Align α,α-trehalase (MSMEG_4535;MSMEG4528) (EC 3.2.1.28) (characterized)
to candidate Pf6N2E2_6094 Glucoamylase (EC 3.2.1.3)
Query= CAZy::ABK72415.1 (668 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6094 Length = 529 Score = 328 bits (841), Expect = 4e-94 Identities = 197/493 (39%), Positives = 268/493 (54%), Gaps = 12/493 (2%) Query: 154 ILLRTVRCVSGTVELVMSCEPAFDYHRVSATWEYSGPAYGEAIARASRNPDSHPTLRLTT 213 +L+R V G+ M C DY R + T A P+LRL + Sbjct: 30 VLMRKVHMTVGSATFRMRCAVRHDYARAATTARQDA-------AHICFEAPGQPSLRLCS 82 Query: 214 NLRIGIEGREARARTRLTEGDNVFVALSWSKHPAPQTYEEAADKMWKTSEAWRQWINVGD 273 + + ++G A A L +G + L P Q + +A + +T WR WI Sbjct: 83 DQPMTLDGNAAVAEFTLAQGQSAEFLLGGIDDPRLQD-DVSAICLERTLAFWRGWIGQST 141 Query: 274 FPDHPWRAYLQRSALTLKGLTYSPTGALLAAPTTSLPETPQGERNWDYRYSWIRDSTFAL 333 + WR + RSAL LK LT GA+LAA T LPET GERNWDYRY+WIRDS+F + Sbjct: 142 YRGR-WREVVNRSALALKLLTSRKHGAILAAATFGLPETRGGERNWDYRYTWIRDSSFTV 200 Query: 334 WGLYTLGLDREADDFFSFIADVSGANNGERHPLQVMYGVGGERSLVEEELHHLSGYDNSR 393 + LG EA+ + ++ + L ++YG+ G L E EL HLSG+ N+R Sbjct: 201 YAFMRLGFVEEANAYMRWLRGRVSDCCDQPTKLNILYGLDGRLELPETELPHLSGFGNAR 260 Query: 394 PVRIGNGAYNQRQHDIWGTMLDSVYLHAKSREQIPDALWPVLKNQVEEAIKHWKEPDRGI 453 PVRIGN AY Q Q DI+G ++D+VYL K E I W + V++ K W++ D GI Sbjct: 261 PVRIGNLAYKQVQLDIFGELMDAVYLVNKYGEAISHQGWKHTVDVVDQVCKVWQDKDVGI 320 Query: 454 WEVRGEPQHFTSSKIMCWVALDRGSKLAELQGEKSYAQQWRAIAEEIKADVLAR-GVDKR 512 WE+RG+ QHF S++MCWVA+DR +LAE + + +W + I D+ D+ Sbjct: 321 WEMRGDKQHFLHSRLMCWVAVDRAIRLAEKRSLPAPFARWDETRQAIYQDIWTNFWNDEH 380 Query: 513 GVLTQRYGDDALDASLLLAVLTRFLPADDPRIRATVLAIADELTEDGLVLRYRVEETD-D 571 QR G ALD S+LL L RF+ A DPR +T+ AI L DG+V RYR +++ D Sbjct: 381 QHFIQRLGSTALDGSMLLMPLVRFVSARDPRWLSTLDAIEKNLVRDGMVYRYRNDDSPID 440 Query: 572 GLAGEEGTFTICSFWLVSALVEIGEISRAKHLCERLLSFASPLHLYAEEIEPRTGRHLGN 631 GL G EG+F CSFW V L G + +A+ E+LL +A+PL LYAEE + G HLGN Sbjct: 441 GLRGIEGSFAACSFWYVECLARAGRVEKAQLEFEQLLRYANPLGLYAEEFDSH-GYHLGN 499 Query: 632 FPQAFTHLALINA 644 PQA HLALI+A Sbjct: 500 TPQALPHLALISA 512 Lambda K H 0.319 0.135 0.426 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: 980 Number of extensions: 48 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: 668 Length of database: 529 Length adjustment: 37 Effective length of query: 631 Effective length of database: 492 Effective search space: 310452 Effective search space used: 310452 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 (21.7 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