Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_012469877.1 GLOV_RS09030 C4-dicarboxylate ABC transporter permease
Query= SwissProt::O07838 (440 letters) >NCBI__GCF_000020385.1:WP_012469877.1 Length = 460 Score = 653 bits (1685), Expect = 0.0 Identities = 326/438 (74%), Positives = 377/438 (86%), Gaps = 14/438 (3%) Query: 2 SALIIFGLLIALMLTGMPISISLGLTVLTFLFTMTQVPIDTVALKLFTGIEKFEIMAIPF 61 +A I+F LLI LMLTGMPISISLGLTVLTFLF M+QVP++TVA+KLFTGIEKFEIMAIPF Sbjct: 35 NAGIVFALLIGLMLTGMPISISLGLTVLTFLFFMSQVPVETVAMKLFTGIEKFEIMAIPF 94 Query: 62 FILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGSV 121 FILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGV+ACALFAAVSGSSPATVVAIGS+ Sbjct: 95 FILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVMACALFAAVSGSSPATVVAIGSI 154 Query: 122 ILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSASV 181 +LPAMV GFPK FGAGVI+TSG+LGILIPPSIVMV+YAVAT+ +SV Sbjct: 155 LLPAMVKAGFPKNFGAGVISTSGSLGILIPPSIVMVIYAVATN--------------SSV 200 Query: 182 GELFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLRQRWTAFREAAWGLMLIVVVI 241 G LFMAG++PGLMLA L W RARKF YPR+ KA++++R AF+E+ WGL+LIV+V+ Sbjct: 201 GALFMAGIIPGLMLATLLGSVAWYRARKFNYPRMPKATMKERLKAFKESIWGLLLIVIVL 260 Query: 242 GGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITNAVL 301 GGIY+G+FTPTEAAAMSAVYAFF++VFVYKD+T + +P+VLL SANMSAMLLYIITNAVL Sbjct: 261 GGIYSGMFTPTEAAAMSAVYAFFVAVFVYKDMTFKGIPKVLLDSANMSAMLLYIITNAVL 320 Query: 302 FSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILFPVA 361 FS+LM E IPQ + +WM+ FL + N+LLL AGN MEPSSI+LI+APILFPVA Sbjct: 321 FSYLMTSEQIPQIMADWMIAHNFGVIAFLAVTNVLLLLAGNVMEPSSIILILAPILFPVA 380 Query: 362 VRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLAFL 421 ++LGIDP+HFGI+I VNMEVGMCHPPVGLNLYVASGITKMGITELTVAV PWL+ M+ F+ Sbjct: 381 MKLGIDPIHFGILITVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVLPWLIAMVGFM 440 Query: 422 VLVTYVPAISLALPNLLG 439 +LVTYVP ISL LP L+G Sbjct: 441 LLVTYVPEISLWLPRLMG 458 Lambda K H 0.329 0.142 0.431 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: 793 Number of extensions: 36 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: 440 Length of database: 460 Length adjustment: 33 Effective length of query: 407 Effective length of database: 427 Effective search space: 173789 Effective search space used: 173789 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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