Align α,α-trehalase (MSMEG_4535;MSMEG4528) (EC 3.2.1.28) (characterized)
to candidate AO356_21075 AO356_21075 glucoamylase
Query= CAZy::ABK72415.1 (668 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_21075 Length = 607 Score = 380 bits (976), Expect = e-109 Identities = 235/613 (38%), Positives = 330/613 (53%), Gaps = 35/613 (5%) Query: 38 PFPPIADYGFLSDCETTCLISSAGSVEWLCVPRPDSPSVFGAILDRG-AGHFRLGPYGVS 96 P PI ++G + D T L++ GSV++ C P DSPS+F ++LD AG F+L P Sbjct: 7 PQSPIENHGIIGDMRTAALVNDRGSVDFFCWPEFDSPSIFCSLLDTAQAGIFQLAP---D 63 Query: 97 VPAARR---YLPGSLILETTWQTHTGWLIVRDALVMGPWHDIDTRSRTHRRTPMDWDAEH 153 +P ARR YLP + +L+T W + + + D L +G D Sbjct: 64 LPDARRQQIYLPDTNVLQTRWLSDGAVVELTDLLPIGDSED----------------DLP 107 Query: 154 ILLRTVRCVSGTVELVMSCEPAFDYHRVSATWEYSGPAYGEAIARASRNPDSHPTLRLTT 213 +L+R VR G+ + C DY R + T G A P+LRL Sbjct: 108 VLIRRVRMTIGSATFRLRCAVRHDYARAATTARQDG-------AHICFEAPGQPSLRLCA 160 Query: 214 NLRIGIEGREARARTRLTEGDNVFVALSWSKHPAPQTYEEAADKMWKTSEAWRQWINVGD 273 + + ++G A A LT+G + L P Q + +A + +T WR WI + Sbjct: 161 DQPLTLDGNAAVAEFTLTQGQSAEFLLGGIDDPRLQD-DVSAICLERTLAFWRGWIGQSN 219 Query: 274 FPDHPWRAYLQRSALTLKGLTYSPTGALLAAPTTSLPETPQGERNWDYRYSWIRDSTFAL 333 + WR + RSAL LK LT GA+LAA T LPET GERNWDYRY+WIRD++F + Sbjct: 220 YRGR-WREMVNRSALALKLLTSRKHGAILAAATFGLPETRGGERNWDYRYTWIRDASFTV 278 Query: 334 WGLYTLGLDREADDFFSFIADVSGANNGERHPLQVMYGVGGERSLVEEELHHLSGYDNSR 393 + LG EA+ + ++ + L ++YG+ G L E EL HLSG+ N++ Sbjct: 279 YAFMRLGFVEEANAYMRWLRGRVSDCCDQPTKLNILYGLDGRLELPETELPHLSGFGNAQ 338 Query: 394 PVRIGNGAYNQRQHDIWGTMLDSVYLHAKSREQIPDALWPVLKNQVEEAIKHWKEPDRGI 453 PVRIGN AY Q Q DI+G ++D+VYL K E I W + V++ + W++ D GI Sbjct: 339 PVRIGNLAYQQVQLDIFGELMDAVYLVNKYGEAISHEGWKHTVDVVDQVCEVWQDKDVGI 398 Query: 454 WEVRGEPQHFTSSKIMCWVALDRGSKLAELQGEKSYAQQWRAIAEEIKADVLAR-GVDKR 512 WE+RG+ QHF S++MCWVA+DR +LAE + + +W + I D+ D+ Sbjct: 399 WEMRGDKQHFLHSRLMCWVAVDRAIRLAEKRSLPAPFARWDETRQAIYQDIWTNFWNDEH 458 Query: 513 GVLTQRYGDDALDASLLLAVLTRFLPADDPRIRATVLAIADELTEDGLVLRYRVEETD-D 571 QR G ALD S+LL L RF+ A DPR +T+ AI L DG+V RYR +++ D Sbjct: 459 QHFIQRLGSTALDGSMLLMPLVRFVSARDPRWLSTLDAIEKHLVRDGMVYRYRNDDSPID 518 Query: 572 GLAGEEGTFTICSFWLVSALVEIGEISRAKHLCERLLSFASPLHLYAEEIEPRTGRHLGN 631 GL+G EG+F CSFW V L G + +A+ E+LL +A+PL LYAEE + G HLGN Sbjct: 519 GLSGIEGSFAACSFWYVECLARAGRVEKAQLEFEQLLRYANPLGLYAEEFDSH-GYHLGN 577 Query: 632 FPQAFTHLALINA 644 PQA THLALI+A Sbjct: 578 TPQALTHLALISA 590 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: 1164 Number of extensions: 57 Number of successful extensions: 9 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: 607 Length adjustment: 38 Effective length of query: 630 Effective length of database: 569 Effective search space: 358470 Effective search space used: 358470 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: 54 (25.4 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