Align Putative bacterial solute-binding protein 1 family (characterized, see rationale)
to candidate GFF772 PGA1_c07860 alpha-glucosides-binding periplasmic protein AglE
Query= uniprot:A8LLL6 (452 letters) >FitnessBrowser__Phaeo:GFF772 Length = 450 Score = 634 bits (1636), Expect = 0.0 Identities = 299/452 (66%), Positives = 361/452 (79%), Gaps = 2/452 (0%) Query: 1 MRHTLHASAAALALSAGMAGAGGHLAFTPGEGEFNWDSYQAFAEATDLSGQDLSIFGPWL 60 M+ +L A+A LALSAG+A A G L F GEGEFNW+S++A +ATDLSG+ +++FGPWL Sbjct: 1 MKRSLLAAAGVLALSAGLAQAEGALTFPVGEGEFNWESFEAL-KATDLSGEQVTVFGPWL 59 Query: 61 AGEADAFSNLVAFFNEATGANATYVGSDSLEQQIVIDAEAGSAPDLTVFPQPGLATTMAA 120 + + ++A+F EATGA+ Y GSDS EQQIV+DAEAGSAP++ VFPQPGL + MAA Sbjct: 60 GPDQELVEKVLAYFAEATGADVRYTGSDSFEQQIVVDAEAGSAPNVAVFPQPGLVSDMAA 119 Query: 121 RGFLTPLPDGTDDWLRENYAAGQSWIDLGTYADGSGNDQLYGFFFNVNVKSLVWYIPENF 180 RGF+ PL T DW+RENYAAG SW+DL T+ GN+ ++G F+ V+VKSLVWY+PE F Sbjct: 120 RGFIAPLGSETADWVRENYAAGDSWVDLSTFTGPDGNEDVFGLFYKVDVKSLVWYVPETF 179 Query: 181 EDFDYEVPETMEEFKALMDQMVEDGQTPLCVGLGSGGATGWPATDWVEDLMLRTQPPEVY 240 EDF Y++P++MEE KAL DQMV DG TP C+GLGSGGATGWPATDWVED+MLRTQ P VY Sbjct: 180 EDFGYDIPQSMEELKALTDQMVADGNTPWCIGLGSGGATGWPATDWVEDMMLRTQDPGVY 239 Query: 241 DAWVSNEMPFDDPRVVAAIEEYGSFTRNDDYVVGNANDTASVDFRESPLGLFASPPACMM 300 D WVSNE+PF DPRVV AIEE+G F RNDDYV G A AS DFR+SP GLFASPP C+M Sbjct: 240 DQWVSNEIPFTDPRVVNAIEEFGYFARNDDYVSGGAGAVASTDFRDSPKGLFASPPQCLM 299 Query: 301 HRQASFIPAYFPEGTELGEDADFFYFPAFEEKDLGRPVLGAGTLFAITNENPAASAFIEF 360 HRQASFIPA+FPEGTE+G DADFFYFPA+ EKDLG PVLGAGTL++ITN++ A A +EF Sbjct: 300 HRQASFIPAFFPEGTEVGLDADFFYFPAYAEKDLGSPVLGAGTLWSITNDSKGARALMEF 359 Query: 361 LKTPFAHEIMMAQDGFLTPFKGANPAAYASDTLRGQGEILTNATTFRFDGSDLMPGGVGA 420 LK+P HE+ MAQ GFLTP KG N YA+DTL+ GEIL +A TFRFD SDLMPGGVGA Sbjct: 360 LKSPIGHEVWMAQQGFLTPHKGVNTDVYATDTLKKMGEILLSADTFRFDASDLMPGGVGA 419 Query: 421 GTFWTGMVDYSSGAKSAADVASEIQASWESLK 452 G+FWTGMV Y+ G A +VA+EIQ+SW++LK Sbjct: 420 GSFWTGMVGYAGGT-PAEEVAAEIQSSWDALK 450 Lambda K H 0.317 0.134 0.413 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: 854 Number of extensions: 42 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: 452 Length of database: 450 Length adjustment: 33 Effective length of query: 419 Effective length of database: 417 Effective search space: 174723 Effective search space used: 174723 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: 51 (24.3 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