Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate AO356_25645 AO356_25645 ABC transporter substrate-binding protein
Query= SwissProt::Q9HU18 (331 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25645 Length = 339 Score = 177 bits (449), Expect = 3e-49 Identities = 105/325 (32%), Positives = 168/325 (51%), Gaps = 6/325 (1%) Query: 2 LKHTAKALVCALSLTVAGIVQAADPI---VIKFSHVVAEHTPKGQGALLFKKLVEERLPG 58 L T A CA L + G+ AD I ++F+ + P+GQGA F L+ E+ G Sbjct: 4 LMKTLLAGACATGLLLTGVASHADEIRERTLRFAFQNVKEHPQGQGAQKFADLLSEKSGG 63 Query: 59 KVKVEVYPNSSLFGDGKEMEALLLGDVQIIAPSLAKFEQYTKKLQIFDLPFLFDNIQAVD 118 K+KV ++P +L GD + + AL G + I + + D PFLF+N++ Sbjct: 64 KIKVRLFPGGTLGGDVQTVSALQGGTLDITVLNSGILAAQAPDYAMLDFPFLFNNVEEAH 123 Query: 119 RFQQSPQGKELLTSMQDKGITGLGYWHNGMKQLSANK-PLREPKDARGLKFRVQASKVLE 177 P G++L + KG+ GLGYW G + L+ +K P+ + +D +GLK RV S + Sbjct: 124 AVIDGPVGQKLAAQLDSKGLVGLGYWDLGFRNLTNSKHPVTKLEDMQGLKIRVIQSPIYL 183 Query: 178 EQFKAVRANPRKMSFAEVYQGLQTGVVNGTENPWSNIYSQKMHEVQKYITESDHGVLDYM 237 E F A+ ANP M+F EVY GL+ ++G ENP++ I K +EVQKY++ + H Sbjct: 184 ETFSALGANPVPMAFPEVYTGLEQHTIDGQENPFTVIEGNKFYEVQKYLSVTGHIFNPQS 243 Query: 238 VITNTKFWNGLPEDVRGVLAKTMDEVTVEVNKQAEALNQGDKQRIVEAKTSEIIELTPEQ 297 +I + K WN L +D + ++ E ++ A + DK + A + E+TP + Sbjct: 244 LIISQKTWNRLNDDEKAMIRAAAAEAQA-FQREVTAASM-DKAKATLAAAMTVNEITPAE 301 Query: 298 RAEWRKAMQPVWKKFEGEIGADLIK 322 + R+ ++PV KF + DL+K Sbjct: 302 KDRLRERVKPVVDKFAKSLDGDLVK 326 Lambda K H 0.316 0.132 0.376 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: 258 Number of extensions: 15 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: 331 Length of database: 339 Length adjustment: 28 Effective length of query: 303 Effective length of database: 311 Effective search space: 94233 Effective search space used: 94233 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 (21.6 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