Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate SMc00265 SMc00265 periplasmic binding protein
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__Smeli:SMc00265 Length = 336 Score = 160 bits (405), Expect = 4e-44 Identities = 106/336 (31%), Positives = 168/336 (50%), Gaps = 15/336 (4%) Query: 2 LTRRILGALVGATALSLALSVPALAEPIVIKFSHVVAPDTPKGKGAAKFEELAEKY---T 58 +TRR + GA AL ++ A A K ++ + P + +E A+K T Sbjct: 3 MTRRTMLLGTGAVALGASIRTKAHAADFTYKLANNLPVTHPLN---IRLKEAADKILEET 59 Query: 59 NGAVDVEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYE 118 G + + ++P+SQL D E L L+ GA + + S L V + + + + F DY+ Sbjct: 60 GGRLKINIFPSSQLGNDTETLSQLRNGATEFFSLSPLILSTL-VPNAAISGIGFAFPDYD 118 Query: 119 ALHKVTQGEAGKMLLSKLEAKGITGLA-FWDNGFK-IMSANTPLTMPDDFLGLKMRIQSS 176 + K GE G ++E KG+ + WDNGF+ I S+N P+ P+D G K+R+ S Sbjct: 119 TVWKAMDGELGAYARGEIEKKGLVPMEKIWDNGFRQITSSNKPINTPEDLKGFKIRVPPS 178 Query: 177 KVLEAEMNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGY 236 + ++ A GA P + F+EVY AL TG VDG ENP + T K+ EVQKH ++NH + Sbjct: 179 PLWQSMFTAFGAAPTTINFAEVYTALSTGTVDGQENPLAIASTAKLYEVQKHCAMTNHMW 238 Query: 237 LGYAVIVNKQFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQAMKDAGTTEFHEL 296 G+ ++ NKQ W+ LP D+R K + ES + N+ + + +G T Sbjct: 239 DGFWMLANKQAWETLPEDIREIAAKHLNESAIAQRTDTAKVNDTVREQLTQSGMT----F 294 Query: 297 TAEERAAWEEVLTPV--HDEMAERIGAETIAAVKAA 330 T ++AA+ E L + E + G E A ++ A Sbjct: 295 TDPDKAAFRETLRSAGFYAEWKGKFGDEAWAILEKA 330 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: 272 Number of extensions: 14 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: 336 Length adjustment: 28 Effective length of query: 305 Effective length of database: 308 Effective search space: 93940 Effective search space used: 93940 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