Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate PfGW456L13_3040 Various polyols ABC transporter, permease component 2
Query= reanno::Dino:3607127 (272 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3040 Length = 276 Score = 206 bits (524), Expect = 4e-58 Identities = 106/256 (41%), Positives = 155/256 (60%) Query: 17 IITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALFEDGVLRTLINSLIIAI 76 I + FP +WMV TS KT+I A PP +IF PTL NY NS++I+ Sbjct: 21 IAILIFFPIFWMVLTSFKTEIDAFATPPQFIFMPTLENYLHINERSDYFSFAWNSVVISF 80 Query: 77 STTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLIARNLGLLDKH 136 S T L L++ VPAA+++A +E + + W ++ +M+ P+ + +P +L+A++ GLLD Sbjct: 81 SATALCLLIAVPAAYSMAFYETQRTRGTLLWMLSTKMLPPVGVLMPIYLLAKSFGLLDTR 140 Query: 137 ITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPLAMPGVAVS 196 I LI+IY NLPIV+W++ F+ IP D+ EAARL+GA+ M ++ LP+A G+A + Sbjct: 141 IALIVIYTLINLPIVVWMIYTYFKDIPRDILEAARLDGATLAQEMLRVLLPIAKGGLAST 200 Query: 197 AIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYGKIMATSTLIVIPVLIFAL 256 + S I WNE + L LT S+A A+ S+ L + K+ A STL P+LIF Sbjct: 201 VLLSLILCWNEAFWSLNLTSSKAAPLTALIASYSSPEGLFWAKLSAVSTLACAPILIFGW 260 Query: 257 IASKQLVRGLTMGAVK 272 I+ KQLVRGL+ GAVK Sbjct: 261 ISQKQLVRGLSFGAVK 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: 243 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: 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 Apr 09 2024. 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