Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate WP_011842336.1 RSPH17029_RS17115 DctP family TRAP transporter solute-binding subunit
Query= SwissProt::P37735 (333 letters) >NCBI__GCF_000015985.1:WP_011842336.1 Length = 331 Score = 164 bits (416), Expect = 2e-45 Identities = 99/298 (33%), Positives = 155/298 (52%), Gaps = 3/298 (1%) Query: 31 IKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVDVEVYPNSQLYKDKEELEALQLGAVQML 90 IKF+ TP +G F + E+ + G + V+ N L D + L +LQ G V+M+ Sbjct: 27 IKFAATGQEGTPPVQGMHIFAQKLEEQSGGKLKTRVFANGVLGGDVQVLSSLQGGVVEMM 86 Query: 91 APSLAKFGPLGVQDFEVFDLPYIFKDYEALHKVTQGEAGKMLLSKLEAKGITGLAFWDNG 150 + QDF + DLP+I++D E + + GE G+ L +L G+ GL+FW+ G Sbjct: 87 VWNAGNM-MTQAQDFGILDLPFIYQDEEVMDTLLDGEVGRKLTDQLPEHGVIGLSFWEQG 145 Query: 151 FKIMSANT-PLTMPDDFLGLKMRIQSSKVLEAEMNALGAVPQVMAFSEVYQALQTGVVDG 209 F+ ++ +T + +D GLK+R+Q + +L ALGA P MA +E+Y AL+TG VDG Sbjct: 146 FRQLTNDTREVHRLEDIAGLKVRVQQNPLLVDMWKALGANPTPMAVTELYTALETGAVDG 205 Query: 210 TENPPSNMFTQKMNEVQKHATVSNHGYLGYAVIVNKQFWDGLPADVRTGLEKAMAESTDY 269 E T K EVQK+ +V+ H Y V++ K FWD L D + ++K E+ Sbjct: 206 QECTAPFALTAKYTEVQKYLSVTRHNYNPQIVLIGKPFWDKLTDDEKALIQKVAQETAVE 265 Query: 270 ANGIAKEENEKALQAMKDAGTTEFHELTAEERAAWEEVLTPVHDEMAERIGAETIAAV 327 I++ + AL+ ++ AG E+T EE A +E + PV A+ E + V Sbjct: 266 QRRISRAAQDSALEEIRAAGNV-VTEITPEELARMQEAVAPVIRTYAQTFDPELVRTV 322 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: 224 Number of extensions: 10 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: 331 Length adjustment: 28 Effective length of query: 305 Effective length of database: 303 Effective search space: 92415 Effective search space used: 92415 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 Apr 10 2024. 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