Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate AO353_25890 AO353_25890 sugar ABC transporter permease
Query= reanno::Dino:3607127 (272 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25890 Length = 276 Score = 212 bits (540), Expect = 6e-60 Identities = 113/274 (41%), Positives = 164/274 (59%), Gaps = 2/274 (0%) Query: 1 MTSTRSLFSQI--ALLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREA 58 + TR L S + L I + FP +WMV TS KT+I A PP +IF PTL NY Sbjct: 3 LQQTRRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYLHV 62 Query: 59 LFEDGVLRTLINSLIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIV 118 G NS++I+ S T L L++ VPAA+++A +E + K W ++ +M+ P+ Sbjct: 63 NERSGYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWMLSTKMLPPVG 122 Query: 119 LALPFFLIARNLGLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQF 178 + +P +L+A++ GLLD I LI+IY NLPIV+W++ F+ IP D+ EAARL+GA+ + Sbjct: 123 VLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMIYTYFKDIPKDILEAARLDGATLW 182 Query: 179 TIMRKICLPLAMPGVAVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYG 238 M ++ LP+A G+A + + S I WNE + L LT S+A A+ S+ L + Sbjct: 183 QEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSKAAPLTALIASYSSPEGLFWA 242 Query: 239 KIMATSTLIVIPVLIFALIASKQLVRGLTMGAVK 272 K+ A STL P+LIF I+ KQLVRGL+ GAVK Sbjct: 243 KLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 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: 251 Number of extensions: 10 Number of successful extensions: 1 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: 276 Length adjustment: 25 Effective length of query: 247 Effective length of database: 251 Effective search space: 61997 Effective search space used: 61997 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