Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate Echvi_2850 Echvi_2850 Glycosidases
Query= CAZy::AAS80455.1 (528 letters) >FitnessBrowser__Cola:Echvi_2850 Length = 519 Score = 221 bits (564), Expect = 4e-62 Identities = 164/521 (31%), Positives = 255/521 (48%), Gaps = 90/521 (17%) Query: 2 WWKEA-VIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGY 60 +W EA + Y+++ +SF DT+GDG+GD+ GV ++L +++ LG +A+W P SP Y Sbjct: 33 YWPEAGITYEIFIQSFYDTDGDGIGDINGVTKKLDHVQELGANAIWFMPLMPSPSYH-KY 91 Query: 61 DVADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASRNSPKR 120 DV DY + P +GT+ DF ++L+EAH +KV++D++ NHTS EHPWF E++ R++P R Sbjct: 92 DVTDYKAIHPDYGTMDDFKQMLDEAHKRDIKVVIDMIINHTSDEHPWFQEAKKGRDNPYR 151 Query: 121 DWYIWKDPAPDGGPPNNWQSFFGGPAWTLDEAT-------GQ---YYLHQFLPEQPDLNW 170 D+Y+W + Q + TLD GQ YY F + PDLN+ Sbjct: 152 DYYVW-------AQYDTIQDYLDKKVVTLDSDNIRQWHDPGQGDDYYYGFFTGDMPDLNF 204 Query: 171 RNPEVREAIYEVMRFWLRR-GVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLH 229 NP+VRE IYE+ R+WL GVDGFR+D + D DR H Sbjct: 205 DNPKVREEIYEIGRYWLAEVGVDGFRLDAAKHIYPD-----------------DRAADSH 247 Query: 230 IFTEDQPETYAYVREMRQVLDEFSEPGRERVMVGEIYLPYPQLVRYYQAGCHLPFNFHLI 289 F E+ + EM +V + +VGE+Y ++V Y G FNF Sbjct: 248 EFWEE------FRAEMEKVKPDV-------YLVGEVY-DMKEVVAPYLTGLRALFNFDFH 293 Query: 290 FRGLPDWRPENLARIVEEYESLLTRWDW------PNWVLGNHDQPRLASRLGEAQARV-- 341 + L ++ E+ + ++ +L ++ + NHDQPRL + LG+++ ++ Sbjct: 294 YTLLEAYKKEDGMLLAKKQHDILAFYNGITDDFIDATISSNHDQPRLLNELGKSKDKLKQ 353 Query: 342 AAMLLFTLRGTPTWYYGDEIGMKNGEIPPEKVQDPAALRQKDRLGEHNLPPGRDPERTPM 401 A +L T+ G P YYG+EIGM G+ P +++P + +D RT Sbjct: 354 AIAILMTMPGAPYIYYGEEIGML-GKKPDPNIREPFLWDVAE----------QDEGRT-- 400 Query: 402 QWDDTPFAGFSTVEPWLPVNPDYKTRNVAAQEQDPRSMLHLVRRLIALRK-DPDLLYGAY 460 +W F+ +TV P +A Q++D S + +R+I LR P L G+ Sbjct: 401 KWITPAFSTDNTVTP------------LAIQKEDADSYFNHYKRVIQLRNTHPALAIGSL 448 Query: 461 R--TYRAREGVYAYLRGEG---WLVALNLTEKEKALELPRG 496 + + V AY R G V NL +K + LP+G Sbjct: 449 ELPAEKYPKAVMAYQRKTGEQELYVFHNLGKKSVEIPLPQG 489 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: 863 Number of extensions: 55 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: 528 Length of database: 519 Length adjustment: 35 Effective length of query: 493 Effective length of database: 484 Effective search space: 238612 Effective search space used: 238612 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