Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate PfGW456L13_3148 L-proline glycine betaine ABC transport system permease protein ProW (TC 3.A.1.12.1)
Query= SwissProt::P14176 (354 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3148 Length = 283 Score = 198 bits (503), Expect = 2e-55 Identities = 99/262 (37%), Positives = 163/262 (62%), Gaps = 4/262 (1%) Query: 66 SWVTEGIDWVVTHFRPVFQGVRVPVDYILNGFQQLLLGMPAPVAIIVFALIAWQISGVGM 125 +++ +DW+ + +F+ + ++ +L G + LL P P A+I ++ + Sbjct: 12 AFLAPAVDWLNANLHGLFKVISQVIEAVLGGVEGALLA-PHPYALIG-GVVVLALFFANK 69 Query: 126 GVATLVSLIAIGAI--GAWSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKIIRPL 183 VA L+ + G W +M T+ALV A+L + I PLG+ AR R + P+ Sbjct: 70 KVALFAGLMLAFCLFSGLWVASMQTIALVSVAVLISVSIAFPLGVLAARVKRVDEAFLPI 129 Query: 184 LDAMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEASRS 243 L+ MQT P +VYL+P VMLF +G VP ++ TI++ +PP++RLT L Q+P + +E ++ Sbjct: 130 LNIMQTVPPWVYLIPAVMLFSLGRVPAIIATIVYGIPPMLRLTTLAFKQLPKEFLELGQA 189 Query: 244 FGASPRQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGRLDM 303 GASPR +LFK++LP A PT++ G+NQ ++L+L+MVV+A ++ GGLG V RG+ R++M Sbjct: 190 IGASPRAILFKIELPTAAPTLLVGLNQCILLSLAMVVLAGLVGAGGLGAEVTRGLTRMEM 249 Query: 304 GLATVGGVGIVILAIILDRLTQ 325 GL G+ IV +A++LDRL++ Sbjct: 250 GLGLRAGLAIVAVALLLDRLSR 271 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: 271 Number of extensions: 15 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: 354 Length of database: 283 Length adjustment: 27 Effective length of query: 327 Effective length of database: 256 Effective search space: 83712 Effective search space used: 83712 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