Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate 3610517 Dshi_3898 alpha amylase catalytic region (RefSeq)
Query= uniprot:H3K096 (538 letters) >FitnessBrowser__Dino:3610517 Length = 526 Score = 374 bits (960), Expect = e-108 Identities = 209/495 (42%), Positives = 285/495 (57%), Gaps = 13/495 (2%) Query: 7 WWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGYD 66 W VIYQ+YPRSFLD+ G G GDL G+T +LDY+A L VDGIWLSPF+ SP D GYD Sbjct: 7 WPENPVIYQVYPRSFLDTTGTGEGDLPGVTRQLDYIAGLGVDGIWLSPFYPSPFCDGGYD 66 Query: 67 VSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKAD 126 ++D+ VD FGTL+DF AL+ +AH L L+VMID V++HTSD H WF +S R D Sbjct: 67 IADHCAVDRRFGTLDDFDALVARAHDLDLRVMIDLVLNHTSDTHDWFAKSLA-REEGFED 125 Query: 127 WFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQLD 186 ++WADP DG+PP+NWLS FG +AW + +R QY LH FL QP +N ++ + Sbjct: 126 VYIWADPCKDGSPPSNWLSFFGEAAWRWHPQRAQYCLHKFLPCQPCLNHYNDRVHERLNR 185 Query: 187 NMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDLSR 246 RFW D GVDGFR D V +F+D RDNPP + EA + P NPYT+Q H++D+ Sbjct: 186 ITRFWRDRGVDGFRYDAVTSFFYDPGFRDNPPAAEAEAALIPGPSNNPYTFQEHIHDVLP 245 Query: 247 PENLDFLKDLRALMDEYPGTTTVGEIGD-DNPLERMAEYTAGGDKLHMAYTFDLLNMPHS 305 E F + LR + P +GEI + +E ++T G D+L Y DL S Sbjct: 246 NECAAFAETLREMAG--PDAYLLGEINNGPRSVEVTCKFT-GPDRLDAGYAIDLPERGPS 302 Query: 306 ASYLREVIERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLFSLRGSV 365 LR+++ R + G W W S HD R+ + +G + A K++ A L +L G + Sbjct: 303 TEVLRDLLTRLEDAEG--WTWWLNS-HDQKRAVSSFG--DGGAADAKMLAAFLCALPGPL 357 Query: 366 CLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPWTDGEQG-GFSPVEPWL 424 L+QGEELG P+A++ + DPY + WP+ GR+G R PM W D + GFS PWL Sbjct: 358 LLFQGEELGQPQAELEKVELTDPYDLMYWPDSVGRNGARAPMAWDDTQPACGFSKAVPWL 417 Query: 425 PMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTRQKG 484 PM AR + V++Q+ DP + L R LA RR L + + L D D + F + G Sbjct: 418 PM-ARAEQGGVAQQEADPASVLAFYRDALA-RRRDLGLAEATMELEDAPDACIRFRLRVG 475 Query: 485 DETLLCVFNLTGQEQ 499 + N++G Q Sbjct: 476 TLVVQVAANMSGAPQ 490 Lambda K H 0.320 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: 909 Number of extensions: 53 Number of successful extensions: 5 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: 538 Length of database: 526 Length adjustment: 35 Effective length of query: 503 Effective length of database: 491 Effective search space: 246973 Effective search space used: 246973 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: 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