Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 185 bits (470), Expect = 1e-51 Identities = 114/310 (36%), Positives = 181/310 (58%), Gaps = 20/310 (6%) Query: 25 LVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVIATGGIDL 84 L+AL+++ LV SL++ F + L +G +++ + + +++GMTLVI T GIDL Sbjct: 10 LIALIILCLVLSLLSDRF--LTLANGW------NVMRQVSVNICISVGMTLVILTAGIDL 61 Query: 85 SVGAVMAIAGATTAAM-----TVAGFSLPI------VLLSALGTGILAGLWNGILVAILK 133 SVG+++A+ GA TA++ V G +L I ++ +G G G +NG + K Sbjct: 62 SVGSILALCGAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWTITRFK 121 Query: 134 IQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFW 193 + PFVATL ++ RG+ L T G + D ++ G+G L +P PV I + + L Sbjct: 122 VPPFVATLAMLTIARGLTMLWTGGFPINGLGEDFAFLGTGWFLGIPMPVWITAVIVALAV 181 Query: 194 LLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADA 253 LLT+KT G ++ A+G N RAA+ +G+N + M Y ++G AA+ G+IV + + A Sbjct: 182 LLTKKTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLDSAQP 241 Query: 254 NNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVK 313 NAG+ ELDAI AVVIGG SL GG+ ++ +V+G +II +N G++L P QVVK Sbjct: 242 -NAGISYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQVVK 300 Query: 314 AVVVLCVLIV 323 V+L +++ Sbjct: 301 GAVILLAVVI 310 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: 317 Number of extensions: 21 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: 318 Length adjustment: 28 Effective length of query: 313 Effective length of database: 290 Effective search space: 90770 Effective search space used: 90770 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