Align Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate H281DRAFT_02631 H281DRAFT_02631 carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= TCDB::Q72KX3 (369 letters) >FitnessBrowser__Burk376:H281DRAFT_02631 Length = 300 Score = 105 bits (262), Expect = 2e-27 Identities = 104/362 (28%), Positives = 149/362 (41%), Gaps = 91/362 (25%) Query: 7 AFLVLLPSVLAVGVFVYGFIGQNLWVSLTDW-GKDPAQALALRPELRFVGLENYRELFTG 65 AF LLP + V I ++ +S +W G P F+GL NY ELF Sbjct: 27 AFFFLLPGCALFALCVIYPIFSSIALSFYNWDGMTPRT---------FIGLANYVELF-- 75 Query: 66 FVDVRFRQSVVNLIFFTLFFMAGSLGLGLLLALAVDKAPRGEGFFRTVFLFPMALSFVVT 125 D + NLI+ F +A LGL L AL +++ +G +++F P LS VV Sbjct: 76 HADTFYLALKNNLIWLVFFLLAPPLGL--LFALYLNQQIKGMRVVKSLFFAPFVLSGVVV 133 Query: 126 GTIWRWLLQPQGGVNVLPTLFGLPPLSFPWLATREQVLVFDWNRLPFYTALVVGLVLLYV 185 G LVF W P + GL+ L V Sbjct: 134 G------------------------------------LVFSWFYDPAF-----GLLKLIV 152 Query: 186 AYTAYREGERRRALWGLASAGVLLLWAFAFGQGLRLLPYPEVHGFSLALVGVILAAVWQM 245 G G+ +L P F G++ AA+W Sbjct: 153 ------------------------------GHGIPVLGDPRTVTF-----GIVFAALWPQ 177 Query: 246 SGYTMALYLAGLRGIPVEVLEAARVDGASEWQLFRRVIFPMLAPITLSAMIVLGHIALKI 305 + Y M LYL GL I EV+EAAR++GA W L VI P L P T A+++ AL+ Sbjct: 178 TPYCMVLYLTGLTSINPEVVEAARMEGAKGWSLLWHVILPQLRPATFMAVVLTVIGALRS 237 Query: 306 FDLVFAMA-GLDYAPTDVPAIYMYLLAFRGNQFAKGAAIGILLLLLVAVVVVPYLATQLR 364 FDL+ M+ G + + V A YMY A + + A+I ++L ++ V +V +L LR Sbjct: 238 FDLISVMSGGGPFDSSTVLAYYMYDQAIKYYREGYSASIAVVLFAIMLVYIVFHLRRMLR 297 Query: 365 KE 366 +E Sbjct: 298 EE 299 Lambda K H 0.331 0.146 0.458 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: 296 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 369 Length of database: 300 Length adjustment: 28 Effective length of query: 341 Effective length of database: 272 Effective search space: 92752 Effective search space used: 92752 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 49 (23.5 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