Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate Dsui_2532 Dsui_2532 tripartite ATP-independent periplasmic transporter solute receptor, DctP family
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__PS:Dsui_2532 Length = 341 Score = 145 bits (367), Expect = 1e-39 Identities = 104/337 (30%), Positives = 178/337 (52%), Gaps = 16/337 (4%) Query: 10 LVGATALSLAL-----SVPALAE-PIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVD 63 LV A +L+LAL SV A+ + S V+ P P GK ++ EL ++ T G ++ Sbjct: 4 LVAAASLALALLPLGHSVAHAADYKSEYRLSTVLGPAFPWGKAGERWAELVKQKTEGRIN 63 Query: 64 VEVYPNSQLYKDKE--ELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEALH 121 +++YP + L + E A++ G + + S + P V+ +F LP++ D ++L Sbjct: 64 IKLYPGTSLVGGDQTREFSAIRQGVIDLAIGSSINWSPQ-VKQLNLFSLPFLTPDEKSLD 122 Query: 122 KVTQGEAGKMLLSKLEAKGITGLAFWDNGFKIMS-ANTPLTMPDDFLGLKMRIQSSKVLE 180 + +G GK L + LE +G+ LA+ +NGF+ +S + P+ P D G+K+R+ S + Sbjct: 123 ALIKGPVGKDLFAVLEKQGVVPLAYGENGFRELSNSRHPIRTPADLKGMKIRVVGSPIFI 182 Query: 181 AEMNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEV-QKHATVSNHGYLGY 239 +ALGA P M++++ AL T VDG ENP S K++ + Q+H T+ + Sbjct: 183 DAFSALGANPTQMSWADAQPALATKAVDGQENPLSVFNAAKLHTLGQQHLTLWGYMTDPL 242 Query: 240 AVIVNKQFWDG-LPAD---VRTGLEKAMAESTDYANGIAKEENEKALQAMKDAGTTEFHE 295 +VN+ W+ AD VR E+A AE+ A ++ L+ ++ G T Sbjct: 243 IFVVNRNVWNNWSEADRKAVREAAEQAAAENLVAARKGVSPGDDALLKDIEKNGVT-ITR 301 Query: 296 LTAEERAAWEEVLTPVHDEMAERIGAETIAAVKAATA 332 LTAE+R A++++ PV+D+ AE +G + + +AA A Sbjct: 302 LTAEQRKAFKDLTRPVYDKWAETVGKDLVKKAEAAIA 338 Lambda K H 0.314 0.130 0.364 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: 184 Number of extensions: 8 Number of successful extensions: 4 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: 333 Length of database: 341 Length adjustment: 28 Effective length of query: 305 Effective length of database: 313 Effective search space: 95465 Effective search space used: 95465 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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