Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate RR42_RS06535 RR42_RS06535 C4-dicarboxylate ABC transporter
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__Cup4G11:RR42_RS06535 Length = 342 Score = 150 bits (379), Expect = 4e-41 Identities = 101/335 (30%), Positives = 178/335 (53%), Gaps = 11/335 (3%) Query: 7 LGALVGATALSLALSVPALAEPIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVDVEV 66 L A + A AL+ A ++ A + K S V+ P P GKG + +L + T+G +++++ Sbjct: 10 LAATIAAAALAPAGAM-AQSYKAEYKMSLVLGPAFPWGKGGEIWADLVRQRTSGRINIKL 68 Query: 67 YPNSQLYKDKE--ELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEALHKVT 124 YP + L + E A++ G + M S + P V++ +F LP++ DY+AL +T Sbjct: 69 YPGTSLVAGDQTREFSAIRQGVIDMAVGSTINWSPQ-VKELNLFSLPFLMPDYKALDALT 127 Query: 125 QGEAGKMLLSKLEAKGITGLAFWDNGFK-IMSANTPLTMPDDFLGLKMRIQSSKVLEAEM 183 QGE GK + + L+ G+ LA+ +NGF+ + ++ + P+D G+K+R+ S + Sbjct: 128 QGEVGKSIFATLDKSGVVPLAWGENGFREVSNSKREIRKPEDLKGMKLRVVGSPLYIETF 187 Query: 184 NALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEV-QKHATVSNHGYLGYAVI 242 NALGA P M++++ A+ +G VDG ENP S K+ V QK+ T + + Sbjct: 188 NALGANPTQMSWADAQPAMASGAVDGQENPQSVFAAAKLYTVGQKYVTTWGYVADPLIFV 247 Query: 243 VNKQFWDG-LPADVRTGLEKAMAESTDYANGIAKEE-NEKALQAMKD--AGTTEFHELTA 298 VNKQ W+ PAD R +++A ++ +A++ E A KD A + +LT Sbjct: 248 VNKQIWESWTPAD-REIVKQAAIDAGKQETALARKGLVEAGAPAWKDMEAHGVKVAQLTP 306 Query: 299 EERAAWEEVLTPVHDEMAERIGAETIAAVKAATAE 333 E A+ + V+D+ ++IG + ++ +A+ A+ Sbjct: 307 AEHDAFRKATAKVYDKWKKQIGVDLVSKAEASIAK 341 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: 218 Number of extensions: 12 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: 342 Length adjustment: 28 Effective length of query: 305 Effective length of database: 314 Effective search space: 95770 Effective search space used: 95770 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