Align trehalose-6-phosphate hydrolase (TreC) (EC 3.2.1.93) (characterized)
to candidate GFF775 PGA1_c07890 putative alpha-glucosidase AglA
Query= CAZy::AAC77196.1 (551 letters) >FitnessBrowser__Phaeo:GFF775 Length = 552 Score = 297 bits (761), Expect = 6e-85 Identities = 180/508 (35%), Positives = 268/508 (52%), Gaps = 48/508 (9%) Query: 5 PHWWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQVDNG 64 P WW+ VIYQIYP+S+QD+ G G GDLRG+ Q L ++ LGVDAIW++PF+ SP D G Sbjct: 17 PDWWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVDAIWISPFFTSPMKDFG 76 Query: 65 YDVANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREA-LNKESPY 123 YDV++Y +DP +G+L +FD+LV A G+R+++D+V +HTS QHAWF E+ ++++ Sbjct: 77 YDVSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSDQHAWFGESRQSRDNAR 136 Query: 124 RQFYIWRDGEPE-TPPNNWRSKFGGSAWRWHAESEQYYLHLFAPEQADLNWENPAVRAEL 182 +Y+W D +P+ TPPNNW S FGGSAW+W EQYYLH F Q DLN+ +PAV+ L Sbjct: 137 ADWYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLVSQPDLNFHSPAVQDAL 196 Query: 183 KKVCEFWADRGVDGLRLDVVNL------ISKDPRFPEDLDGDGRRFYTDGPRAHEFLHEM 236 V FW +RGVDG RLD +N + +P P + +R T P + + H+ Sbjct: 197 LDVTRFWLERGVDGFRLDTINFYYHDAELRSNPALPPE-----QRNATIAPSVNPYNHQE 251 Query: 237 N-RDVFTPRGLMTVGEMSSTSLEHCQRYA------ALTGSELSMTFNFHHLKVDYPGGEK 289 + P L +G + E+ + A A G E+ ++ + V + Sbjct: 252 HLYSKNQPENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGSYTAANTGVHMCYAFE 311 Query: 290 WTLAKPDFVA--LKTLFRHWQQGMHNVAWNALFWCNHDQPRIVSRFGDEGEYRVPAAKML 347 LAK A L +F + N W + NHD R SR+G A ++ Sbjct: 312 -LLAKDVLTASRLAEVFAEVDRVAAN-GWACWAFSNHDVIRHSSRWG----LNPAAQRLF 365 Query: 348 AMVLHGMQGTPYIYQGEEIGMTNPHFTRITDYRDVESLNMFAELRNDGRDADELLAILAS 407 ++ ++GT IYQGEE+G+ D +D + + E Sbjct: 366 TTMMMCLRGTTCIYQGEELGLPEADIA-FEDLQDPYGIEFWPEF---------------- 408 Query: 408 KSRDNSRTPMQW--SNGDNAGFTAGEPWIGLGDNYQQINVEAALADDSSVFYTYQKLIAL 465 K RD RTPM W SNG + GF+AG+PW+ + + ++V + AD ++ + Y++ IAL Sbjct: 409 KGRDGCRTPMVWEPSNG-SGGFSAGKPWLPVSPEHLNLSVASQEADPDAMLHHYRRAIAL 467 Query: 466 RKQEAILTWGNYQDLLPNSPVLWCYRRE 493 RK L G + L V + R++ Sbjct: 468 RKAHPALAVGTHDQLRAEGNVAFFTRQD 495 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: 1033 Number of extensions: 42 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 551 Length of database: 552 Length adjustment: 36 Effective length of query: 515 Effective length of database: 516 Effective search space: 265740 Effective search space used: 265740 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