Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_004318964.1 C665_RS14795 TRAP transporter large permease
Query= SwissProt::O07838 (440 letters) >NCBI__GCF_000310185.1:WP_004318964.1 Length = 426 Score = 373 bits (957), Expect = e-108 Identities = 189/439 (43%), Positives = 282/439 (64%), Gaps = 15/439 (3%) Query: 1 MSALIIFGLLIALMLTGMPISISLGLTVLTFLFTMTQVPIDTVALKLFTGIEKFEIMAIP 60 M +LI+FGL LM+ G+PI ISLG+ + L V +A L T I+ F +MA+P Sbjct: 1 MISLILFGLFALLMIVGVPIGISLGIAAMAALGYGGVVDSSYLAQSLVTSIDSFPLMAVP 60 Query: 61 FFILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGS 120 FFILAG+ + HGG+++R++ + G + GGLGL V C FAA+SGS PATV AIG Sbjct: 61 FFILAGDLMGHGGISRRLLEVGEILFGRYTGGLGLVAVATCMFFAAISGSGPATVAAIGG 120 Query: 121 VILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSAS 180 ++ PAM+ +G+ + F G++ ++G +G++IPPSI MV+YA + S AS Sbjct: 121 ILFPAMLQRGYDRNFSVGLVASAGCIGVVIPPSIPMVIYATS--------------SGAS 166 Query: 181 VGELFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASL-RQRWTAFREAAWGLMLIVV 239 V LF+AGVVPG+++ L +W ARK GY +E++ + + +A W L++ V+ Sbjct: 167 VSSLFLAGVVPGVLIGVVLMLMSWFIARKAGYHGIERSYTGAEIFRILWDAKWALLVPVI 226 Query: 240 VIGGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITNA 299 ++GGIY GIFTPTEAAA++ Y FF+ VFVYKDL L DV +VL SA SA ++ I+ A Sbjct: 227 ILGGIYGGIFTPTEAAAVAVAYGFFVGVFVYKDLKLADVYKVLAHSALTSATVMVIVGTA 286 Query: 300 VLFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILFP 359 +F ++A EGIP L +V M L+++N+L L G FME + ++I+ PIL P Sbjct: 287 TVFGRVLAIEGIPVKLANEIVALTSDPIMILLLINVLFLVVGCFMETLAAIIILTPILLP 346 Query: 360 VAVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLA 419 V +++G+DPVHFGI+++VN+ +GM PP+G+NL+V S + + + P+LL+M+ Sbjct: 347 VVLKVGVDPVHFGILMIVNLAIGMVTPPMGINLFVGSRVGNAQLEGVIRGATPFLLSMIV 406 Query: 420 FLVLVTYVPAISLALPNLL 438 L+++TYVP I+L LPNL+ Sbjct: 407 VLLVLTYVPQITLWLPNLM 425 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: 603 Number of extensions: 40 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 24 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