Align α,α-trehalase (MSMEG_4535;MSMEG4528) (EC 3.2.1.28) (characterized)
to candidate Pf1N1B4_153 Glucoamylase (EC 3.2.1.3)
Query= CAZy::ABK72415.1 (668 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_153 Length = 607 Score = 371 bits (952), Expect = e-107 Identities = 237/607 (39%), Positives = 324/607 (53%), Gaps = 37/607 (6%) Query: 45 YGFLSDCETTCLISSAGSVEWLCVPRPDSPSVFGAILDRG-AGHFRLGPYGVSVPAARR- 102 +G + D + L++ GSV++ C P DSPS+F A+LD AG F+L P +P ARR Sbjct: 14 HGIIGDMRSAALVNDKGSVDFFCWPEFDSPSIFCALLDSPEAGIFQLAP---DLPDARRE 70 Query: 103 --YLPGSLILETTWQTHTGWLIVRDALVMGPWHDIDTRSRTHRRTPMDWDAEHILLRTVR 160 YLP + +L+T W + + V D L +G D PM L+R VR Sbjct: 71 QIYLPDTNVLQTRWMSDHAVVEVTDLLPIGDSED---------DLPM-------LMRRVR 114 Query: 161 CVSGTVELVMSCEPAFDYHRVSATWEYSGPAYGEAIARASR-NPDSHPTLRLTTNLRIGI 219 VSG + M C DY R P A R+ P ++L +N + I Sbjct: 115 VVSGQATIRMRCAVRHDYARA--------PTKARARDRSVYFEATGQPAMQLCSNQSLRI 166 Query: 220 EGREARARTRLTEGDNVFVALSWSKHPAPQTYEEAADKMWKTSEAWRQWINVGDFPDHPW 279 EG A A L E D L A AA + +T + WR WI ++ W Sbjct: 167 EGHAAVAEFIL-EQDQSAEFLLGGVDDARFKEGAAALCLERTLKFWRDWIGQSNYRGR-W 224 Query: 280 RAYLQRSALTLKGLTYSPTGALLAAPTTSLPETPQGERNWDYRYSWIRDSTFALWGLYTL 339 R + RSAL LK LT GA+LAA T LPETP GERNWDYRY+WIRD++F ++ L Sbjct: 225 REMVNRSALALKLLTSRKHGAILAAATFGLPETPGGERNWDYRYTWIRDASFTVYAFMRL 284 Query: 340 GLDREADDFFSFIADVSGANNGERHPLQVMYGVGGERSLVEEELHHLSGYDNSRPVRIGN 399 G EA+ + ++ +G+ L ++Y + G + L E EL HL+G+ + PVRIGN Sbjct: 285 GFVEEANAYTRWLRGRVRDCHGKTMKLNILYAIDGRQELPEVELPHLAGHGGATPVRIGN 344 Query: 400 GAYNQRQHDIWGTMLDSVYLHAKSREQIPDALWPVLKNQVEEAIKHWKEPDRGIWEVRGE 459 AY+Q Q DI+G ++D+VYL K E I W V++ + W++ D GIWE+RGE Sbjct: 345 QAYDQIQLDIFGELMDAVYLVNKHGEAISHEGWKHTVEVVDQVCETWQQKDVGIWEMRGE 404 Query: 460 PQHFTSSKIMCWVALDRGSKLAELQGEKSYAQQWRAIAEEIKADVLAR-GVDKRGVLTQR 518 HF S++MCWVA+DR +LA + + +W + I AD+ + ++RG Q Sbjct: 405 QYHFLHSRLMCWVAVDRAIRLASKRSLPAPFARWDQTRQAIYADIWSNFWNEERGHFVQH 464 Query: 519 YGDDALDASLLLAVLTRFLPADDPRIRATVLAIADELTEDGLVLRYRVEETD-DGLAGEE 577 G LD S+LL L RF+ A DPR AT+ AI L G+V RYR +++ DGL G E Sbjct: 465 IGGTGLDGSMLLMPLVRFVSAKDPRWIATLEAIEKSLVRAGMVYRYRNDDSQIDGLPGTE 524 Query: 578 GTFTICSFWLVSALVEIGEISRAKHLCERLLSFASPLHLYAEEIEPRTGRHLGNFPQAFT 637 G F CSFW V L G++ +A E+LL +A+PL LYAEE + RHLGN PQA T Sbjct: 525 GAFAACSFWYVECLARAGQVEKAHLEFEQLLKYANPLGLYAEEFDSH-ARHLGNTPQALT 583 Query: 638 HLALINA 644 HLALI+A Sbjct: 584 HLALISA 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: 1121 Number of extensions: 44 Number of successful extensions: 7 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