Align Putative alpha-glucosidase AglA (characterized, see rationale)
to candidate 3610517 Dshi_3898 alpha amylase catalytic region (RefSeq)
Query= uniprot:I7EUW4 (552 letters) >FitnessBrowser__Dino:3610517 Length = 526 Score = 372 bits (956), Expect = e-107 Identities = 206/504 (40%), Positives = 287/504 (56%), Gaps = 11/504 (2%) Query: 19 WWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVDAIWISPFFTSPMKDFGYD 78 W VIYQ+YPRS+ D+ G G GDL G+T++L +IA LGVD IW+SPF+ SP D GYD Sbjct: 7 WPENPVIYQVYPRSFLDTTGTGEGDLPGVTRQLDYIAGLGVDGIWLSPFYPSPFCDGGYD 66 Query: 79 VSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSDQHAWFGESRQSRDNARAD 138 ++D+C VD FG+L +FD LVA AH L LRVMIDLVL+HTSD H WF +S +R+ D Sbjct: 67 IADHCAVDRRFGTLDDFDALVARAHDLDLRVMIDLVLNHTSDTHDWFAKS-LAREEGFED 125 Query: 139 WYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLVSQPDLNFHSPAVQDALLD 198 Y+WADP DG+PP+NWLS FG +AW+W P+R QY LH FL QP LN ++ V + L Sbjct: 126 VYIWADPCKDGSPPSNWLSFFGEAAWRWHPQRAQYCLHKFLPCQPCLNHYNDRVHERLNR 185 Query: 199 VTRFWLERGVDGFRLDTINFYYHDAELRSNPALPPEQRNATIAPSVNPYNHQEHLYSKNQ 258 +TRFW +RGVDGFR D + +++D R NP + PS NPY QEH++ Sbjct: 186 ITRFWRDRGVDGFRYDAVTSFFYDPGFRDNPPAAEAEAALIPGPSNNPYTFQEHIHDVLP 245 Query: 259 PENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGSYTAANTGVHMCYAFELLAKDVL 318 E AF R + P +GE+ + R +E+ +T + + YA +L + Sbjct: 246 NECAAFAETLREMAG--PDAYLLGEINNGPRSVEVTCKFTGPDR-LDAGYAIDLPERGPS 302 Query: 319 TASRLAEVFAEVDRVAANGWACWAFSNHDVIRHSSRWGLNPAAQRLFTTMMMC-LRGTTC 377 T L ++ ++ A GW W ++HD R S +G AA +C L G Sbjct: 303 T-EVLRDLLTRLE--DAEGWTWW-LNSHDQKRAVSSFGDGGAADAKMLAAFLCALPGPLL 358 Query: 378 IYQGEELGLPEADIAFEDLQDPYGIEFWPEFKGRDGCRTPMVWEPSNGSGGFSAGKPWLP 437 ++QGEELG P+A++ +L DPY + +WP+ GR+G R PM W+ + + GFS PWLP Sbjct: 359 LFQGEELGQPQAELEKVELTDPYDLMYWPDSVGRNGARAPMAWDDTQPACGFSKAVPWLP 418 Query: 438 VSPEHLNLSVASQEADPDAMLHHYRRAIALRKAHPALAVGTHDQLRAEGNVAFFTRQDRD 497 ++ VA QEADP ++L YR A+A R+ LA T + A F + Sbjct: 419 MARAEQG-GVAQQEADPASVLAFYRDALA-RRRDLGLAEATMELEDAPDACIRFRLRVGT 476 Query: 498 EVIFCAFNLGDIPAEITLPEGTWR 521 V+ A N+ P ++ +G R Sbjct: 477 LVVQVAANMSGAPQDLAPRQGAKR 500 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: 998 Number of extensions: 61 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: 526 Length adjustment: 35 Effective length of query: 517 Effective length of database: 491 Effective search space: 253847 Effective search space used: 253847 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