Align trehalose-6-phosphate hydrolase (TreC) (EC 3.2.1.93) (characterized)
to candidate GFF3716 Psest_3785 Glycosidases
Query= CAZy::AAC77196.1 (551 letters) >FitnessBrowser__psRCH2:GFF3716 Length = 511 Score = 337 bits (863), Expect = 9e-97 Identities = 203/549 (36%), Positives = 288/549 (52%), Gaps = 62/549 (11%) Query: 7 WWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQVDNGYD 66 WW+ +YQIYP+SF D+ G G GDL GV++HLD+L +LGVDA+WL+P + SP D GYD Sbjct: 9 WWKGATVYQIYPRSFADSNGDGIGDLNGVLRHLDHLQQLGVDALWLSPIFRSPMADAGYD 68 Query: 67 VANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREA-LNKESPYRQ 125 +++Y IDP +G+L D D L+ +A +R IR++LD V NHTS +H WF E+ ++++P R Sbjct: 69 ISDYCDIDPLFGSLADIDRLIAEAHARNIRVLLDFVPNHTSDEHPWFVESRSSRDNPKRD 128 Query: 126 FYIWRDGEPETPPNNWRSKFG-GSAWRWHAESEQYYLHLFAPEQADLNWENPAVRAELKK 184 +YIWRD PNNWR+ G GSAW W ++QYYLHLF +Q DLNW NP V + Sbjct: 129 WYIWRD-----QPNNWRAALGAGSAWTWDEHTQQYYLHLFLAKQPDLNWRNPEVVEAMHD 183 Query: 185 VCEFWADRGVDGLRLDVVNLISKDPRFPED---LDGDGRRFYTDGPRAHEFLHEMNRDVF 241 V FW DRG+DG R+DV++ KD F +D G + D P +HE L + + V Sbjct: 184 VLRFWLDRGIDGFRIDVIHCTGKDLSFADDPRCQAGQPLSDFNDQPYSHEVLRGLRKLVD 243 Query: 242 T-PRGLMTVGEMSSTSLEHCQRYAALTGSELSMTFNFHHLKVDYPGGEKWTLAKPDFVAL 300 + P M VGE++ S E +Y G EL + FNF+ L + D V Sbjct: 244 SYPGDRMLVGEVNIRSTERVLQYYG-AGDELHLAFNFNPLDAPW-----------DPVLF 291 Query: 301 KTLFR---HWQQGMHNVAWNALFWCNHDQPRIVSRFGDEGEYRVPAAKMLAMVLHGMQGT 357 +T R HW Q AW NHD R SR+ G R AA+ A++L ++GT Sbjct: 292 RTCIREVEHWLQPAG--AWPTWVLSNHDNVRQRSRY--RGSER--AARAAAVLLLTLRGT 345 Query: 358 PYIYQGEEIGMTNPHFTRITDYRDVESLNMFAELRNDGRDADELLAILASKSRDNSRTPM 417 P+IYQGEE+G+ + H +R++ R + RD R P+ Sbjct: 346 PFIYQGEELGLEDAH------------------IRDEAR--------IDPGGRDGCRAPI 379 Query: 418 QWSNGDNAGFTAGEPWIGLGDNYQQINVEAALADDSSVFYTYQKLIALRKQEAILTWGNY 477 W G+ EPW+ + ++ E +S+F YQ+L+A RK L G++ Sbjct: 380 PWQAEPPHGWQGAEPWLPFPPDAAELAAERQTGAANSIFALYQRLLAARKASPALHHGDF 439 Query: 478 QDLLPNSPVLWCYRREWKGQTLLVIANLSREIQPWQAGQMRGNWQLVMHNYEEASPQPCA 537 ++L + VL YRR+ LV N S QP A G+W + + + P Sbjct: 440 EELASHPEVL-AYRRQHGDDCRLVCINFSE--QP-HAHPHAGDWHVEIASDGVGENAPYN 495 Query: 538 MNLRPFEAV 546 L P +AV Sbjct: 496 GTLNPGQAV 504 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: 1067 Number of extensions: 65 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: 511 Length adjustment: 35 Effective length of query: 516 Effective length of database: 476 Effective search space: 245616 Effective search space used: 245616 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