Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate Dsui_0629 Dsui_0629 branched-chain amino acid ABC-type transport system, permease component
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__PS:Dsui_0629 Length = 307 Score = 61.2 bits (147), Expect = 3e-14 Identities = 78/281 (27%), Positives = 126/281 (44%), Gaps = 31/281 (11%) Query: 67 ALLAIGMTLVIATGG-IDLSVGAVMAIAGAT--TAAMTVAGFSLPIVLLSALGTGILAGL 123 AL+A+G T+V G I+ + G V+ I T T +AG LP +++ +G A + Sbjct: 19 ALVALGYTMVYGILGLINFAHGEVVMIGALTALTVVKLLAGSGLPGPVIALIGLMAAAPV 78 Query: 124 WNGILVAILKIQ-----------PFVATLILMVAGRGVAQLITAGQIVTFNS--PDLSWF 170 I I KI P + + + + + +A ++ +F + P + Sbjct: 79 CMAIGYGIEKIAYRPLRKAPRLAPLITAIGVSIVLQNLAMMVWGRSYHSFPAVLPAEAHE 138 Query: 171 GSGSLLFLPTPVIIAVLTLILF---WLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVM 227 G+ F VII ++ + LL +T LG + A N A+ GVN I+ Sbjct: 139 VLGAT-FTDLQVIIVLVAAGMMAGLLLLINRTRLGRAMRATAENPAIAQLMGVNVNHIIS 197 Query: 228 LTYVLSGLCAAIAGIIVAADIRGADANNAGLWLELDAILAVVIGG-----GSLMGGRFNL 282 LT+V+ AA+AG++V+A+ A G L L A A V+GG G+++GG Sbjct: 198 LTFVIGSALAAVAGLMVSANYSIAH-YYMGFILGLKAFTAAVLGGIGNLAGAMIGGILLG 256 Query: 283 LLSVVGALIIQGMNTGILLSGFPPEMNQVVKAVVVLCVLIV 323 L+ +GA I G + GF Q V A VL +++V Sbjct: 257 LIESLGAGYI-----GDITGGFLGSHYQDVFAFFVLILVLV 292 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: 224 Number of extensions: 16 Number of successful extensions: 2 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: 307 Length adjustment: 28 Effective length of query: 313 Effective length of database: 279 Effective search space: 87327 Effective search space used: 87327 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: 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