Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate HSERO_RS04250 HSERO_RS04250 C4-dicarboxylate ABC transporter permease
Query= SwissProt::O07838 (440 letters) >FitnessBrowser__HerbieS:HSERO_RS04250 Length = 426 Score = 667 bits (1720), Expect = 0.0 Identities = 343/438 (78%), Positives = 383/438 (87%), Gaps = 14/438 (3%) Query: 1 MSALIIFGLLIALMLTGMPISISLGLTVLTFLFTMTQVPIDTVALKLFTGIEKFEIMAIP 60 M+ALIIF LL ALMLTGMPISISLGLTVLTFLFTMT+VPI +VALKLFTGIEKFEIMAIP Sbjct: 1 MNALIIFVLLFALMLTGMPISISLGLTVLTFLFTMTEVPIQSVALKLFTGIEKFEIMAIP 60 Query: 61 FFILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGS 120 FFILAGNFLTHGGVA+RMINFAT+MVGHWHGGL LAGV+ACALFAAVSGSSPATVVAIGS Sbjct: 61 FFILAGNFLTHGGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGS 120 Query: 121 VILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSAS 180 +ILPAMV QGFP +FGAGVITTSGALGILIPPSIVMVMY+V+T+ S Sbjct: 121 IILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTN--------------TS 166 Query: 181 VGELFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLRQRWTAFREAAWGLMLIVVV 240 VG+LFMAGVVPGL+LA L TTW ARK YPRL+KA+ +R AFR++ WGL LIV+V Sbjct: 167 VGKLFMAGVVPGLLLAFLLGVTTWFLARKNNYPRLKKATWAERAAAFRKSGWGLFLIVIV 226 Query: 241 IGGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITNAV 300 +GGIY G+FTPTEAAAM+AVYAFFI+VFVYKDLTL+ VP+VLL SA+MSAMLLYIITNAV Sbjct: 227 MGGIYTGVFTPTEAAAMAAVYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAV 286 Query: 301 LFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILFPV 360 LFSFL+ E IPQA+ W+ ++GL FL++VNILLL AGN MEPSSIVLI+APILFPV Sbjct: 287 LFSFLVTSENIPQAMAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPV 346 Query: 361 AVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLAF 420 A++LGIDPVHFGI+IVVNMEVGMCHPPVGLNLYVASGITKMGITELT+AV PWLLTML F Sbjct: 347 AMKLGIDPVHFGILIVVNMEVGMCHPPVGLNLYVASGITKMGITELTIAVMPWLLTMLGF 406 Query: 421 LVLVTYVPAISLALPNLL 438 L LVTY PA+SL LPNL+ Sbjct: 407 LALVTYWPALSLWLPNLI 424 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: 734 Number of extensions: 26 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: 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