Align 6-phospho-α-glucosidase (Pagl;CAC3426) (EC 3.2.1.122) (characterized)
to candidate BWI76_RS27540 BWI76_RS27540 glycoside hydrolase
Query= CAZy::AAK81356.1 (445 letters) >FitnessBrowser__Koxy:BWI76_RS27540 Length = 459 Score = 167 bits (422), Expect = 8e-46 Identities = 121/467 (25%), Positives = 222/467 (47%), Gaps = 55/467 (11%) Query: 6 ICIVGGGSRYTPDMLAMLCNQKERFPLRKIVLYDNESERQETVGNYAKILFKEYYPELEE 65 + ++GGG + + L R L ++V D+ +E G A+ +F P++ Sbjct: 3 LTVLGGGGVRSAFLAKSLAYNAHRIGLTEVVFLDSSAENLAIFGEIARYVFNAIRPDIHF 62 Query: 66 VIWTTDEKEAFEDIDFALMQIRAGRLKMREKDEKISLKHGCLGQETCGAGGFAYGLRSVP 125 + T+D A ++ + + +R G + R +DE+I+L+H LGQET GAGGFA +RS+P Sbjct: 63 SV-TSDPVPALKNSHYVITTLRVGGDESRIRDERIALEHNTLGQETTGAGGFAMAMRSIP 121 Query: 126 AVIDLIKSIRTYSPKCWIL-NYSNPAAIVAEA-TKRVFPNDYRIINICDMPIAIMDIYAA 183 A+++ + I ++ + IL N++NP+ +V EA K F R+ ICD P ++ A Sbjct: 122 AILNYCRLIEEHAAEDAILFNFTNPSGLVTEAIIKSGFKR--RVYGICDAPSELIRELPA 179 Query: 184 VLGLKRRDLEPKYFGLNHFGWFTHILDKKTGENYLPKLREILKTPVDVQTEPLFQEKSWK 243 +LG RDL + +GLNHF WFTH + GE+ +L + + L+++ + + Sbjct: 180 ILGCDERDLGVECYGLNHFSWFTHFTVR--GEDVTERL---------IASPDLYRKTAMQ 228 Query: 244 STFEFMSQMINDYDEYLPNTYLQYYLY-PAKMRNKENPEYTRANEVMDGNE--------- 293 F +++ D+ L N YL YY Y ++ +N TR ++ N Sbjct: 229 ---YFSPELVQLCDKQLLNEYLYYYYYREVALKAIQNAPETRGEQIARINHDMREELRTV 285 Query: 294 ------------------KETYERMHKIISLGKIHGTKYELT-------SDVGCHAEYIV 328 + M K H T+ LT D G +A + Sbjct: 286 DVKANPEAAFTLWMKHYLRRENSYMQNESQQEKFH-TREPLTLKQFIEEPDTGGYAGVAL 344 Query: 329 DLATAIANNTNEIFLIITENKGTINNVSKDMMVEVPCRVGSNGVEPLVVGSIPAFYKGLM 388 D+ A+ + + ++ N GT++ + D ++E+ C + +G++P+ +P K ++ Sbjct: 345 DILEAVNSTATKRIVVSMSNNGTLDFLRPDDVIEISCDLSKDGLKPVTPKHVPTAQKNMI 404 Query: 389 ENQYAYEKLSVDACLEGSYQKALQALVLNRTVVNTDVAKELLKDLIE 435 + YE+L+V A L+ A++AL+ + V + +AK L++ ++ Sbjct: 405 ASVKEYERLAVAAILQRDKSLAVRALMAHPLVGSYSLAKTLVEAYLD 451 Lambda K H 0.319 0.136 0.406 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: 494 Number of extensions: 27 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 445 Length of database: 459 Length adjustment: 33 Effective length of query: 412 Effective length of database: 426 Effective search space: 175512 Effective search space used: 175512 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 (21.7 bits) S2: 51 (24.3 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