Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate Pf6N2E2_3330 L-proline glycine betaine ABC transport system permease protein ProW (TC 3.A.1.12.1)
Query= SwissProt::P14176 (354 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3330 Length = 238 Score = 98.2 bits (243), Expect = 2e-25 Identities = 66/218 (30%), Positives = 106/218 (48%), Gaps = 7/218 (3%) Query: 127 VATLVSLIAIGAIGAWSQAMVT-----LALVLTALLFCIVIGLPLGIWLARSPRAAKIIR 181 +A LV I I I + ++ L LVL ++L +++G+P GI L+R + R Sbjct: 19 LALLVHWIGIDTIQRYHDDLLFYLQAHLLLVLASMLAALLVGIPAGIALSRPGMVGRAER 78 Query: 182 --PLLDAMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIE 239 + + T P L + + GIG+ P + + +L PI+R T G+ V L E Sbjct: 79 FMQVFNIGNTVPPLAVLAIALGILGIGSGPAIFALFLASLLPIVRNTYEGLKNVQGSLKE 138 Query: 240 ASRSFGASPRQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIG 299 A+ G +PRQ+L+KV+LP A+P I+ GV L + + +A +I LG ++ GI Sbjct: 139 AAVGIGMTPRQVLWKVELPNAVPIIVGGVRVALAINVGTAPLAFLIGANSLGSLIFPGIA 198 Query: 300 RLDMGLATVGGVGIVILAIILDRLTQAVGRDSRSRGNR 337 + +G +LA++LD L R RG R Sbjct: 199 LNNQPQLLLGAACTALLALLLDGLVTLASRLWLERGLR 236 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: 225 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: 354 Length of database: 238 Length adjustment: 26 Effective length of query: 328 Effective length of database: 212 Effective search space: 69536 Effective search space used: 69536 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