Align TRAP transporter, subunit DctQ (characterized, see rationale)
to candidate WP_051301796.1 A3GO_RS22360 TRAP transporter small permease
Query= uniprot:I7EY26 (225 letters) >NCBI__GCF_000428045.1:WP_051301796.1 Length = 208 Score = 209 bits (531), Expect = 4e-59 Identities = 102/205 (49%), Positives = 138/205 (67%), Gaps = 18/205 (8%) Query: 12 INTLEETLIALLLGLMTLITFANVVARFVFNSNILWALELTVFLFAWLVLLGASYAVKVH 71 ++ +EET IA+ LGLMTLITFANV+AR++FN+NILWALE TVFLFAWLVL+G SY VK Sbjct: 13 MDQIEETAIAICLGLMTLITFANVIARYLFNNNILWALEATVFLFAWLVLMGCSYGVKKQ 72 Query: 72 AHLGVDAILNMVSPGARRVIGLISVGCCLVFSLLLLKGAYDYWAVFADLPPTSGRWFPTG 131 H+GVD ++NMVSP A RV+ L+SV CL F++LLL G++DYW F Sbjct: 73 FHIGVDVVINMVSPKAHRVMALLSVTACLAFAILLLVGSWDYWYAF-------------- 118 Query: 132 FDMKARSQSFYEVQDVPMVAIFGFLEDLINYGDSYEKLPKVVPYVVLPLSMLLMLLRFAQ 191 A ++F E DVPM F +N G+ YEK+P+ +PY LPL M L+ LRF + Sbjct: 119 ----ATKRAFLETNDVPMPDFLQFFATWLNEGELYEKMPRFIPYAALPLGMGLLTLRFLE 174 Query: 192 AAMQILRGDVDRLVASHEVEDEIAE 216 A ++++G+ D ++ASHE E ++E Sbjct: 175 VAWKVIKGEQDSIIASHEAEAAVSE 199 Lambda K H 0.327 0.142 0.427 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: 120 Number of extensions: 5 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: 225 Length of database: 208 Length adjustment: 22 Effective length of query: 203 Effective length of database: 186 Effective search space: 37758 Effective search space used: 37758 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: 45 (21.9 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