Align TreU, component of Trehalose porter (characterized)
to candidate AZOBR_RS25325 AZOBR_RS25325 polyamine ABC transporter permease
Query= TCDB::Q97ZC1 (267 letters) >FitnessBrowser__azobra:AZOBR_RS25325 Length = 268 Score = 93.6 bits (231), Expect = 4e-24 Identities = 66/222 (29%), Positives = 111/222 (50%), Gaps = 4/222 (1%) Query: 44 PVSLTLNNLLTALQGTAFIDPFIKSLETATLVGIITIALAIPAGYGLSRLPRAIAYSIII 103 P +L + L A I SL A V + + +A PA L+R ++ + Sbjct: 43 PSGWSLRWYVALLADGAMAAALINSLLLAAAVTALALLIAFPAALALAR---GRLTALAV 99 Query: 104 LLLVTNMMPAIVIGIPIAVDFLKLHLFESVVGLALAQTLITLPLATFILQGTFSSIPIDL 163 LL + ++P+IV+G+ + V F++L L S G+A+ LITLP A +L+ +P + Sbjct: 100 LLTLPLLLPSIVLGLALLVLFVRLGLVGSWPGMAVPHLLITLPYALRVLETALRGLPPGV 159 Query: 164 EHQARVDGANLFNRLFSVLLPLAAPGIAAAFLISWMFSWDEFTYAILLI-PYHSTLPVTI 222 E A GA + + LPLAAPG+AAA ++ ++ S+DE ++ + P +TLPV + Sbjct: 160 EEAAASLGARPASVALRITLPLAAPGLAAAAILVFLVSFDEVVVSLFIAGPRLTTLPVAL 219 Query: 223 YQDVTRGNLLAGIAFSLIFTLPVIILTFALQKYLRGEYLAGG 264 Y+ V + A + + L + L AL++ + GG Sbjct: 220 YRHVESSSDPLVAAVAALLVLGTLALVIALERLVGLRRALGG 261 Lambda K H 0.330 0.146 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: 202 Number of extensions: 14 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: 267 Length of database: 268 Length adjustment: 25 Effective length of query: 242 Effective length of database: 243 Effective search space: 58806 Effective search space used: 58806 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 (21.8 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