Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate H281DRAFT_03486 H281DRAFT_03486 osmoprotectant transport system permease protein
Query= SwissProt::P14176 (354 letters) >FitnessBrowser__Burk376:H281DRAFT_03486 Length = 239 Score = 107 bits (267), Expect = 3e-28 Identities = 62/196 (31%), Positives = 101/196 (51%), Gaps = 4/196 (2%) Query: 144 QAMVTLALVLTALLFCIVIGLPLGIWLARSP----RAAKIIRPLLDAMQTTPAFVYLVPI 199 Q++ + +V A IV+ +PLGI+L+R RA + + L+ Q P L Sbjct: 39 QSITQMTMVAIAGGLAIVVAVPLGIYLSRESGKHARAGQALLQTLNMGQAVPKLALLALA 98 Query: 200 VMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEASRSFGASPRQMLFKVQLPL 259 + + GIG P + + L PI+ T+ G+ VP LIEA+ G +PRQ+LF+V+LP Sbjct: 99 MSVLGIGRWPSIFALWVATLLPIVLNTLEGLRAVPRALIEAATGMGMTPRQVLFRVELPN 158 Query: 260 AMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGRLDMGLATVGGVGIVILAII 319 A+ I AG+ L + + +A ++ GGLG+++ GI D + G + +LA++ Sbjct: 159 ALYVIFAGIRTALAITVGTAPLAFLVGGGGLGELIFTGIDMNDFSMLLAGAIPTAVLAVL 218 Query: 320 LDRLTQAVGRDSRSRG 335 D L + SRG Sbjct: 219 TDVLIGQMQVHLVSRG 234 Lambda K H 0.326 0.141 0.435 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: 213 Number of extensions: 7 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: 354 Length of database: 239 Length adjustment: 26 Effective length of query: 328 Effective length of database: 213 Effective search space: 69864 Effective search space used: 69864 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 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