Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate AZOBR_RS27985 AZOBR_RS27985 ABC transporter permease
Query= reanno::Dino:3607127 (272 letters) >FitnessBrowser__azobra:AZOBR_RS27985 Length = 280 Score = 215 bits (547), Expect = 1e-60 Identities = 112/262 (42%), Positives = 165/262 (62%), Gaps = 7/262 (2%) Query: 11 IALLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALFEDGVLRTLIN 70 +ALL+L++ FPF WMV +L+ L+ +F PTL N+ AL++ ++ +N Sbjct: 25 LALLLLVL----FPFAWMVQMALRPADAVLD--DAVLFLPTLENF-VALWQGHFPKSFLN 77 Query: 71 SLIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLIARNL 130 S++++ +T +L LGVPAA+ L R+ FR ++ + W + RM PI L +PFFL R + Sbjct: 78 SVLVSSLSTAASLALGVPAAYVLTRWRFRARRRVALWILATRMAPPIALTIPFFLAYRWV 137 Query: 131 GLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPLAM 190 GL D + L LIY+TFN+ IV+W + F IP L+EAA ++G + R++ LPLA Sbjct: 138 GLQDSVVGLALIYMTFNISIVVWFMQTFFAAIPRSLEEAAWIDGCGVWQAFRRVTLPLAA 197 Query: 191 PGVAVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYGKIMATSTLIVIP 250 PG+A +A+F FIFSWN+ F LILTR+ A TAP +F++ +GKI A TL+++P Sbjct: 198 PGLAATAVFCFIFSWNDFFFALILTRTNAVTAPVAITNFLQYEGWEWGKIAAAGTLVMLP 257 Query: 251 VLIFALIASKQLVRGLTMGAVK 272 VL F L+ K LVRGLT G +K Sbjct: 258 VLAFTLLVRKYLVRGLTAGGLK 279 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: 249 Number of extensions: 11 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 272 Length of database: 280 Length adjustment: 25 Effective length of query: 247 Effective length of database: 255 Effective search space: 62985 Effective search space used: 62985 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