Align Maltose phosphorylase (EC 2.4.1.8); Trehalose phosphorylase (EC 2.4.1.64) (characterized)
to candidate WP_008992569.1 I215_RS13630 glycoside hydrolase family 65 protein
Query= reanno::Pedo557:CA265_RS24655 (772 letters) >NCBI__GCF_000300875.1:WP_008992569.1 Length = 768 Score = 945 bits (2442), Expect = 0.0 Identities = 448/766 (58%), Positives = 577/766 (75%), Gaps = 5/766 (0%) Query: 2 KNYIKADEWNIIEEGFDPHLNKISESIFSLGNGRMGQRANFEETYTGETLPGNYVAGVYY 61 ++YIK +EW++IEEGF+P K SES+FSLGNG MGQRANFEE Y+GE+ G+Y+AGVYY Sbjct: 3 QDYIKPNEWSLIEEGFNPQKVKSSESLFSLGNGAMGQRANFEEDYSGESFQGSYIAGVYY 62 Query: 62 PDKTRVGWWKNGYPEYFAKVLNAANWIGIEVKLDGEILDLATA-EVSDFKRVLNMHAGYL 120 PDKTRVGWWKNGYPEYFAKVLNA NWIGI V+++GE LDL T +VSD+ R LNM G+ Sbjct: 63 PDKTRVGWWKNGYPEYFAKVLNAPNWIGIHVQVEGETLDLNTCTKVSDYARELNMKQGWY 122 Query: 121 ERTFTAKLKSGKTLKVKSTRFCSIADDEVGAIRYSITPLNFDGRLTLMPFIDGDVKNQDS 180 +R+F A + +G LKVK+TRF S+ EVGAI+Y +TPLN + + P++DG + N+DS Sbjct: 123 QRSFVASMPNGVDLKVKATRFLSMTLTEVGAIKYEVTPLNRSVEVVITPYVDGGITNEDS 182 Query: 181 NYDEKFWDKVADEISGTE--AYIKLRTKKTEFEVCTGSNIELYKNAEKLAINPEAVRKEK 238 N+D+ FW +E+S + AY++ T KT F+VCTG ELY + +K+ + E V + + Sbjct: 183 NWDDAFWQ--INEVSSKDDFAYVRSMTNKTAFDVCTGMLNELYLDDQKVEVKGEVVSESR 240 Query: 239 FVGQTFSLEVKANEEISLVKIAANLSSENYPKESLLKETKSIIAKASAKGFDTLLKEQTE 298 VG ++L++ ++ +LVK A ++S N+ E L++ ++ I+ KA GFD LL+ Q + Sbjct: 241 KVGLKYTLKLSQGQKATLVKFAGYVTSLNHKSEVLVEASEQILIKARNYGFDALLESQIQ 300 Query: 299 AWASKWEESDIIIEGDVSAQQAIRFNIFQLFQTYTGKDDRLNIGPKGFTGEKYGGSTYWD 358 W + W+ +DI I+GDV AQQ IRFNIFQL QTY+GKD RLNIGPKGFTGEKYGGSTYWD Sbjct: 301 EWDAIWQMADITIKGDVKAQQGIRFNIFQLNQTYSGKDSRLNIGPKGFTGEKYGGSTYWD 360 Query: 359 TEAYCVPFYLATAPQEVSKNLLVYRHKQLGKAIENAAKLGFKDGAALYPMVTMNGEECHN 418 TEAYC+PFY+AT ++V++NLL YR+ QL KAIENA KLGF DGAALYPMVTM+GEECHN Sbjct: 361 TEAYCIPFYMATKDEKVARNLLTYRYNQLDKAIENAQKLGFTDGAALYPMVTMDGEECHN 420 Query: 419 EWEITFEEIHRNGAIAFAIFNYIRYTGDESYLSDFGLEVLIGIARFWKQRVNWSNDKQQY 478 EWEITFEEIHRNG+I FAI+NY R+T D+SY+ + GLEV+I I+RFWKQR N+S DK QY Sbjct: 421 EWEITFEEIHRNGSILFAIYNYTRFTADKSYIPEMGLEVMIAISRFWKQRANFSTDKNQY 480 Query: 479 VMLGVTGPNEYENNVNNNWYTNILATWCMKYATEAAEIVKTQQPEKYNSLLKSLNFDQKE 538 V+LGVTGPNEYENNVNNNW+TN +A WCM+Y + E+VK + + ++K +E Sbjct: 481 VILGVTGPNEYENNVNNNWFTNYIAKWCMEYTAQTIEMVKEDYADDFARVIKKTKLSDQE 540 Query: 539 FADWADIIEKMYYPQDEKLGIFLQQDGYLDKEQTLVKDLPASERPINQKWSWDRILRSCF 598 A W ++ E MY+P DEK ++LQQDG+LDKE V +L ++RPINQKWSWDRILRS + Sbjct: 541 VAKWLEVAENMYFPFDEKRNVYLQQDGFLDKELVPVSELSKTQRPINQKWSWDRILRSPY 600 Query: 599 IKQADVLQGLYFFEEDYDLDTLKRNFDFYEPRTVHESSLSPCVHSILAAKLNDEARAYEF 658 IKQADVLQG YFFE+ + L+ L+R+FDFYEP TVHESSLSPCVHSI AA L+ +AY F Sbjct: 601 IKQADVLQGFYFFEDQFSLEELERHFDFYEPYTVHESSLSPCVHSIQAAVLDRMDQAYTF 660 Query: 659 YLRTARLDLDDYNNDTEDGLHITSMAGTWMSVVEGFAGMRVREGKLQFNPFLPGKWKSFS 718 YLRT+RLDLDDYN + +GLHITSMAGTWMSVVEGF GMRV+ L F+P +P +W +FS Sbjct: 661 YLRTSRLDLDDYNKEVHEGLHITSMAGTWMSVVEGFGGMRVKNDCLSFDPKIPKEWDAFS 720 Query: 719 FTIGFRGATLKINITESGISIKNNAAVDLEIGIRNQLYKLAGNTEI 764 F + FR LK+ ++ SG + K +L+I I Q L + +I Sbjct: 721 FKVNFRNQILKVEVSHSGTTFKLEGDRELKILINGQSTMLQPDNKI 766 Lambda K H 0.317 0.134 0.401 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: 1803 Number of extensions: 71 Number of successful extensions: 3 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: 772 Length of database: 768 Length adjustment: 41 Effective length of query: 731 Effective length of database: 727 Effective search space: 531437 Effective search space used: 531437 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 55 (25.8 bits)
This GapMind analysis is from Sep 24 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