Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate GFF3716 Psest_3785 Glycosidases
Query= BRENDA::Q5SL12 (529 letters) >FitnessBrowser__psRCH2:GFF3716 Length = 511 Score = 430 bits (1105), Expect = e-125 Identities = 236/500 (47%), Positives = 305/500 (61%), Gaps = 47/500 (9%) Query: 3 WWQRAVIYQVYPRSFQDTNGDGVGDLEGIRRRLPYLKSLGVDALWLSPFYKSPMKDFGYD 62 WW+ A +YQ+YPRSF D+NGDG+GDL G+ R L +L+ LGVDALWLSP ++SPM D GYD Sbjct: 9 WWKGATVYQIYPRSFADSNGDGIGDLNGVLRHLDHLQQLGVDALWLSPIFRSPMADAGYD 68 Query: 63 VADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASRNSPKRD 122 ++DYCD+DP+FG+L D DRL+ EAHA ++VL+D VPNHTS EHPWF+ESR+SR++PKRD Sbjct: 69 ISDYCDIDPLFGSLADIDRLIAEAHARNIRVLLDFVPNHTSDEHPWFVESRSSRDNPKRD 128 Query: 123 WYIWKDPAPDGGPPNNWQSFFG-GPAWTLDEATGQYYLHLFLPEQPDLNWRNPEVREAIK 181 WYIW+D PNNW++ G G AWT DE T QYYLHLFL +QPDLNWRNPEV EA+ Sbjct: 129 WYIWRD------QPNNWRAALGAGSAWTWDEHTQQYYLHLFLAKQPDLNWRNPEVVEAMH 182 Query: 182 EVMRFWLRRGVDGFRVDVLWLLGKDPLFRDEPGSPLWRPGLPDRARHEHLYTEDQPETYA 241 +V+RFWL RG+DGFR+DV+ GKD F D+P +P L D DQP ++ Sbjct: 183 DVLRFWLDRGIDGFRIDVIHCTGKDLSFADDPRCQAGQP-LSD--------FNDQPYSHE 233 Query: 242 YVREMRQVLDEFSEPGRERVMVGEIYL-PLPRLVRYYAAG--CHLPFNFSLVTEGLSDWR 298 +R +R+++D + PG +R++VGE+ + R+++YY AG HL FNF+ + + W Sbjct: 234 VLRGLRKLVDSY--PG-DRMLVGEVNIRSTERVLQYYGAGDELHLAFNFNPLD---APWD 287 Query: 299 PENLARIVETYEGLLS-RWDWPNWVLGNHDQPRLASRL--GEPQARVAAMLLFTLRGTPT 355 P + E L WP WVL NHD R SR E AR AA+LL TLRGTP Sbjct: 288 PVLFRTCIREVEHWLQPAGAWPTWVLSNHDNVRQRSRYRGSERAARAAAVLLLTLRGTPF 347 Query: 356 WYYGDELALPNGLIPPEKVQDPAALRQRDREPTAYHTLGRDPERTPMPWDASPYGGFSTV 415 Y G+EL L + I E DP GRD R P+PW A P G+ Sbjct: 348 IYQGEELGLEDAHIRDEARIDPG---------------GRDGCRAPIPWQAEPPHGWQGA 392 Query: 416 EPWLPLNPDYRTRNVAAQEKDPRSMLHLVKRLIALRK-DPDLLYGAYRTYRAREGVYAYL 474 EPWLP PD Q S+ L +RL+A RK P L +G + + V AY Sbjct: 393 EPWLPFPPDAAELAAERQTGAANSIFALYQRLLAARKASPALHHGDFEELASHPEVLAYR 452 Query: 475 RGEG---WLVALNLTEKEKA 491 R G LV +N +E+ A Sbjct: 453 RQHGDDCRLVCINFSEQPHA 472 Lambda K H 0.320 0.141 0.462 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: 1062 Number of extensions: 59 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: 529 Length of database: 511 Length adjustment: 35 Effective length of query: 494 Effective length of database: 476 Effective search space: 235144 Effective search space used: 235144 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