Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate 8500288 DvMF_1044 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= SwissProt::P14176 (354 letters) >FitnessBrowser__Miya:8500288 Length = 280 Score = 245 bits (625), Expect = 1e-69 Identities = 129/269 (47%), Positives = 173/269 (64%), Gaps = 1/269 (0%) Query: 62 IPLDSWVTEGIDWVVTHFRPVFQGVRVPVDYILNGFQQLLLGMPAPVAIIVFALIAWQIS 121 IPL W+ ID++VTH P + + LN + L +P + I L+AW+++ Sbjct: 8 IPLGQWLEAAIDFLVTHLAPATRAFSAVTESGLNLLEAGLDALPPLLVIAFVGLVAWRVT 67 Query: 122 G-VGMGVATLVSLIAIGAIGAWSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKII 180 V +GV + L + +G W M TLALVL A L +++G+PLGI A S RA ++ Sbjct: 68 RQVALGVFAVAGLALVWNMGLWQATMSTLALVLVATLLAVLVGIPLGIAAAMSDRARAVV 127 Query: 181 RPLLDAMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEA 240 P+LD MQT PAFVYL+P + FG+G V V T+IFA+PP IR T LGI QVPA+L+E Sbjct: 128 MPVLDVMQTMPAFVYLIPAIPFFGLGKVAAVFATVIFAMPPAIRFTCLGIRQVPAELVEC 187 Query: 241 SRSFGASPRQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGR 300 + +FG Q L K++LPLA PT++AGVNQT+MLALSMVVIA+MI GLG V + I R Sbjct: 188 AEAFGTGRFQRLVKLELPLAAPTMLAGVNQTVMLALSMVVIAAMIGARGLGGEVWKAIQR 247 Query: 301 LDMGLATVGGVGIVILAIILDRLTQAVGR 329 L+MG G+GIVI+AI LDR+ Q VG+ Sbjct: 248 LEMGNGFEAGIGIVIVAICLDRILQHVGK 276 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: 331 Number of extensions: 16 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: 280 Length adjustment: 27 Effective length of query: 327 Effective length of database: 253 Effective search space: 82731 Effective search space used: 82731 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