Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate HSERO_RS04240 HSERO_RS04240 C4-dicarboxylate ABC transporter
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__HerbieS:HSERO_RS04240 Length = 334 Score = 442 bits (1136), Expect = e-129 Identities = 222/328 (67%), Positives = 261/328 (79%) Query: 5 RILGALVGATALSLALSVPALAEPIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVDV 64 ++ L+ TA ++ + +PIVIKFSHVVA DTPKGK A +F+ELAEK T G V + Sbjct: 2 KLKSILLAMTAAAIVSTNAFAQQPIVIKFSHVVANDTPKGKAAERFKELAEKATKGRVKI 61 Query: 65 EVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEALHKVT 124 EVYPNS LYKDKEELEALQLGAVQMLAPSLAKFGPLGV++FEVFDLPYIF E L++VT Sbjct: 62 EVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEVLYRVT 121 Query: 125 QGEAGKMLLSKLEAKGITGLAFWDNGFKIMSANTPLTMPDDFLGLKMRIQSSKVLEAEMN 184 +G GK L KLE KGITGLA+WDNGFK+MSAN PL P DF GLKMRIQSSKVL+A+M Sbjct: 122 EGPIGKDLFKKLEPKGITGLAYWDNGFKVMSANKPLHHPADFRGLKMRIQSSKVLDAQMR 181 Query: 185 ALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGYAVIVN 244 ALGA PQV+AFSEVYQALQTGVVDGTENPPSN++TQKM+EVQKH TVSNHGYLGYAVIVN Sbjct: 182 ALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGYAVIVN 241 Query: 245 KQFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQAMKDAGTTEFHELTAEERAAW 304 K+FWDGLP+D+RT LE AM ++T YAN IA++EN+ AL A++ G T + LT E+A W Sbjct: 242 KKFWDGLPSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDAEKAEW 301 Query: 305 EEVLTPVHDEMAERIGAETIAAVKAATA 332 + L PV +MA RIG + I AV +A Sbjct: 302 RKALLPVQQQMASRIGKDLIDAVNKESA 329 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: 348 Number of extensions: 11 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: 334 Length adjustment: 28 Effective length of query: 305 Effective length of database: 306 Effective search space: 93330 Effective search space used: 93330 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