQGEEIGMTNPHFTRITDYRDVESLNMFAELRNDGRDA 398 ++L +L ++G+ +YQGEE+G+ R D D + + E Sbjct: 348 PDPERGRLLMALLLSLRGSVCMYQGEELGLPEAEL-RYEDLVDPYGITFWPEF------- 399 Query: 399 DELLAILASKSRDNSRTPMQW-SNGDNAGFTAGEPWIGLGDNYQQINVEAALADDSSVFY 457 K RD RTPM W S +AGFT +PW+ + D+++ ++V A AD S+ Sbjct: 400 ---------KGRDGCRTPMPWESEAHHAGFTGSQPWLPVDDSHRSLSVAAQDADPHSMLN 450 Query: 458 TYQKLIALRKQEAILTWGNYQDLLPNSPVLWCYRREWKGQTLLVIANL 505 Y++ + R+++ +L G+ ++ + L + R + L + NL Sbjct: 451 CYRRFLGWRREQRLLIEGDIH-MVYHDDALLVFERRLGDEAWLCLFNL 497 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: 1045 Number of extensions: 54 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: 542 Length adjustment: 36 Effective length of query: 515 Effective length of database: 506 Effective search space: 260590 Effective search space used: 260590 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