Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_092483295.1 BM299_RS09255 TRAP transporter large permease
Query= SwissProt::O07838 (440 letters) >NCBI__GCF_900115975.1:WP_092483295.1 Length = 429 Score = 372 bits (955), Expect = e-107 Identities = 178/435 (40%), Positives = 286/435 (65%), Gaps = 14/435 (3%) Query: 3 ALIIFGLLIALMLTGMPISISLGLTVLTFLFTMTQVPIDTVALKLFTGIEKFEIMAIPFF 62 ALI+ +L+ L+L G PI+ SL + + L + +P+ V +LFT + F ++A+PFF Sbjct: 4 ALILLLVLLLLLLVGFPIAFSLAMAAVAALLSKGTIPLTVVPQRLFTATDSFILLAVPFF 63 Query: 63 ILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGSVI 122 +LAG + HGG+++R++NFA+ ++G GGL L + + A FAA+SGSS AT AIG V+ Sbjct: 64 VLAGELMQHGGISRRLVNFASDLLGWISGGLALVSIASAAFFAAISGSSAATTAAIGGVM 123 Query: 123 LPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSASVG 182 P M +G+ F A V G LG++IPPSI +++Y V T AS+G Sbjct: 124 YPEMRQRGYKPDFTAVVQAVGGTLGVVIPPSIPLIIYGVITG--------------ASIG 169 Query: 183 ELFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLRQRWTAFREAAWGLMLIVVVIG 242 +LF+AG++PGL+ A W A K GY ++++SL++ W +FREA+WGL++ V+++G Sbjct: 170 DLFLAGIIPGLLGAAVYMAVAWKMAGKLGYKTMQRSSLKKTWHSFREASWGLLMPVIILG 229 Query: 243 GIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITNAVLF 302 GIY G+FTPTEAA ++ VYA + F+YK+L ++ +L+ S SAM++ +I A LF Sbjct: 230 GIYGGVFTPTEAAVVAVVYALLVGFFIYKELNWKNFYSMLVKSGLTSAMIMLLIATASLF 289 Query: 303 SFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILFPVAV 362 +++M E IPQA+ +++ S +FL++VN++ L AG F++ +I+L++ PI FP+A+ Sbjct: 290 TWIMTIENIPQAITGAILSMTESKLVFLLLVNMVFLIAGMFLDTVAIILLLIPIFFPIAL 349 Query: 363 RLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLAFLV 422 +LG+DPVHFG++ V N+ VG PP G+ L+V+SG++ + + +L AV P+LL ++ Sbjct: 350 QLGVDPVHFGVIAVFNLAVGQMTPPFGVCLFVSSGVSGVSLEKLFKAVLPYLLAAFILIL 409 Query: 423 LVTYVPAISLALPNL 437 L+TYVP++SL + L Sbjct: 410 LLTYVPSLSLGILEL 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: 616 Number of extensions: 36 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: 429 Length adjustment: 32 Effective length of query: 408 Effective length of database: 397 Effective search space: 161976 Effective search space used: 161976 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