Align C4-dicarboxylate TRAP transporter small permease protein DctQ (characterized)
to candidate WP_004321712.1 C665_RS15565 TRAP transporter small permease
Query= SwissProt::O07837 (227 letters) >NCBI__GCF_000310185.1:WP_004321712.1 Length = 234 Score = 230 bits (587), Expect = 2e-65 Identities = 129/239 (53%), Positives = 149/239 (62%), Gaps = 35/239 (14%) Query: 1 MLRILDRAEEVLIAALIATATVLIFVSVTHRFTLGFVADFVGFFRGHGMTGAAAAAKSLY 60 ML+ILD EE LI L+ AT++IFVSV HR+ G+ L Sbjct: 1 MLKILDHLEEWLITFLMGAATLIIFVSVVHRY------------------GSGLEIPGLQ 42 Query: 61 TTLRGINLVWAQELCIILFVWMAKFGAAYGVRTGIHVGIDVLINRLDAPKRRFFILLGLG 120 L G+NL WAQEL II+FVWMAKFGAAYGVRTGIHVG+DVLINRL AP R F+++GL Sbjct: 43 DWLLGLNLGWAQELTIIMFVWMAKFGAAYGVRTGIHVGVDVLINRLSAPNRARFVVIGLA 102 Query: 121 AGALFTGIIATLGANFVLH---MYHASS-------------TSPDLELPMWLVYLAIPMG 164 AGALFTGI+ TLGA FVL Y S T+PDLE P W+VY AIP G Sbjct: 103 AGALFTGIVGTLGATFVLENGAHYQILSWLGMDTGDLFEGPTTPDLEWPTWMVYAAIPFG 162 Query: 165 SSLMCFRFLQVAFGFARTGELPHHDHGHVDGVDTENEGIDAEGDVLLHSPLTPRDLVEK 223 S LMCFRFLQV F RTGELPHHDHGHVDG++ E+ +D + L PRDL K Sbjct: 163 SYLMCFRFLQVMVAFIRTGELPHHDHGHVDGIEEEHVPVDV-NPYDMGDNLHPRDLKHK 220 Lambda K H 0.328 0.143 0.442 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: 169 Number of extensions: 5 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: 227 Length of database: 234 Length adjustment: 23 Effective length of query: 204 Effective length of database: 211 Effective search space: 43044 Effective search space used: 43044 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 (21.7 bits) S2: 46 (22.3 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