Align Inositol transport system sugar-binding protein (characterized)
to candidate SMa0218 SMa0218 ABC transporter substrate-binding protein
Query= reanno::Phaeo:GFF715 (316 letters) >FitnessBrowser__Smeli:SMa0218 Length = 316 Score = 117 bits (292), Expect = 5e-31 Identities = 98/317 (30%), Positives = 149/317 (47%), Gaps = 20/317 (6%) Query: 11 ATTVAAAPMMLATTASAEGEKYILVSHAPDSDSWWNTIKNGIALAGEQMNVE--VEYRNP 68 A A +L +TA A K ++ + S ++N + G A Q V+ V+Y N Sbjct: 9 AALAAGLATLLTSTALAADVKATMIIYLDPSVQFFNPVVKGAQDAAAQFGVDLDVQYAN- 67 Query: 69 PTGDLADMARIIEQAAASGPNGIITTLSDYDVLSGPIKAAVDSGVDVIIMNSGTPDQARE 128 D +IE A ASG +GI +S D I AAV +G+ VI N+ D A+ Sbjct: 68 --NDPVRQNDLIESATASGVDGIAVAISSSDAFDESICAAVKAGIIVIGFNNDDLDGAKG 125 Query: 129 VGALMYVGQPEYDAGHAAGMRA-KADGVGSFLCVNHYISSPSSTERCQGFADGLGVD--- 184 YVG E +G+ G R K G+ S V + P E A G G++ Sbjct: 126 NCRQAYVGMDELASGYELGNRMIKEFGLKSGDVVFNPREIP---EASFAVARGGGIEKAM 182 Query: 185 ----LGDQMIDSGQDPAEIKNRVLAYLNTNPETDAILTLGPTSADPTLLALDENGMAGDI 240 + + + +G DPAE +N + +L NP A+ G ++ A+ + G+ DI Sbjct: 183 TENGIKVETVRAGLDPAEAQNIIAQFLIANPNVKALFGTGSVTSTVGAGAIKDAGV--DI 240 Query: 241 YFGTFDLGEEIVKGLKSGVINWGIDQQPFLQAYLPVVVLTNYHRYGVLPGNNINSGPG-F 299 FG FDL EIV ++SG + +DQQP+LQ Y P+ + +YG+ P +I++G G F Sbjct: 241 PFGGFDLAVEIVNAVESGAMYATMDQQPYLQGYYPIAQIALAKKYGLTP-TDIDTGQGAF 299 Query: 300 VTKDGLEKVEEFAGEYR 316 + K + V+ G YR Sbjct: 300 LDKTRIGSVKPLIGSYR 316 Lambda K H 0.315 0.134 0.393 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: 264 Number of extensions: 14 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: 316 Length of database: 316 Length adjustment: 27 Effective length of query: 289 Effective length of database: 289 Effective search space: 83521 Effective search space used: 83521 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: 42 (22.0 bits) S2: 48 (23.1 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