Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate H281DRAFT_02175 H281DRAFT_02175 monosaccharide ABC transporter membrane protein, CUT2 family
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__Burk376:H281DRAFT_02175 Length = 353 Score = 197 bits (500), Expect = 4e-55 Identities = 117/319 (36%), Positives = 180/319 (56%), Gaps = 15/319 (4%) Query: 11 TPKRRFRWPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLA 70 T R +R +++ LL ++L + + PHFW + + L + + ++ Sbjct: 41 TGVRNWRRLAMQREVIVLLAMVLFNLIFTPHFWSLQTFNVNL--------TQVVTIVIVG 92 Query: 71 IGMTLVIATGGIDLSVGAVMAIAGATTAAMTV-----AGFSLPIVLLSALGTGILAGLWN 125 IGMTLV+ATGGIDLSVGA MAI+GA + + G +L VL + L G++N Sbjct: 93 IGMTLVVATGGIDLSVGASMAISGALAPMLFLNIPVPGGIALAFVL--PVLAAALCGVFN 150 Query: 126 GILVAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIA 185 G+LV L +QP VATL+L +AGRG+AQ++T G + FN+P W G + +P V++ Sbjct: 151 GLLVTRLAVQPIVATLVLFIAGRGIAQVVTDGSLQAFNTPAFQWIALGKVAGVPFQVLLM 210 Query: 186 VLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVA 245 + ++ F + RKT G ++ G N +AA +GV T + ++ Y L A +AG+I Sbjct: 211 LALVVAFAWVVRKTLFGQYLLITGGNEKAAYLSGVPTASVKLIAYTLCAALAGLAGLISI 270 Query: 246 ADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFP 305 + +DAN GL +ELDAI AV +GG +L GG+ + ++VGALIIQ + +L G P Sbjct: 271 SVNSSSDANVVGLGIELDAIAAVAVGGTALTGGKAFIGGTLVGALIIQLLRYTLLAHGIP 330 Query: 306 PEMNQVVKAVVVLCVLIVQ 324 VVKA +++ + VQ Sbjct: 331 DAAALVVKAGIIVAAVYVQ 349 Lambda K H 0.327 0.142 0.416 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: 325 Number of extensions: 12 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: 341 Length of database: 353 Length adjustment: 29 Effective length of query: 312 Effective length of database: 324 Effective search space: 101088 Effective search space used: 101088 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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