Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate Pf1N1B4_4287 Inositol transport system permease protein
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4287 Length = 340 Score = 169 bits (429), Expect = 7e-47 Identities = 110/338 (32%), Positives = 186/338 (55%), Gaps = 24/338 (7%) Query: 4 QSLPDTTTPKRRFRWPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSP--IDILN 61 ++ P K R R+PT + ++ LVL+ LV F +V L S + ++ Sbjct: 6 ENKPAAVPVKSRRRFPTEL----SIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMIL 61 Query: 62 RAAPVALLAIGMTLVIATGGIDLSVGAVMAIAGATTAAM------------TVAGFSLPI 109 + + + LLAIG+T VI T GIDLS G+V+A++ A++ ++ + I Sbjct: 62 QVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWI 121 Query: 110 VLLSALGTGILAGLWNGILVAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSW 169 ++ LG G+LAG NG ++AI I PF+ATL +MV+ RG+A+ T GQ V+ S + Sbjct: 122 PVIVGLGVGLLAGAINGSIIAITGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTA 181 Query: 170 FGSGSLLFLPTPVIIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLT 229 G G++ PVII ++ ++F + R T G + A+G N++AA+ +G+N + +++ Sbjct: 182 IGHGAM-----PVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIV 236 Query: 230 YVLSGLCAAIAGIIVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGA 289 Y ++GL A +AG++ +A A G+ ELDAI A VIGG SL GG + +V+GA Sbjct: 237 YSIAGLLAGLAGVVASARAATGQA-GMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGA 295 Query: 290 LIIQGMNTGILLSGFPPEMNQVVKAVVVLCVLIVQSQR 327 LI+ M +G G + ++K ++++ +++ R Sbjct: 296 LILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYR 333 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: 310 Number of extensions: 17 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: 340 Length adjustment: 28 Effective length of query: 313 Effective length of database: 312 Effective search space: 97656 Effective search space used: 97656 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