Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_086508157.1 BZY95_RS01095 maltose/maltodextrin ABC transporter substrate-binding protein MalE
Query= reanno::psRCH2:GFF849 (395 letters) >NCBI__GCF_002151265.1:WP_086508157.1 Length = 395 Score = 443 bits (1140), Expect = e-129 Identities = 206/368 (55%), Positives = 275/368 (74%) Query: 26 AIEEGKLVVWINGDKGYKGLAEVGKKFTAETGIPVEVAHPDSATDKFQQAAATGNGPDIF 85 A + +L +W+ +KGY G+ EV ++F +TGI V + +PD+ TD+FQQAA +G GPDI Sbjct: 26 AFDGDRLTIWMGDNKGYDGIREVARQFADDTGIEVRIVNPDNLTDRFQQAAGSGQGPDIV 85 Query: 86 IWAHDRIGEWAKSGLLTPVTPSADTKSGIADFSWQAVTYDNKLWGYPISVETIGLIYNKA 145 IWAHDRIGEWA+SGLL PV+PS+D + DF+W A + + +GYPISVE +GLIYNKA Sbjct: 86 IWAHDRIGEWAQSGLLAPVSPSSDFRERYFDFTWDATLWSGEHYGYPISVEALGLIYNKA 145 Query: 146 LVDTPPKTFDDVMALNEKLAAQGKRAILWDYNNTYFTWPLLSAKGGYVFEHADGGYDVKS 205 LV+TPP++F ++ L+ +LA QG++AIL+DY Y+ W LL+A GGY F + G+DV Sbjct: 146 LVETPPESFAELAQLDAELAEQGRKAILFDYGEPYYGWTLLAANGGYPFRRTEEGFDVDD 205 Query: 206 TGVNNAGAKAGAQVLRDLIDKGVMPKGADYSVAEAAFNKGDSAMMISGPWAWSNIEKSGI 265 GVNN GA GA++L +LI+ GV+P+G DYS+ + FN+G+ A MISGPWAWSN+E+SGI Sbjct: 206 IGVNNEGALQGAELLVELIESGVLPRGTDYSIMDTRFNRGEVAAMISGPWAWSNLEQSGI 265 Query: 266 DFGVAPIPAIDGEPGKPFVGVAAALLNAASPNKDLAVEFLENYLLQVEGLKTVNADVPLG 325 D+GVA +P + E KP GV AA++N ASPN LAVEFLENYLL EG++T N+D LG Sbjct: 266 DYGVALLPKVGEERAKPMFGVMAAMINTASPNDFLAVEFLENYLLSEEGMRTFNSDSTLG 325 Query: 326 AVANTAYMEELSANPHIKATFENAQMGEPMPNVPEMGAFWSSMAAALTNITSGRQDVDAA 385 AVA+ AY +EL ++P+I AT ENA++G PMPN+PEMGAFW++M AL NI SGRQ A Sbjct: 326 AVAHIAYQQELESDPNIAATLENAELGMPMPNIPEMGAFWAAMEPALQNIGSGRQSPREA 385 Query: 386 LDDAAKRI 393 LD AA+R+ Sbjct: 386 LDAAARRM 393 Lambda K H 0.315 0.132 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: 555 Number of extensions: 30 Number of successful extensions: 1 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: 395 Length of database: 395 Length adjustment: 31 Effective length of query: 364 Effective length of database: 364 Effective search space: 132496 Effective search space used: 132496 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 (21.5 bits) S2: 50 (23.9 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