Align α-glucosidase (AG31A;BspAG31A) (EC 3.2.1.20) (characterized)
to candidate N515DRAFT_3227 N515DRAFT_3227 alpha-D-xyloside xylohydrolase
Query= CAZy::BAQ19546.1 (790 letters) >FitnessBrowser__Dyella79:N515DRAFT_3227 Length = 956 Score = 241 bits (614), Expect = 2e-67 Identities = 168/534 (31%), Positives = 265/534 (49%), Gaps = 51/534 (9%) Query: 222 FSAEGGQIDYYTLAGPTPKAVLEQYTFLTGRAPIPPKWAIGYHQSRYSYKTEQEVRLLAK 281 FS G +DYY +AG V+ Y +TG+A + P+WA G+ QSR YKT+ E+ AK Sbjct: 377 FSEVGHAVDYYFVAGDNLDQVIAGYREITGKATLLPRWAYGFWQSRERYKTQAEILDTAK 436 Query: 282 TFKEKEIPLDAIHLDIHYM--DGYRVFTFDRSRFPKPEKMVEELKQEGVHIVSIVDPGVK 339 ++E +PLD + D Y D + FD+SRFP + +V++L +H+ ++ K Sbjct: 437 RYRELGLPLDNVVEDWSYWPEDAWGSHDFDKSRFPDAKGLVDQL--HAMHVQLMISVWPK 494 Query: 340 QDPEYHIYKEGIQNDYFCKYLEGEVFFGDV-WPGR---SAFPDFTNEKVRE-WWGQKHAY 394 P Y+E Y + V G+V W G+ +AF D E+ R +W Q Sbjct: 495 FYPTTKNYQELDAKGYIYR---RNVEKGEVDWIGKGYLNAFYDPYAEEARHIYWRQIQEK 551 Query: 395 YANMGIEGIWNDMNEPSVFNE----TKTMDMNVVHENDGDPRTHRELHNIYGMMMGKATY 450 +GI+ W D +EP + + + M G N Y +M Y Sbjct: 552 LGAVGIDAWWLDASEPDTHSNLDIAERKLRMGPTALGPGG-----AFFNSYPLMHTTGVY 606 Query: 451 EGMKKQLGNKRPFLLTRAGFAGVQR-YSAVWTGDNRSFWEHLELSLPMCMNLGVSGVPFV 509 +G ++ G++R F+LTR+ FAG QR +A W+GD S W +L + +N ++G+P Sbjct: 607 DGWRRDHGDRRAFILTRSAFAGQQRNAAATWSGDVASRWSNLHDQISAGLNFSLAGIPNW 666 Query: 510 GPDVGGFA------------HDSNGQLLTRWTQVGAFYPFFRNHSVIESVRQEPW----- 552 D+GGFA D +L RW Q GAF P FR+H Q P+ Sbjct: 667 TTDIGGFALEPRYEKPGAADLDEWRELNLRWFQFGAFSPLFRSHG------QFPYREIYN 720 Query: 553 --AFGEEYEQIIKRYIQLRYQWLPHLYSLFAEANETGVPIMRPLFLEYPDDPHVMNLATQ 610 + G + + Y +LRY+ +P++Y+L + IMR L +++P D V + + Sbjct: 721 LASPGSPVYEALAYYDRLRYRLMPYIYTLAGDTYWKDGTIMRGLAMDFPGDAKVRGIDDE 780 Query: 611 FMVGDNVIVAPIMRPDTYHRVIYLPEG-NWVDYWNEEVLEGGKHHLVEAPLDKLPIYVKQ 669 +M G +VAP+ R +YLP G W ++ + EGG +APL ++P++V+ Sbjct: 781 YMFGPAFLVAPVTEYKATSRPVYLPAGAGWYEFHTGKYHEGGAAIQADAPLARMPLFVRA 840 Query: 670 GTMLVHG-DIKSSTAIPDEKLTLHIYAQTSGEASYSLYEDDGMSFDYEQGSYLR 722 G ++ G DI+ + PD +TL +YA G+ +SLYED+G ++ YE+G Y R Sbjct: 841 GAIVPTGPDIQYTGEKPDAPVTLLVYAGADGQ--FSLYEDEGTTYGYEKGRYSR 892 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: 2047 Number of extensions: 126 Number of successful extensions: 10 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: 956 Length adjustment: 42 Effective length of query: 748 Effective length of database: 914 Effective search space: 683672 Effective search space used: 683672 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