Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate AO353_15985 AO353_15985 trehalose-6-phosphate hydrolase
Query= uniprot:A8LLL3 (552 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15985 Length = 549 Score = 269 bits (688), Expect = 2e-76 Identities = 180/535 (33%), Positives = 268/535 (50%), Gaps = 69/535 (12%) Query: 20 WRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKDFGYDI 79 W+ +VIYQIYP+SF G+ GDLLG+V ++ Y+ LGVD +WI+PF SP +D GYDI Sbjct: 4 WQRSVIYQIYPKSFHSHAGNPTGDLLGVVAKLDYLQWLGVDCLWITPFLRSPQRDNGYDI 63 Query: 80 SDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDNPKADW 139 SDY+ +DP +G++AD + LI A G+++M+D+V++HTS +H WF+++RSS DNP D+ Sbjct: 64 SDYYAIDPSYGTMADCELLIAEAGKRGIKLMLDIVVNHTSIEHSWFQQARSSLDNPYRDF 123 Query: 140 YVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLTSQPDLNFHCADVQDALLGV 199 Y+W D PNNW S FGGS W ++A+ QY+LH F +Q DLN+ V+ + + Sbjct: 124 YIWRD------QPNNWESKFGGSAWEYEAQTGQYFLHLFDHTQADLNWDNPQVRAEVFKL 177 Query: 200 GRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPEERNSNIAPEVNPYNHQRHLYSKNQP 259 RFW D+GV GFRLD IN A+ PE+ R Y+ + P Sbjct: 178 MRFWRDKGVGGFRLDVINLISKPADF-------PEDHTDG-----------RRFYT-DGP 218 Query: 260 ENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILGQYTRGET-GVHMCYAFEFLAQEK- 317 E+L + + E + VGE+ LE +Y+R ++ + M + F L + Sbjct: 219 NVHEYLQEMHREVFEGHDLINVGEMSST--SLEHCIRYSRPDSKELSMTFNFHHLKVDYP 276 Query: 318 ------------LTAKRVAEVLNKVDEVASDGWACWAFSNHDVMRHVSRW----DLTPGA 361 L KR+ + A GW + NHD R VSR+ + + Sbjct: 277 NMQKWVRADFDFLELKRILSDW-QTGMQAGGGWNALFWCNHDQPRVVSRFGDDGEHRVVS 335 Query: 362 QRGMLTLLMCLRGSVCLYQGEELGLPEAEVAFDDLQDPYGIEFWPEY------------- 408 + + T L L+G+ +YQGEELG+ F+ ++ +E Y Sbjct: 336 AKMLGTALHFLQGTPFIYQGEELGM--TNPGFERIEQYRDVETLNIYRLKREAGESEASS 393 Query: 409 ------KGRDGCRTPMVWQSDNMSGGFSIHRPWLPVSTEHLGLAVAVQEEAPDALLHHYR 462 K RD RTPM W S + GFS PW+ V + + V Q + ++LHHYR Sbjct: 394 MAAIMQKSRDNSRTPMQW-SALPNAGFSSSEPWIGVPANAMQINVENQLDDTTSVLHHYR 452 Query: 463 RALAFRRAHPALVKGDISDVTVV-GDVISFLRKDPEETVFVAINMSDAPGAVDLP 516 + +A RR+ P + G + V +LR+ E + V N V+LP Sbjct: 453 QLIALRRSEPLIQDGVYRQLLPTHKQVWVYLREGEGERLLVVNNFYGTACEVELP 507 Lambda K H 0.321 0.138 0.451 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: 918 Number of extensions: 54 Number of successful extensions: 6 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: 552 Length of database: 549 Length adjustment: 36 Effective length of query: 516 Effective length of database: 513 Effective search space: 264708 Effective search space used: 264708 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: 53 (25.0 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