Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate 3609944 Dshi_3326 TRAP dicarboxylate transporter, DctP subunit (RefSeq)
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__Dino:3609944 Length = 325 Score = 157 bits (398), Expect = 3e-43 Identities = 107/326 (32%), Positives = 166/326 (50%), Gaps = 18/326 (5%) Query: 10 LVGATALSLALSVPALAEP-IVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVDVEVYP 68 L+GA A A PA+A +V++F HV AP + F E A A +V+ + Sbjct: 7 LLGAVA---ACVTPAIASAEMVLRFGHVGAPGSLFEASVNAFAECANGKLGDAAEVQTFG 63 Query: 69 NSQLYKDKEELEALQLGAVQMLAPS--LAKFGPLGVQDFEVFDLPYIFKDYEALHKVTQG 126 SQL D+E L+ L+LG V M PS ++ P +F +F++PYI +D E + +V Q Sbjct: 64 ASQLGNDREMLQKLKLGQVHMSLPSSVMSSVAP----EFGIFEMPYIIRDREHMKRV-QA 118 Query: 127 EAGKMLLSKLEAKGITGLAFWDNGFKIMSANT-PLTMPDDFLGLKMRIQSSKVLEAEMNA 185 E G +G + + +NGF+ ++ N P+ P+D G+K+R + + Sbjct: 119 ELGDTFQEAALGQGYRIIGYMENGFRHITNNVRPINTPEDLAGVKLRTPNGEWRVKMFQE 178 Query: 186 LGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGYAVIVNK 245 GA P M+FSEV+ ALQT V+DG ENP + + + K EVQ + +++ H Y V+V + Sbjct: 179 YGANPTPMSFSEVFTALQTKVIDGQENPYAQIASAKFQEVQSYLSITGHVYTPAYVLVAE 238 Query: 246 QFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQAMKDAGTTEFHELTAEERAAWE 305 W P DVR LE E+ D IA + L +K AG E+ ++AA+ Sbjct: 239 NQWQSWPEDVRAALESCGTETQDTVYEIAANLETELLDVIKAAGV----EVNEADKAAFV 294 Query: 306 EVLTPVHDEMAERI--GAETIAAVKA 329 TP++D A ++ AE I V++ Sbjct: 295 AASTPIYDAFAAQVEGAAEMIETVQS 320 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: 249 Number of extensions: 13 Number of successful extensions: 3 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: 325 Length adjustment: 28 Effective length of query: 305 Effective length of database: 297 Effective search space: 90585 Effective search space used: 90585 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