Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate Pf1N1B4_835 Trehalose-6-phosphate hydrolase (EC 3.2.1.93)
Query= uniprot:A8LLL3 (552 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_835 Length = 549 Score = 280 bits (715), Expect = 1e-79 Identities = 184/536 (34%), Positives = 273/536 (50%), Gaps = 69/536 (12%) Query: 20 WRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKDFGYDI 79 W+ +VIYQIYP+SF G+ GDLLG+V ++ Y+ LGVD +WI+PF SP +D GYDI Sbjct: 4 WQRSVIYQIYPKSFHSHAGNPTGDLLGVVAKLDYLHWLGVDCLWITPFLRSPQRDNGYDI 63 Query: 80 SDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDNPKADW 139 SDY+ +DP +G++AD + LI A G+++M+D+V++HTS +H WF+++RSS DNP D+ Sbjct: 64 SDYYAIDPSYGTMADCELLIAEAGKRGIKLMLDIVVNHTSIEHTWFQQARSSLDNPYRDF 123 Query: 140 YVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLTSQPDLNFHCADVQDALLGV 199 Y+W D PNNW S FGGS W ++A+ QYYLH F +Q DLN+ V+ + + Sbjct: 124 YIWRD------QPNNWESKFGGSAWEYEAQTGQYYLHLFDHTQADLNWDNPQVRAEVFKM 177 Query: 200 GRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPEERNSNIAPEVNPYNHQRHLYSKNQP 259 RFW D+GV GFRLD IN A+ PE+ + R Y+ + P Sbjct: 178 MRFWRDKGVGGFRLDVINLISKPADF-------PEDNSDG-----------RRFYT-DGP 218 Query: 260 ENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILGQYTRGET-GVHMCYAFEFLAQEK- 317 E+L + + E + VGE+ LE +Y+R E+ + M + F L + Sbjct: 219 NVHEYLQQMHREVFEGHDLINVGEMSST--SLEHCIRYSRPESKELSMTFNFHHLKVDYP 276 Query: 318 ------------LTAKRVAEVLNKVDEVASDGWACWAFSNHDVMRHVSRW----DLTPGA 361 L KR+ + A GW + NHD R VSR+ + + Sbjct: 277 NLQKWVRADFDFLALKRILSDW-QTGMQAGGGWNALFWCNHDQPRVVSRFGHDGEHRVVS 335 Query: 362 QRGMLTLLMCLRGSVCLYQGEELGLPEAEVAFDDLQDPYGIEFWPEY------------- 408 + + T L L+G+ +YQGEELG+ FD + +E + Sbjct: 336 AKMLGTALHFLQGTPFVYQGEELGM--TNPGFDHIDQYRDVETLNIFRLKREAGSSDVDN 393 Query: 409 ------KGRDGCRTPMVWQSDNMSGGFSIHRPWLPVSTEHLGLAVAVQEEAPDALLHHYR 462 K RD RTPM W ++ + GFS PW+ V + VA Q + PD++LHHYR Sbjct: 394 MAAIMQKSRDNGRTPMHWNTE-PNAGFSAVEPWIGVPANAAQINVAHQLDDPDSVLHHYR 452 Query: 463 RALAFRRAHPALVKGDISDVTVVGDVI-SFLRKDPEETVFVAINMSDAPGAVDLPP 517 + +A RR+ + G + I +++R+ E + V N P V+LPP Sbjct: 453 QLIALRRSETLMSDGVYRQLLPEHTQIWAYVREGQGERLLVLNNFYGTPCEVELPP 508 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: 999 Number of extensions: 63 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