Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate AZOBR_RS09605 AZOBR_RS09605 C4-dicarboxylate ABC transporter
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__azobra:AZOBR_RS09605 Length = 336 Score = 468 bits (1205), Expect = e-137 Identities = 237/326 (72%), Positives = 273/326 (83%), Gaps = 1/326 (0%) Query: 6 ILGALVGATALSLALSVPALAEPIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVDVE 65 +L A V A L A + A EPIVIKFSHVVAP+TPKGKGA KF++LAE+ T G V VE Sbjct: 6 LLCATVAAGCLMAATAATA-QEPIVIKFSHVVAPETPKGKGAEKFKQLAEQRTAGKVKVE 64 Query: 66 VYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEALHKVTQ 125 VYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLG ++FE+FDLPYIF AL KVT Sbjct: 65 VYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGAKEFEIFDLPYIFPCKTALVKVTT 124 Query: 126 GEAGKMLLSKLEAKGITGLAFWDNGFKIMSANTPLTMPDDFLGLKMRIQSSKVLEAEMNA 185 G GK L KLE KGITGLA+WDNGFKIMSAN PL DF GLKMRIQSSKVL+A+M A Sbjct: 125 GPIGKQLFQKLENKGITGLAYWDNGFKIMSANKPLHATADFKGLKMRIQSSKVLDAQMRA 184 Query: 186 LGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGYAVIVNK 245 LGA+PQVMAFSEVYQALQTGVVDGTENPPSNM+TQKM+EVQ HAT+S+HGYLGYAVIVNK Sbjct: 185 LGALPQVMAFSEVYQALQTGVVDGTENPPSNMYTQKMHEVQSHATLSDHGYLGYAVIVNK 244 Query: 246 QFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQAMKDAGTTEFHELTAEERAAWE 305 +FWDGLPADVRT L+ AM E+T+YAN IA+EEN+KAL+AMK AG T+F+ELT +ERA+W Sbjct: 245 KFWDGLPADVRTQLDGAMKEATEYANNIAQEENDKALEAMKAAGKTKFYELTKDERASWR 304 Query: 306 EVLTPVHDEMAERIGAETIAAVKAAT 331 + + PVH++MA R+G E +A++K T Sbjct: 305 QAMLPVHEDMASRVGKELLASIKTET 330 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: 374 Number of extensions: 10 Number of successful extensions: 1 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: 336 Length adjustment: 28 Effective length of query: 305 Effective length of database: 308 Effective search space: 93940 Effective search space used: 93940 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