Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate HSERO_RS04240 HSERO_RS04240 C4-dicarboxylate ABC transporter
Query= SwissProt::A3QCW5 (336 letters) >FitnessBrowser__HerbieS:HSERO_RS04240 Length = 334 Score = 244 bits (624), Expect = 2e-69 Identities = 135/323 (41%), Positives = 196/323 (60%), Gaps = 4/323 (1%) Query: 10 IKQIVKMTSIAALLGASLNSWAA-PTEIKFSHVVAENTPKGQMALKFKQLVEERLPGEYQ 68 +K I+ + AA++ S N++A P IKFSHVVA +TPKG+ A +FK+L E+ G + Sbjct: 3 LKSILLAMTAAAIV--STNAFAQQPIVIKFSHVVANDTPKGKAAERFKELAEKATKGRVK 60 Query: 69 VNVFPNSQLFGDNNELSALLLNDVQFVAPSLSKFERY-TKKLQLFDLPFLFKDMDAVNRF 127 + V+PNS L+ D EL AL L VQ +APSL+KF K+ ++FDLP++F + + R Sbjct: 61 IEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEVLYRV 120 Query: 128 QQSDAGQQLLNSMKRKGVVGLGYLHNGMKQFSASSPLVLPEDAQGKKFRIMASDVLAAQF 187 + G+ L ++ KG+ GL Y NG K SA+ PL P D +G K RI +S VL AQ Sbjct: 121 TEGPIGKDLFKKLEPKGITGLAYWDNGFKVMSANKPLHHPADFRGLKMRIQSSKVLDAQM 180 Query: 188 QAVEAIPVKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQSNITESNHGVLDYMVVT 247 +A+ A P FSEV+ LQT +DG EN SN+Y++K +EVQ ++T SNHG L Y V+ Sbjct: 181 RALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGYAVIV 240 Query: 248 SNTFWKSLPADKRKVIKASLDEAIAYGNEIAAAKVNKDKQAIIDSKRSEVTYLTPEQRAA 307 + FW LP+D R ++ ++ +A Y N IA + + A+ + ++ V LT ++A Sbjct: 241 NKKFWDGLPSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDAEKAE 300 Query: 308 WVNAMKPVWAQFEDKIGKDLIDA 330 W A+ PV Q +IGKDLIDA Sbjct: 301 WRKALLPVQQQMASRIGKDLIDA 323 Lambda K H 0.317 0.130 0.368 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: 256 Number of extensions: 11 Number of successful extensions: 2 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: 336 Length of database: 334 Length adjustment: 28 Effective length of query: 308 Effective length of database: 306 Effective search space: 94248 Effective search space used: 94248 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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