Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate HSERO_RS14035 HSERO_RS14035 C4-dicarboxylate ABC transporter
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__HerbieS:HSERO_RS14035 Length = 344 Score = 404 bits (1039), Expect = e-117 Identities = 205/324 (63%), Positives = 249/324 (76%), Gaps = 5/324 (1%) Query: 9 ALVGATALSLALSVPALA-----EPIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVD 63 AL ++L L PA +PI+IKFSHVVA DTPKGKGA +F+ELAEK T G V Sbjct: 9 ALAACAFVTLGLPQPAALAQQPQQPIIIKFSHVVANDTPKGKGAERFKELAEKATQGRVK 68 Query: 64 VEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEALHKV 123 VEVYPNS LYKDKEELEALQLG+VQMLAPSLAKFGPLG ++FEVFDLPYIF D L +V Sbjct: 69 VEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAREFEVFDLPYIFPDKAVLKRV 128 Query: 124 TQGEAGKMLLSKLEAKGITGLAFWDNGFKIMSANTPLTMPDDFLGLKMRIQSSKVLEAEM 183 T+G G+ L KLE KGI GLA+WDNG K+M+AN PL DF LKMRIQSSKVL+ + Sbjct: 129 TEGPIGQGLFQKLEGKGIKGLAYWDNGMKVMTANRPLHKVADFRALKMRIQSSKVLDEQF 188 Query: 184 NALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGYAVIV 243 AL A PQV+AFSEVYQA+QTGVVDG+EN PSN++TQKM+EVQ + TVS+HGY+GYAVIV Sbjct: 189 RALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTVSDHGYIGYAVIV 248 Query: 244 NKQFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQAMKDAGTTEFHELTAEERAA 303 NK+FW+ LPAD+R+ LE AM ++T YAN IA++EN+ AL A+K +G T + L+ +E+A Sbjct: 249 NKKFWEALPADIRSQLEAAMKQATLYANTIAQKENDDALAAIKASGKTRVYTLSEQEKAE 308 Query: 304 WEEVLTPVHDEMAERIGAETIAAV 327 W L PVH MA R+GA+ I A+ Sbjct: 309 WRRALLPVHKSMAARVGADLIEAI 332 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: 346 Number of extensions: 9 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: 344 Length adjustment: 28 Effective length of query: 305 Effective length of database: 316 Effective search space: 96380 Effective search space used: 96380 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