Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate Ac3H11_4787 Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3)
Query= reanno::Smeli:SM_b21653 (298 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4787 Length = 293 Score = 127 bits (319), Expect = 3e-34 Identities = 85/279 (30%), Positives = 144/279 (51%), Gaps = 13/279 (4%) Query: 17 WLFVAPALGLITLFMVYPIAWSLWMSFQ--SGRGMTLKFAGFANIVRLWNDPVFIKALTN 74 W+ +AP L +I++F +P +L SFQ GM+ ++ G N L+ DP ++ + Sbjct: 14 WVLLAPQLAIISVFFFWPAGQALVQSFQMQDSFGMSTEWVGLDNFKHLFEDPGYLASFKT 73 Query: 75 TMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCVSSLVAYSVLFKGMFATD 134 T + ++ + I L+LILA + + + G V++TA+ LP + VL+ MF+ Sbjct: 74 TAFFSILVAAVGIGLSLILA-IFADRIIKGAMVYKTALLLPYAVAPAVAGVLWMFMFSPS 132 Query: 135 -GIVNSTLQAIGLAASPIPWLTHPFWAKVLVILAITWRWTGYNMIFYLAALQNIDKSIYE 193 G+V L+ G + + H A L+++A W+ YN +F+LA LQ+I KS+ E Sbjct: 133 LGVVAYMLRQSGFDWNHMLNSDH---AMGLIVIAAVWKQISYNFLFFLAGLQSIPKSLIE 189 Query: 194 VARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDEVYNLTEG--KGGPSNATL 251 A IDG W R + PLL P F VI+ + F + + + + +GGP T Sbjct: 190 AAAIDGAGPWRRFWSIQFPLLSPTTFFLLVINVV---YAFFDTFAIVDATTQGGPGRDTA 246 Query: 252 TLSLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQF 290 L +Y+ F+ M ++G +A S V++ +V +L +QF Sbjct: 247 ILVYKVYHDGFKAM-DMGGSAAQSVVLMAIVVVLTVIQF 284 Lambda K H 0.330 0.142 0.447 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: 223 Number of extensions: 13 Number of successful extensions: 5 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: 298 Length of database: 293 Length adjustment: 26 Effective length of query: 272 Effective length of database: 267 Effective search space: 72624 Effective search space used: 72624 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 (21.9 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