Align Putative alpha-glucosidase AglA (characterized, see rationale)
to candidate Ga0059261_1580 Ga0059261_1580 Glycosidases
Query= uniprot:I7EUW4 (552 letters) >FitnessBrowser__Korea:Ga0059261_1580 Length = 541 Score = 528 bits (1359), Expect = e-154 Identities = 258/506 (50%), Positives = 327/506 (64%), Gaps = 11/506 (2%) Query: 9 PAQVLAADPDWWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVDAIWISPFF 68 P + DWWRGAVIYQIYPRS+ DSNGDGIGDL G+ L H+A+LG DAIW+SPFF Sbjct: 6 PMPATETNRDWWRGAVIYQIYPRSFADSNGDGIGDLPGVAAHLDHVAALGADAIWLSPFF 65 Query: 69 TSPMKDFGYDVSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSDQHAWFGES 128 TSPM+DFGYD++DYC VDP+FG+L++FD ++ AH LGL+V+ID V SHTSDQH WF ES Sbjct: 66 TSPMRDFGYDIADYCGVDPVFGTLADFDAVIEKAHALGLKVIIDQVYSHTSDQHEWFKES 125 Query: 129 RQSRDNARADWYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLVSQPDLNFH 188 R SRDNA+ADWYVWAD + DG+PP NW S+FGG AW WD RR QYYLHNFL QPDLN H Sbjct: 126 RSSRDNAKADWYVWADAKADGSPPTNWQSVFGGPAWTWDARRGQYYLHNFLSEQPDLNLH 185 Query: 189 SPAVQDALLDVTRFWLERGVDGFRLDTINFYYHDAELRSNPALPPEQRNATIAPSVNPYN 248 +P VQ+A L RFWL+RGVDGFR+D INF HD E R NP P T P P++ Sbjct: 186 NPQVQNAALAAARFWLDRGVDGFRVDAINFAMHDPEFRDNPPAP-----YTGTPRTRPFD 240 Query: 249 HQEHLYSKNQPENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGSYTAANTGVHMCY 308 Q+HLY+++ P+ + FL R R L D Y + V EVG E M ++T ++ Y Sbjct: 241 FQQHLYNQSHPDIVRFLERHRELTDSYGGRFTVAEVGGPTPEAE-MHAFTQGQKRLNSAY 299 Query: 309 AFELLAKDVLTASRLAEVFAEVDRVAANGWACWAFSNHDVIRHSSRWGLNPAAQRLFTTM 368 F+ L + LT + + + GW WAF NHD R SRW ++ + F M Sbjct: 300 GFDFLYANKLTPALVKKAVETWPDTHGTGWPSWAFENHDAPRALSRW-VDAEHRDAFAAM 358 Query: 369 ----MMCLRGTTCIYQGEELGLPEADIAFEDLQDPYGIEFWPEFKGRDGCRTPMVWEPSN 424 +MCLRG ++QGEELGL + +IA++ LQDP I WP RDG RTPM W+ Sbjct: 359 KMLLLMCLRGNAILFQGEELGLTQVEIAYDQLQDPEAIANWPLTLSRDGVRTPMPWKADA 418 Query: 425 GSGGFSAGKPWLPVSPEHLNLSVASQEADPDAMLHHYRRAIALRKAHPALAVGTHDQLRA 484 + GF+AG+PWLP+ P+H L+V Q A ++L+ R IALR A+PAL G + L A Sbjct: 419 ENLGFTAGRPWLPLGPDHGALAVDRQIAQNGSLLNLTRGLIALRAANPALRAGAMEVLAA 478 Query: 485 EGNVAFFTRQDRDEVIFCAFNLGDIP 510 + + FTR + + CAFNLG P Sbjct: 479 DEALLVFTRIADGQALTCAFNLGKTP 504 Lambda K H 0.321 0.137 0.444 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: 1039 Number of extensions: 53 Number of successful extensions: 4 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: 541 Length adjustment: 36 Effective length of query: 516 Effective length of database: 505 Effective search space: 260580 Effective search space used: 260580 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 (21.9 bits) S2: 52 (24.6 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