Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate GFF4195 Psest_4268 tripartite ATP-independent periplasmic transporter solute receptor, DctP family
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__psRCH2:GFF4195 Length = 331 Score = 174 bits (440), Expect = 4e-48 Identities = 108/323 (33%), Positives = 175/323 (54%), Gaps = 10/323 (3%) Query: 8 LLATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKLKVK 67 L A LA A+ +A A P I+F + ++E++ +G+ F + + +R GK++V+ Sbjct: 4 LTAKALACALSLSIAGLAHAADPITIKFSHVVAENTPKGQGALMFKKLVEERLAGKVEVQ 63 Query: 68 GFADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQEADAVFDG 127 + ++SL D + AL+ G +++ S A K V+DLPFLF++ D G Sbjct: 64 VYPNSSLFGDGKEMEALLLGDVQLIAPSLAKFEHYSKGVQVYDLPFLFDDIAAVDRFQKG 123 Query: 128 PFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDMFNG 187 GQ L + DK + GL YW NG + L+ +K P+ + +D +G+K RV + V + F Sbjct: 124 EAGQSLLRSMEDKNITGLGYWHNGMKQLSANK-PLREPKDARGLKFRVQASAVLDEQFKA 182 Query: 188 FGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVLASK 247 AN +SF+E++ ++TG V+G ENP + I S K +EVQKY+T S H ++V+ + Sbjct: 183 VRANPRKMSFAEVYQGLQTGVVNGAENPYSNIYSQKMHEVQKYITESNHGLLDYMVITNT 242 Query: 248 RWYDGLSADER----KIINEAAVASRDFERKDSREASKQSIAYLKDKG-MQINELSDAEL 302 ++++GL AD R I+NE VA + + +A KQ I D G +I L+ + Sbjct: 243 KFWNGLPADVRSELESILNEVTVAVNK-QADELNQADKQRIV---DAGTTEIINLTPEQR 298 Query: 303 GRMREMVKPAMDKFAADGGADLL 325 RE +KP KF + GADL+ Sbjct: 299 EMWREAMKPVWKKFEGEIGADLI 321 Lambda K H 0.317 0.134 0.372 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: 241 Number of extensions: 12 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: 337 Length of database: 331 Length adjustment: 28 Effective length of query: 309 Effective length of database: 303 Effective search space: 93627 Effective search space used: 93627 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