Align TRAP dicarboxylate transporter, DctP subunit (characterized, see rationale)
to candidate WP_090439690.1 BLS63_RS03220 C4-dicarboxylate ABC transporter
Query= uniprot:Q88NN8 (323 letters) >NCBI__GCF_900100495.1:WP_090439690.1 Length = 324 Score = 526 bits (1355), Expect = e-154 Identities = 258/324 (79%), Positives = 294/324 (90%), Gaps = 1/324 (0%) Query: 1 MTFKRKLLLAVLPFAFSVA-MPASALDIKFAEIHPAGYPTVVAEQNMGKKLEDASNGEIT 59 M KRKLL+A LP AF +A + +A +K AEIHPAGYPTVVA +N+GKKL+ A+NGEIT Sbjct: 1 MNCKRKLLIAALPLAFCLAGLAQAATTLKIAEIHPAGYPTVVAMENLGKKLDAATNGEIT 60 Query: 60 FKMFAGGVLGSEKEVIEQAQIGAVQMTRVSLGIVGPVVPDVNVFNMPFVFRDHDHMRKII 119 +++FAGGVLGSEKEVIEQ QIGAVQ+TRVSLG VGPVVPDVNVFNMPFVFRDH HMRK+I Sbjct: 61 YRLFAGGVLGSEKEVIEQTQIGAVQLTRVSLGAVGPVVPDVNVFNMPFVFRDHAHMRKVI 120 Query: 120 DGEIGQEILDKITNSDFNLVALAWMDGGSRSIYTKKPVRSLEDLKGMKIRVQGNPLFIDM 179 DG IGQEILDKIT S+FN+V LAWMDGG+R++YTKKPVRSLEDLKGMKIRV GNPLFID Sbjct: 121 DGAIGQEILDKITASEFNMVGLAWMDGGTRNLYTKKPVRSLEDLKGMKIRVMGNPLFIDT 180 Query: 180 MNAMGGNGIAMDTGEIFSALQTGVIDGAENNPPTLLEHNHFQSAKYYTLTGHLILPEPVV 239 +NAMG NGIAMDTGEIFSALQTGVIDGAENNPPT+LEHNH+++A YY+LTGHLI+PEP++ Sbjct: 181 LNAMGANGIAMDTGEIFSALQTGVIDGAENNPPTMLEHNHYRNANYYSLTGHLIIPEPLM 240 Query: 240 MSKTTWNKLSPEQQALVKKVAREAQMEERALWDAKSAASEEKLKAAGVEFITVDKKPFYD 299 MSKTTW++L+PEQQALVKK AREAQMEER LWDAKSA+SE KLK AGVEFI VDK+PFYD Sbjct: 241 MSKTTWDQLTPEQQALVKKFAREAQMEERVLWDAKSASSETKLKEAGVEFIEVDKQPFYD 300 Query: 300 ATASVREKYGAQYADLMKRIDAVQ 323 ATA VREKYGA YA+L+KRI+AVQ Sbjct: 301 ATAPVREKYGAPYAELIKRIEAVQ 324 Lambda K H 0.318 0.134 0.381 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: 363 Number of extensions: 15 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: 323 Length of database: 324 Length adjustment: 28 Effective length of query: 295 Effective length of database: 296 Effective search space: 87320 Effective search space used: 87320 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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