Align Probable alpha-glucosidase; EC 3.2.1.20 (uncharacterized)
to candidate 3610517 Dshi_3898 alpha amylase catalytic region (RefSeq)
Query= curated2:Q9Z3R8 (551 letters) >FitnessBrowser__Dino:3610517 Length = 526 Score = 401 bits (1030), Expect = e-116 Identities = 224/495 (45%), Positives = 295/495 (59%), Gaps = 18/495 (3%) Query: 17 WWRGAVIYQIYPRSFQDTNGDGIGDLQGITARLPHIAGLGADAIWISPFFTSPMRDFGYD 76 W VIYQ+YPRSF DT G G GDL G+T +L +IAGLG D IW+SPF+ SP D GYD Sbjct: 7 WPENPVIYQVYPRSFLDTTGTGEGDLPGVTRQLDYIAGLGVDGIWLSPFYPSPFCDGGYD 66 Query: 77 VSNYVDVDPIFGTLEDFDALIAEAHRLGLRVMIDLVLSHTSDRHPWFVESRSSRSNAKAD 136 ++++ VD FGTL+DFDAL+A AH L LRVMIDLVL+HTSD H WF +S +R D Sbjct: 67 IADHCAVDRRFGTLDDFDALVARAHDLDLRVMIDLVLNHTSDTHDWFAKS-LAREEGFED 125 Query: 137 WYVWADSKPDGTPPNNWLSIFGGSAWQWDPTRLQYYLHNFLTSQPDLNLHNPQVQEALLA 196 Y+WAD DG+PP+NWLS FG +AW+W P R QY LH FL QP LN +N +V E L Sbjct: 126 VYIWADPCKDGSPPSNWLSFFGEAAWRWHPQRAQYCLHKFLPCQPCLNHYNDRVHERLNR 185 Query: 197 VERFWLERGVDGFRLDTINFYFHDRELRDNPALVPERRNASTAPAVNPYNYQEHIYDKNR 256 + RFW +RGVDGFR D + +F+D RDNP P+ NPY +QEHI+D Sbjct: 186 ITRFWRDRGVDGFRYDAVTSFFYDPGFRDNPPAAEAEAALIPGPSNNPYTFQEHIHDVLP 245 Query: 257 PENLEFLKRFRAVMDEFPAIAAVGEVGDSQRGLEIAGEYTSGGDKVHMCYAFEFLAPDRL 316 E F + R + P +GE+ + R +E+ ++T G D++ YA + P+R Sbjct: 246 NECAAFAETLREMAG--PDAYLLGEINNGPRSVEVTCKFT-GPDRLDAGYAIDL--PER- 299 Query: 317 TPQRVAEVLRDF--HRAAPEGWACWAFSNHDVVRHVSRWADGVTDHDAHAKLLASLLMSL 374 EVLRD EGW W ++HD R VS + DG A AK+LA+ L +L Sbjct: 300 --GPSTEVLRDLLTRLEDAEGWTWW-LNSHDQKRAVSSFGDGGA---ADAKMLAAFLCAL 353 Query: 375 RGTVCIYQGEELALAEAELDYEDLQDPYGIQFWPDFKGRDGCRTPMVW-ESLPDGGFSSA 433 G + ++QGEEL +AEL+ +L DPY + +WPD GR+G R PM W ++ P GFS A Sbjct: 354 PGPLLLFQGEELGQPQAELEKVELTDPYDLMYWPDSVGRNGARAPMAWDDTQPACGFSKA 413 Query: 434 TPWLPISQSHIPRAVAVQEGDPASVLHHYRRFLAFRKANPALAKGEIEFVETRGSLLGFL 493 PWLP++++ VA QE DPASVL YR LA R+ + LA+ +E + + + F Sbjct: 414 VPWLPMARAE-QGGVAQQEADPASVLAFYRDALA-RRRDLGLAEATMELEDAPDACIRFR 471 Query: 494 RSHGNEKVFCLFNMS 508 G V NMS Sbjct: 472 LRVGTLVVQVAANMS 486 Lambda K H 0.321 0.138 0.443 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: 938 Number of extensions: 51 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: 551 Length of database: 526 Length adjustment: 35 Effective length of query: 516 Effective length of database: 491 Effective search space: 253356 Effective search space used: 253356 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