Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_092058810.1 BQ4888_RS16820 TRAP transporter large permease subunit
Query= SwissProt::O07838 (440 letters) >NCBI__GCF_900111775.1:WP_092058810.1 Length = 425 Score = 251 bits (642), Expect = 2e-71 Identities = 146/432 (33%), Positives = 245/432 (56%), Gaps = 13/432 (3%) Query: 4 LIIFGLLIALMLTGMPISISLGLTVLTFLFTMTQVPIDTVALKLFTGIEKFEIMAIPFFI 63 LI GL + L L G P+ + L + ++ + +A+++F E ++AIP F Sbjct: 3 LIALGLFL-LALLGAPLFAIIAAGALLG-YQRAEIDLAALAVEVFRLAEMPVLLAIPLFT 60 Query: 64 LAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGSVIL 123 LAG L G +R++N A+ G G L ++ACA F A +G+S T+VA+G+++ Sbjct: 61 LAGYLLGESGAPRRLVNLTQALFGWLPGSLAAVALVACAFFTAFTGASGVTIVALGALLY 120 Query: 124 PAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSASVGE 183 PA+ G+ + F G+ITTSG+LG+L PS+ +++Y + V G+ V + + Sbjct: 121 PALQQAGYDEHFNLGLITTSGSLGLLFAPSLPLILYGIVAQQTEV----GRGVG---IDQ 173 Query: 184 LFMAGVVPGL-MLAGFLAFTTWNRARKFGYPRLEKASLRQRWTAFREAAWGLMLIVVVIG 242 LF+AG++PGL ML L + W+ R PR K + A +AAW L L +V+G Sbjct: 174 LFVAGLLPGLLMLVLLLGYAFWHSRR---LPRERKTAAVGPGRALVDAAWELPLPFIVLG 230 Query: 243 GIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITNAVLF 302 GIY+G F +EAAA++A+Y + V + +++TL +P ++ + M +L I+ ++ Sbjct: 231 GIYSGYFAVSEAAAVTALYVLVVEVVILREITLLQLPGIVRQAMVMVGGILIILGVSLAS 290 Query: 303 SFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILFPVAV 362 + ++ G+P+ L +W+ S FL+ +N+ LL G ++ S ++++ P++ PVAV Sbjct: 291 TNVLIDAGVPERLFDWVQAHVSSRLTFLLWLNLFLLLLGCLLDIFSALVLVVPLILPVAV 350 Query: 363 RLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLAFLV 422 +DP+H GI+ + NM++G PPVGLNL++AS I L A P+LL +L ++ Sbjct: 351 GFNVDPLHLGIIFLANMQIGYLTPPVGLNLFIASYRFDQPILTLYRATLPFLLLLLFCVL 410 Query: 423 LVTYVPAISLAL 434 L+TY P +SL L Sbjct: 411 LITYWPWLSLGL 422 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: 596 Number of extensions: 42 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: 440 Length of database: 425 Length adjustment: 32 Effective length of query: 408 Effective length of database: 393 Effective search space: 160344 Effective search space used: 160344 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 Apr 09 2024. 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