Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate 207785 DVU2298 glycine/betaine/L-proline ABC transporter, permease protein
Query= SwissProt::P14176 (354 letters) >MicrobesOnline__882:207785 Length = 283 Score = 221 bits (562), Expect = 2e-62 Identities = 124/271 (45%), Positives = 166/271 (61%), Gaps = 1/271 (0%) Query: 62 IPLDSWVTEGIDWVVTHFRPVFQGVRVPVDYILNGFQQLLLGMPAPVAIIVFALIAWQIS 121 IPL +W+ D +V + ++ + LL +P I V AL+AW+ + Sbjct: 9 IPLGAWLEAFTDNMVEWCSGATRAFSTVAGNGIDMLESLLGSIPPWAFIPVVALLAWRAT 68 Query: 122 GV-GMGVATLVSLIAIGAIGAWSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKII 180 G+G L+ I +G W M T+ALVL A +V G+PLGI A + K++ Sbjct: 69 RKPGIGAFALLGFGLIWNLGLWEATMSTIALVLVATALAVVTGVPLGIAAAVNVTVRKVL 128 Query: 181 RPLLDAMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEA 240 P+LD MQT PAFVYL+P + FG+G V V T++FA+PP IR T LGI QVP DL+E Sbjct: 129 MPVLDLMQTMPAFVYLIPAIPFFGLGKVAAVFATVVFAMPPAIRFTCLGIRQVPDDLVEC 188 Query: 241 SRSFGASPRQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGR 300 + +FG S Q L K++LPLA PTI+AGVNQT+MLALSMVVIA+MI GLG V + I R Sbjct: 189 AEAFGTSRWQRLVKLELPLAAPTILAGVNQTIMLALSMVVIAAMIGARGLGGEVWKAIQR 248 Query: 301 LDMGLATVGGVGIVILAIILDRLTQAVGRDS 331 L++G G+GIVI+AI LDR+ Q +GR S Sbjct: 249 LELGSGFEAGIGIVIVAICLDRVLQHIGRRS 279 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: 316 Number of extensions: 21 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: 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