Align TreU, component of Trehalose porter (characterized)
to candidate GFF507 PGA1_c05190 ABC transporter, inner membrane component
Query= TCDB::Q97ZC1 (267 letters) >FitnessBrowser__Phaeo:GFF507 Length = 265 Score = 101 bits (252), Expect = 1e-26 Identities = 73/261 (27%), Positives = 124/261 (47%), Gaps = 9/261 (3%) Query: 10 IVVGIYFLFPLYILVLLAFNSPKYTVLAKFPSLLPVSLTLNNLLTALQGTAFIDPFIKSL 69 IV ++ + P+Y LV ++F + +L+ F SL P + TL N T ++ +I S+ Sbjct: 9 IVYILFLMLPIYWLVAMSFKTTN-EILSGF-SLFPQTFTLENYATIFTDPSWYWGYINSI 66 Query: 70 ETATLVGIITIALAIPAGYGLSRLPRAIAYSIIILLLVTNMMPAIVIGIPIAVDFLKLHL 129 ++ +I++A+A+PA Y SR + LL M PA V +P + + L Sbjct: 67 IYVSINTVISVAVALPAAYAFSRYRFLGDKQLFFWLLTNRMAPAAVFALPFFQLYSAVGL 126 Query: 130 FESVVGLALAQTLITLPLATFILQGTFSSIPIDLEHQARVDGANLFNRLFSVLLPLAAPG 189 F++ + +ALA L +PLA +IL+G IP +L+ A VDG + ++ +P G Sbjct: 127 FDTHLAVALAHCLFNIPLAVWILEGFMGGIPKELDETAYVDGYSFPRFFATIFIPSIKAG 186 Query: 190 IAAAFLISWMFSWDEFTYAILLI-----PYHSTLPVTIYQDVTRGNLLAGIAFSLIFTLP 244 + A +MFSW E A L P +T+ T LLA A + +P Sbjct: 187 VGVAAFFCFMFSWVELLLAKTLTAVAAKPIAATMTKTASSAGYELGLLA--AAGTLTIIP 244 Query: 245 VIILTFALQKYLRGEYLAGGI 265 I+ + ++ Y+ + G + Sbjct: 245 GAIVIYFVRNYIAKGFAMGRV 265 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: 220 Number of extensions: 14 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: 267 Length of database: 265 Length adjustment: 25 Effective length of query: 242 Effective length of database: 240 Effective search space: 58080 Effective search space used: 58080 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