Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate Ac3H11_4175 TRAP-type C4-dicarboxylate transport system, large permease component
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4175 Length = 421 Score = 304 bits (779), Expect = 3e-87 Identities = 167/420 (39%), Positives = 262/420 (62%), Gaps = 4/420 (0%) Query: 3 ILFLFLLLFLLMFIGVPIAVSLGLSGALTIL-LFSPDSVRSLAIKLFETSEHYTLLAIPF 61 I LF L L+ +GVPI V L LSGA+ IL + SP +S +++F + Y L+AIP Sbjct: 2 ITTLFFLAALM--VGVPIGVCLCLSGAVYILSIGSPVLFQSFPMQMFGGVDSYGLIAIPL 59 Query: 62 FLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSI 121 F+L G M +GG+ RRL+D + A +G ++GGLA +LA ML +++ GS+ A VA + + Sbjct: 60 FILIGEIMNSGGITRRLVDLSMAFIGSVKGGLAYVNILANMLVSSIIGSATAQVAIMSQV 119 Query: 122 AIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLL 181 + M + GY + F AG+ G LG +IPPS++ VVY+ + +VG + IAG++PG+LL Sbjct: 120 MVPEMEKQGYDKTFAAGLTVYGGMLGPIIPPSVMFVVYSVLAQVAVGDMLIAGILPGVLL 179 Query: 182 GLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAA 241 L+ VVI ++ V P + +L + + +A LL+ +II+G I SG PTE+A Sbjct: 180 TLLFFVVIALMGFVYNYPRSEKRTLAQRARTVVQASPTLLIPIIIVGSILSGLANPTESA 239 Query: 242 AVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSI 301 AV A+ SA V +V ++ R S P +LL S + +++F++A A +F+ +L ++PQ + Sbjct: 240 AVGALASALVGRYVTKEFRFSAMPAILLRSAIYSAIVLFLVAAAAVFSWLLIYGKVPQMV 299 Query: 302 ASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMEL-GIDPIHLGII 360 A+WV + P FLL+ N++LL+ G ++ +++ API PIA E+ IDP H G++ Sbjct: 300 AAWVQTVAHDPVTFLLLTNVILLVIGTVIDGIPGLIMTAPILLPIATEVYHIDPRHFGVV 359 Query: 361 MVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLAL 420 +VVN+ +GL+TPPVGL+ FV SAVTG G LP+ +I V L++++ P++SL L Sbjct: 360 IVVNLVLGLMTPPVGLSFFVASAVTGAKPGKMFIVTLPFFIISCVALVMLSLFPSLSLGL 419 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: 448 Number of extensions: 23 Number of successful extensions: 3 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: 421 Length adjustment: 32 Effective length of query: 395 Effective length of database: 389 Effective search space: 153655 Effective search space used: 153655 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