Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate Pf6N2E2_1302 TRAP-type C4-dicarboxylate transport system, large permease component
Query= SwissProt::O07838 (440 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1302 Length = 426 Score = 278 bits (712), Expect = 2e-79 Identities = 142/432 (32%), Positives = 244/432 (56%), Gaps = 14/432 (3%) Query: 1 MSALIIFGLLIALMLTGMPISISLGLTVLTFLFTMTQVPIDTVALKLFTGIEKFEIMAIP 60 M+ +I G L+ M GMPI+ +L + + +F + +A L G + F +MA+P Sbjct: 1 MTLVIFLGSLVGSMALGMPIAFALLVVSVALMFYLDLFDAQIIAQNLLNGADSFPLMAVP 60 Query: 61 FFILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGS 120 FF+LAG + GG++KR++N A A+VGH GGLG +IA L A++SGS+ A A+ + Sbjct: 61 FFMLAGEIMNVGGLSKRIVNIAMALVGHKRGGLGYVAIIASCLLASLSGSAVADAAALAA 120 Query: 121 VILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSAS 180 +++P MV G + AG+I + +IPPSI +++ VA S S Sbjct: 121 LLVPMMVLAGHNRGRSAGLIAAGSIIAPVIPPSIGFIVFGVA--------------SGVS 166 Query: 181 VGELFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLRQRWTAFREAAWGLMLIVVV 240 + +LF+AG+VPGLML LA W +R K S + + +W + L +++ Sbjct: 167 ISKLFLAGIVPGLMLGASLAVAWWYISRSENVETPPKRSRAEVLRTLLDGSWAMGLPLII 226 Query: 241 IGGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITNAV 300 I G+ GIFTPTEAA ++AVY+ F+S+ +Y+++ + + V+LSSA +++++ ++ A+ Sbjct: 227 ILGLKFGIFTPTEAAVVAAVYSLFVSLVIYREMKVSQLYEVILSSAKTTSVVMLLVAAAM 286 Query: 301 LFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILFPV 360 + S+L+ +P L E + + + L+++ L++ G M+ + +LI+ P+L P Sbjct: 287 VSSWLVTIADLPGQLAEMLAPFMDNQTLLLLVMMTLIILVGTVMDMTPTILILTPVLMPA 346 Query: 361 AVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLAF 420 ++ GIDPV+FG++ ++N +G+ PPVG L V G+ K+ E+ VWP++ Sbjct: 347 VIQAGIDPVYFGVLFLINTAIGLITPPVGTVLNVVCGVAKLDFEEIVRGVWPFMFAQFVV 406 Query: 421 LVLVTYVPAISL 432 L L+ P + L Sbjct: 407 LFLLVLFPQLVL 418 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: 574 Number of extensions: 38 Number of successful extensions: 4 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