Align Inner-membrane translocator (characterized, see rationale)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 152 bits (384), Expect = 1e-41 Identities = 106/308 (34%), Positives = 168/308 (54%), Gaps = 21/308 (6%) Query: 16 LLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSGV 75 L+ + LV + D F + N++R + + ++GMTLVI++ GIDLSVG+++AL G Sbjct: 13 LIILCLVLSLLSDRFLTLANGWNVMRQVSVNICISVGMTLVILTAGIDLSVGSILALCGA 72 Query: 76 VTSLLITE----------YQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGM 125 VT+ LI + PL A ++ + LG G G I +K+ PF+ TLA + Sbjct: 73 VTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWTITRFKVPPFVATLAML 132 Query: 126 FLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNG---ALDLSSLIFILFFVIIAVVMH 182 +ARGL T L I+ D A G G + + I + + ++ Sbjct: 133 TIARGL-TMLWTGGFPINGLGED------FAFLGTGWFLGIPMPVWITAVIVALAVLLTK 185 Query: 183 YTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAI 242 T+FG VYAIGGN+ +A L GI+I++ +++YAI+ LA + G++ T S I Sbjct: 186 KTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLDSAQPNAGI 245 Query: 243 GVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLL 302 ELDAIAAVVIGGT L+GG G ++G VLG I++GV+ + ++S +W ++V G ++ Sbjct: 246 SYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVL-LNVSPFWQQVVKGAVI 304 Query: 303 FFFILLQK 310 +++ K Sbjct: 305 LLAVVIDK 312 Lambda K H 0.330 0.145 0.424 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: 360 Number of extensions: 24 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: 320 Length of database: 318 Length adjustment: 28 Effective length of query: 292 Effective length of database: 290 Effective search space: 84680 Effective search space used: 84680 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 (21.8 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