Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate BWI76_RS02960 BWI76_RS02960 glucohydrolase
Query= CAZy::AAS80455.1 (528 letters) >FitnessBrowser__Koxy:BWI76_RS02960 Length = 551 Score = 341 bits (875), Expect = 4e-98 Identities = 208/521 (39%), Positives = 284/521 (54%), Gaps = 52/521 (9%) Query: 1 MWWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGY 60 +WW+ VIYQ+YP+SFQDT G G GDL GV RL YL+ LGVDA+WL+PFY SP D GY Sbjct: 6 LWWQNGVIYQIYPKSFQDTTGTGTGDLRGVTSRLDYLQKLGVDAIWLTPFYVSPQVDNGY 65 Query: 61 DVADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASRNSPKR 120 DVA+Y +DP +GTL DFD L+ +AHA G+++++D+V NHTS+EH WF E+ ++ SP R Sbjct: 66 DVANYTAIDPTYGTLDDFDELVAQAHARGIRIVLDMVLNHTSTEHAWFREA-LNKESPYR 124 Query: 121 DWYIWKDPAPDGGPPNNWQSFFGGPAWTLDEATGQYYLHQFLPEQPDLNWRNPEVREAIY 180 +YIW+D P PPNNW+S FGG AW + QYYLH F EQ DLNW NP VR + Sbjct: 125 QFYIWRDGEPT-TPPNNWRSKFGGNAWQWHAESEQYYLHLFAVEQADLNWENPAVRAELK 183 Query: 181 EVMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPETYA 240 +V FW RGVDG R+DV+ L+++D F P + D GR F D P + Sbjct: 184 KVCEFWADRGVDGLRLDVVNLISKDQTF---PSDTD------GDGRR---FYTDGPRAHE 231 Query: 241 YVREMRQVLDEFSEPGRERVMVGEIYLPYPQLVRYYQA----GCHLPFNFHLIFRGLPDW 296 +++EM + D F+ G + VGE+ + Y A + FNFH + P Sbjct: 232 FLQEMSR--DVFTPRG--LMTVGEMSSTTLAHCQQYAALDGGELSMTFNFHHLKVDYPGG 287 Query: 297 RPENLAR-IVEEYESLLTRWD-------WPNWVLGNHDQPRLASRLGE------AQARVA 342 LAR +SL W W NHDQPR+ SR G+ A++ Sbjct: 288 EKWTLARPDFVALKSLFRHWQQGMHNRAWNALFWCNHDQPRIVSRFGDEGEYRVPAAKML 347 Query: 343 AMLLFTLRGTPTWYYGDEIGMKNG-----------EIPPEKVQDPAALRQKDRLGEHNLP 391 AM+L ++GTP Y G+EIGM N E ++ A + D L Sbjct: 348 AMVLHGMQGTPYIYQGEEIGMTNPHFMRITDYRDVESHNMFIERAAQGQDPDELLAILAS 407 Query: 392 PGRDPERTPMQWDDTPFAGFSTVEPWLPVNPDYKTRNVAAQEQDPRSMLHLVRRLIALRK 451 RD RTPMQW++ GFS EPW+ + +Y+ N A + DP S+ + ++LIALRK Sbjct: 408 KSRDNSRTPMQWNNADHGGFSAGEPWIALCDNYREINAEAAQADPESVFYTYQQLIALRK 467 Query: 452 D-PDLLYGAYRTYRARE-GVYAYLR---GEGWLVALNLTEK 487 P L +G Y+ ++ Y R G+ +V NL+ + Sbjct: 468 SAPVLTWGDYQDLLPEHPSLWCYRRQWQGQTLVVVANLSRE 508 Lambda K H 0.321 0.141 0.466 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: 1084 Number of extensions: 73 Number of successful extensions: 7 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: 528 Length of database: 551 Length adjustment: 35 Effective length of query: 493 Effective length of database: 516 Effective search space: 254388 Effective search space used: 254388 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