Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate AO356_09245 AO356_09245 ABC transporter permease
Query= SwissProt::P14176 (354 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_09245 Length = 283 Score = 198 bits (503), Expect = 2e-55 Identities = 102/267 (38%), Positives = 166/267 (62%), Gaps = 7/267 (2%) Query: 72 IDWVVTHFRPVFQGVRVPVDYILNGFQQLLLGMPAP---VAIIVFALIAWQISGVGMGVA 128 +DW+ + +F + V+ +L + LLL P P +AI+ A + V + A Sbjct: 18 VDWLNANLHGLFVVISQVVEAVLGLVEHLLLA-PHPYMMIAIVFVAAFIFATKRVAVFAA 76 Query: 129 TLVSLIAIGAIGAWSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKIIRPLLDAMQ 188 +++ G W +M T+ALV ++L + I PLG+ AR R P+L+ MQ Sbjct: 77 LMLAFCLFS--GLWVASMQTIALVSVSVLISVAIAFPLGVLAARVKRVDDAFLPILNIMQ 134 Query: 189 TTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEASRSFGASP 248 T P +VYL+P V+LF +G VP ++ TI++ +PP++RLT L Q+P DL+E ++ GASP Sbjct: 135 TVPPWVYLIPAVILFSLGRVPAIIATIVYGIPPMLRLTTLAFKQLPKDLLELGQASGASP 194 Query: 249 RQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGRLDMGLATV 308 + +LFK++LP A PT++ G+NQ ++++L+MVV+A ++ GGLG V RG+ R++MGL Sbjct: 195 KDILFKIELPTAAPTLLVGLNQCILMSLAMVVLAGLVGAGGLGAEVTRGLSRMEMGLGLR 254 Query: 309 GGVGIVILAIILDRLTQ-AVGRDSRSR 334 G+ IV +A++LDRL++ A+ R S S+ Sbjct: 255 AGLAIVAIALLLDRLSRGALQRHSPSK 281 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: 272 Number of extensions: 18 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