Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate Pf6N2E2_1961 Various polyols ABC transporter, permease component 2
Query= reanno::Dino:3607127 (272 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1961 Length = 277 Score = 202 bits (515), Expect = 5e-57 Identities = 103/250 (41%), Positives = 151/250 (60%) Query: 23 FPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALFEDGVLRTLINSLIIAISTTFLA 82 FP +WMV TS KT+I A PP +IF PTL NY NS++I+ S T L Sbjct: 28 FPIFWMVLTSFKTEIDAFATPPQFIFMPTLENYLHIQERSDYFHFAWNSVLISFSATALC 87 Query: 83 LVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLIARNLGLLDKHITLILI 142 +++ VPAA+++A +E + K W ++ +M+ P+ + +P +L+A+ GLLD I LI+I Sbjct: 88 MLIAVPAAYSMAFYETKRTKQTLLWMLSTKMLPPVGVLMPIYLLAKGAGLLDTRIALIVI 147 Query: 143 YLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPLAMPGVAVSAIFSFI 202 Y NLPIV+W++ F+ IP ++ EAARL+GA+ M ++ LP++ G+A + + S I Sbjct: 148 YTLINLPIVVWMIYTYFKDIPREILEAARLDGATLGQEMLRVLLPISKGGLASTMLLSMI 207 Query: 203 FSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYGKIMATSTLIVIPVLIFALIASKQL 262 WNE + L LT S A A+ S+ L + K+ A STL P+LIF I+ KQL Sbjct: 208 LCWNEAFWSLNLTSSSAAPLTALIASYSSPEGLFWAKLSAVSTLACAPILIFGWISQKQL 267 Query: 263 VRGLTMGAVK 272 VRGL+ GAVK Sbjct: 268 VRGLSFGAVK 277 Lambda K H 0.331 0.143 0.431 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: 231 Number of extensions: 11 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: 272 Length of database: 277 Length adjustment: 25 Effective length of query: 247 Effective length of database: 252 Effective search space: 62244 Effective search space used: 62244 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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