Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate Dsui_1262 Dsui_1262 TRAP transporter, DctM subunit
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__PS:Dsui_1262 Length = 488 Score = 187 bits (475), Expect = 6e-52 Identities = 130/429 (30%), Positives = 223/429 (51%), Gaps = 18/429 (4%) Query: 3 ILFLFLLLFLLMFIGVPIAVSLGLSG------ALTILLFSPDSVRSLAIKLFETSEHYTL 56 ++F L+LFLL G P+A +L +G + + L P ++L ++F + TL Sbjct: 11 VMFGALVLFLLF--GYPVAFALAANGMVFGFIGMELGLLHPALFQALPERVFGIMANDTL 68 Query: 57 LAIPFFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVA 116 LAIPFF G + G+A L+D G +RGGLA A + L AA +G A+V Sbjct: 69 LAIPFFTFMGLVLERSGMAEDLLDTIGQLFGPMRGGLAYAVIFVGALLAATTGVVAASVI 128 Query: 117 AVGSIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVV 176 ++G I++ M+R GY + +G++ +GTL +IPPS+V+++ A SVG ++ +V Sbjct: 129 SMGLISLPIMLRYGYDKRLASGVIAASGTLAQIIPPSLVLIIMADQLGKSVGDMYEGAMV 188 Query: 177 PGLLLGLILM--VVIYIVARVKKLPAMP--RVSLREWLASAR---KALWGLLLMVIILGG 229 PGL+L + + VVI + + PA+P SLR R + L+L+ ++LG Sbjct: 189 PGLILTSLYVGYVVILTLIKPNAAPALPLEARSLRGAKLLMRVLTSLVPPLVLIFLVLGT 248 Query: 230 IYSGAFTPTEAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFA 289 I+ G TPTE A+ A + +AL R + +S + + + KL+ ++FI+ + +F Sbjct: 249 IFMGIATPTEGGAMGASGALILALMRKR-LSVSLLKQAMDTTAKLSSFVVFILVGSTVFG 307 Query: 290 HVLTTEQIPQSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAME 349 V + +T L FL+VVNI++ + F++ + I+ P+ P+A + Sbjct: 308 LVFRAVNGDLWVEHLLTSLPGGQLGFLIVVNILVFVLAFFLDFFELSFIIVPLLGPVAEK 367 Query: 350 LGIDPIHLGIIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGAT--IRAALPWLMILLVFL 407 LGID I G+++ VNM+ + PP G LF +V + T A+P++ I ++ + Sbjct: 368 LGIDLIWFGVLLGVNMQTSFMHPPFGFALFYLRSVAPASIKTTDIYWGAVPFVCIQIIMV 427 Query: 408 IIVTYIPAV 416 ++ P + Sbjct: 428 ALIIIFPGI 436 Lambda K H 0.330 0.144 0.425 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: 461 Number of extensions: 22 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: 427 Length of database: 488 Length adjustment: 33 Effective length of query: 394 Effective length of database: 455 Effective search space: 179270 Effective search space used: 179270 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 (21.9 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