Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate 3606962 Dshi_0389 Monosaccharide-transporting ATPase (RefSeq)
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__Dino:3606962 Length = 357 Score = 114 bits (285), Expect = 4e-30 Identities = 96/294 (32%), Positives = 146/294 (49%), Gaps = 29/294 (9%) Query: 50 GRLFGSPID---ILNRAAPVALLAIGMTLVIATGGIDLSVGAVMAIAGATTAAMTVAGFS 106 G F SP IL + V ++A +LVI T GIDLSVGA+M ++ T + Sbjct: 64 GSKFFSPFALTLILQQVQIVGIVAAAQSLVILTAGIDLSVGAIMVMSSVVMGQFTFR-YG 122 Query: 107 LPIVLLSALGT--GILAGLWNGILVAILKIQPFVATLILMVAGRGVAQLITAG------- 157 LP+ + A G G L G NG LVA +K+ PF+ TL G+ Q++ A Sbjct: 123 LPVEVAVACGLLCGTLLGFINGWLVAKVKLPPFIVTL-------GMWQIVLAANFLYSRN 175 Query: 158 -----QIVTFNSPDLSWFGSGSLLF---LPTPVIIAVLTLILFWLLTRKTALGMFIEAVG 209 Q + +P L +FG+ + L VI VL +I+ R TA G + AVG Sbjct: 176 ETIRSQDIRDQAPLLQFFGTTLEIGGARLTYGVIFMVLLVIVLAYALRHTAWGRHVYAVG 235 Query: 210 INIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNAGLWLELDAILAVV 269 + AA+ +GV ++ Y+LSGL A AG + I G+ + +G +++I AVV Sbjct: 236 DDPEAAELSGVQVSRTLISVYMLSGLICAFAGWALIGRI-GSVSPTSGQLANIESITAVV 294 Query: 270 IGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVKAVVVLCVLIV 323 IGG SL GGR ++L + GALI+ G+ L G + ++ ++++ + V Sbjct: 295 IGGISLFGGRGSILGAFFGALIVGVFTLGLRLLGADAQWTFLLIGLLIIAAVAV 348 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: 272 Number of extensions: 15 Number of successful extensions: 4 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: 357 Length adjustment: 29 Effective length of query: 312 Effective length of database: 328 Effective search space: 102336 Effective search space used: 102336 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