Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate CCNA_01515 CCNA_01515 C4-dicarboxylate transporter large subunit
Query= SwissProt::O07838 (440 letters) >FitnessBrowser__Caulo:CCNA_01515 Length = 426 Score = 305 bits (781), Expect = 2e-87 Identities = 160/439 (36%), Positives = 256/439 (58%), Gaps = 13/439 (2%) Query: 1 MSALIIFGLLIALMLTGMPISISLGLTVLTFLFTMTQVPIDTVALKLFTGIEKFEIMAIP 60 M ++ GLL L++ G+P++ +LGL L M P+ ++ TG+ F +MAIP Sbjct: 1 MELTLLLGLLALLLIIGVPVAFALGLASLVTFIFMDIAPV-VAFQRIATGVNVFSLMAIP 59 Query: 61 FFILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGS 120 FFI AG+ + G+A+R++ A A +G GGLG+ V A +F VSGS+ A+V A+GS Sbjct: 60 FFIFAGDLMQQAGIAERLVRVADAAMGRIRGGLGVVDVGASMMFGGVSGSAVASVSALGS 119 Query: 121 VILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSAS 180 ++P M +G+ + V +TS LGILIPPS M++YA A S S Sbjct: 120 TLIPLMKEKGYDADYAVNVTSTSAILGILIPPSHNMIIYAAAAG------------VSVS 167 Query: 181 VGELFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLRQRWTAFREAAWGLMLIVVV 240 V +LF+AGV+PG++ FLA W A + GYP+ E AF A GL+ V++ Sbjct: 168 VADLFLAGVLPGILTGIFLAAAAWIIAVRRGYPKGEFPGWPAFAAAFASALPGLLTAVII 227 Query: 241 IGGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITNAV 300 GG+ G+FTPTE++A++ +Y I+V VY+ L R ++ +AM++ II +A Sbjct: 228 FGGVLGGVFTPTESSAVAVIYTLVIAVIVYRTLGFRGFTTAAQNAVKTTAMVMLIIGSAA 287 Query: 301 LFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILFPV 360 F +L+A P+ L + + + L+++N++LL G FM+ + +++I +PI PV Sbjct: 288 AFGWLLALLEAPEQLATLLQTLTDNPILILLLINLILLILGTFMDMAPLIVITSPIFLPV 347 Query: 361 AVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLAF 420 A+ G+DPV FGIM+++N+ +G+ PPVG L+V + K+ + + +WP+ L + A Sbjct: 348 AMATGMDPVQFGIMMMLNLGIGLVTPPVGSVLFVGCAVGKIKVEQAVRTIWPFYLALFAA 407 Query: 421 LVLVTYVPAISLALPNLLG 439 L+ +T+VPA++L LP L G Sbjct: 408 LMAITFVPALTLTLPGLAG 426 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: 597 Number of extensions: 37 Number of successful extensions: 5 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: 426 Length adjustment: 32 Effective length of query: 408 Effective length of database: 394 Effective search space: 160752 Effective search space used: 160752 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 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