Align Probable alpha-glucosidase; EC 3.2.1.20 (uncharacterized)
to candidate Ga0059261_1580 Ga0059261_1580 Glycosidases
Query= curated2:Q9Z3R8 (551 letters) >FitnessBrowser__Korea:Ga0059261_1580 Length = 541 Score = 534 bits (1375), Expect = e-156 Identities = 261/497 (52%), Positives = 328/497 (65%), Gaps = 8/497 (1%) Query: 12 EPDRDWWRGAVIYQIYPRSFQDTNGDGIGDLQGITARLPHIAGLGADAIWISPFFTSPMR 71 E +RDWWRGAVIYQIYPRSF D+NGDGIGDL G+ A L H+A LGADAIW+SPFFTSPMR Sbjct: 11 ETNRDWWRGAVIYQIYPRSFADSNGDGIGDLPGVAAHLDHVAALGADAIWLSPFFTSPMR 70 Query: 72 DFGYDVSNYVDVDPIFGTLEDFDALIAEAHRLGLRVMIDLVLSHTSDRHPWFVESRSSRS 131 DFGYD+++Y VDP+FGTL DFDA+I +AH LGL+V+ID V SHTSD+H WF ESRSSR Sbjct: 71 DFGYDIADYCGVDPVFGTLADFDAVIEKAHALGLKVIIDQVYSHTSDQHEWFKESRSSRD 130 Query: 132 NAKADWYVWADSKPDGTPPNNWLSIFGGSAWQWDPTRLQYYLHNFLTSQPDLNLHNPQVQ 191 NAKADWYVWAD+K DG+PP NW S+FGG AW WD R QYYLHNFL+ QPDLNLHNPQVQ Sbjct: 131 NAKADWYVWADAKADGSPPTNWQSVFGGPAWTWDARRGQYYLHNFLSEQPDLNLHNPQVQ 190 Query: 192 EALLAVERFWLERGVDGFRLDTINFYFHDRELRDNPALVPERRNASTAPAVNPYNYQEHI 251 A LA RFWL+RGVDGFR+D INF HD E RDNP + P P+++Q+H+ Sbjct: 191 NAALAAARFWLDRGVDGFRVDAINFAMHDPEFRDNPP-----APYTGTPRTRPFDFQQHL 245 Query: 252 YDKNRPENLEFLKRFRAVMDEFPAIAAVGEVGDSQRGLEIAGEYTSGGDKVHMCYAFEFL 311 Y+++ P+ + FL+R R + D + V EVG E+ +T G +++ Y F+FL Sbjct: 246 YNQSHPDIVRFLERHRELTDSYGGRFTVAEVGGPTPEAEMHA-FTQGQKRLNSAYGFDFL 304 Query: 312 APDRLTPQRVAEVLRDFHRAAPEGWACWAFSNHDVVRHVSRWADGVTDHDAHAKLLASLL 371 ++LTP V + + + GW WAF NHD R +SRW D DA A + LL Sbjct: 305 YANKLTPALVKKAVETWPDTHGTGWPSWAFENHDAPRALSRWVD-AEHRDAFAAMKMLLL 363 Query: 372 MSLRGTVCIYQGEELALAEAELDYEDLQDPYGIQFWPDFKGRDGCRTPMVWESLPDG-GF 430 M LRG ++QGEEL L + E+ Y+ LQDP I WP RDG RTPM W++ + GF Sbjct: 364 MCLRGNAILFQGEELGLTQVEIAYDQLQDPEAIANWPLTLSRDGVRTPMPWKADAENLGF 423 Query: 431 SSATPWLPISQSHIPRAVAVQEGDPASVLHHYRRFLAFRKANPALAKGEIEFVETRGSLL 490 ++ PWLP+ H AV Q S+L+ R +A R ANPAL G +E + +LL Sbjct: 424 TAGRPWLPLGPDHGALAVDRQIAQNGSLLNLTRGLIALRAANPALRAGAMEVLAADEALL 483 Query: 491 GFLRSHGNEKVFCLFNM 507 F R + + C FN+ Sbjct: 484 VFTRIADGQALTCAFNL 500 Lambda K H 0.321 0.138 0.443 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: 1018 Number of extensions: 54 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: 551 Length of database: 541 Length adjustment: 35 Effective length of query: 516 Effective length of database: 506 Effective search space: 261096 Effective search space used: 261096 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 (21.9 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