Align α-glucosidase (AG31A;BspAG31A) (EC 3.2.1.20) (characterized)
to candidate Echvi_4038 Echvi_4038 Alpha-glucosidases, family 31 of glycosyl hydrolases
Query= CAZy::BAQ19546.1 (790 letters) >FitnessBrowser__Cola:Echvi_4038 Length = 955 Score = 264 bits (674), Expect = 2e-74 Identities = 176/535 (32%), Positives = 273/535 (51%), Gaps = 49/535 (9%) Query: 220 YSFSAEGGQ-IDYYTLAGPTPKAVLEQYTFLTGRAPIPPKWAIGYHQSRYSYKTEQEVRL 278 Y+F +E G+ +DYY +AG ++ Y LTG+A I PKWA+G+ QSR YKT++E+ Sbjct: 367 YAFRSEAGKMLDYYFVAGQDMDELISGYRQLTGKAQIMPKWAMGFWQSRERYKTQEELLS 426 Query: 279 LAKTFKEKEIPLDAIHLDIHYM--DGYRVFTFDRSRFPKPEKMVEEL-KQEGVHIVSIVD 335 ++++ IPLD I D Y D + FD +RFP P M++++ Q HI+ V Sbjct: 427 TVAEYRKRHIPLDNIVQDWSYWPEDAWGSHDFDPARFPDPVGMIDQVHDQYHAHIMISVW 486 Query: 336 PGVKQDPEYH--------IYKEGIQNDYFCKYLEGEVFFGDVWPGRSAFPDFTNEKVRE- 386 P + E++ +YK+ I N EG + S F D N RE Sbjct: 487 PKFYEGIEHYKQFDEKGWLYKQNILNRQRDWIGEGYI---------STFYDAFNPGAREL 537 Query: 387 WWGQKHAYYANMGIEGIWNDMNEPSVFNETKTMDMNVVHENDGDPRTHRELHNIYGMMMG 446 +W Q + GI+ W D EP V + + N T E N Y ++ Sbjct: 538 FWKQINEKLYQKGIDAWWLDATEPDVLSNASIQHRKTL-MNPTALGTATEYFNGYPLVNA 596 Query: 447 KATYEGMKKQLGNKRPFLLTRAGFAGVQRY-SAVWTGDNRSFWEHLELSLPMCMNLGVSG 505 K Y G + + R F+LTR+ F G+QRY +A W+GD + ++ LE +P +N +SG Sbjct: 597 KGIYHGQRATNPDDRVFILTRSAFPGIQRYGAATWSGDISARFDELEQQIPAGLNFSLSG 656 Query: 506 VPFVGPDVGGF-------AHDSNGQLL-------TRWTQVGAFYPFFRNHSVIESVRQEP 551 +P+ D+GGF D G+ L TRW Q G F P +R+H + +E Sbjct: 657 LPYWTTDIGGFFVEDKYDRPDPKGEALEEWRELNTRWYQYGTFTPLYRSHG--QYPYREV 714 Query: 552 WAFGEE----YEQIIKRYIQLRYQWLPHLYSLFAEANETGVPIMRPLFLEYPDDPHVMNL 607 + E Y I+ Y +LRY+ +P++YSL + + IMRPL +++ DP V + Sbjct: 715 FNIAPEGHPAYRSIV-FYNKLRYRLMPYIYSLTGKVHHDDYTIMRPLIMDFDHDPRVGQI 773 Query: 608 ATQFMVGDNVIVAPIMRPDTYHRVIYLP-EGNWVDYWNEEVLEGGKHHLVEAPLDKLPIY 666 QFM G +++V P+ + +R IY P E W D E GG +EAP DK+P++ Sbjct: 774 KDQFMFGPSILVNPVYHYEATNRDIYFPKETGWYDLLTGEYQAGGVEKNIEAPYDKIPLF 833 Query: 667 VKQGTMLVHG-DIKSSTAIPDEKLTLHIYAQTSGEASYSLYEDDGMSFDYEQGSY 720 VK G+++ G I+ + P +++TL++YA +G + LYED G +++YEQG + Sbjct: 834 VKAGSIIPFGPKIEYTDEKPADEITLYVYAGQNG--YFELYEDQGSNYEYEQGQF 886 Lambda K H 0.320 0.138 0.428 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: 2216 Number of extensions: 154 Number of successful extensions: 9 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: 790 Length of database: 955 Length adjustment: 42 Effective length of query: 748 Effective length of database: 913 Effective search space: 682924 Effective search space used: 682924 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: 56 (26.2 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