Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate GFF2613 Psest_2664 tripartite ATP-independent periplasmic transporter solute receptor, DctP family
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__psRCH2:GFF2613 Length = 329 Score = 161 bits (408), Expect = 2e-44 Identities = 101/324 (31%), Positives = 173/324 (53%), Gaps = 11/324 (3%) Query: 9 LATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKLKVKG 68 LA L+ +I V A P I+F + +++++ +G+ F + +R GK+KV+ Sbjct: 9 LACALSFSIAGLVHAD-----PVTIKFAHVVADNTPKGQGALLFKKLAEERLPGKVKVEV 63 Query: 69 FADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQEADAVFDGP 128 + ++SL D + AL+ G M+ S A K ++DLPFLF++ AD GP Sbjct: 64 YPNSSLFGDGKEMEALLLGDVHMLAPSLAKFEHYAKAIQIYDLPFLFDDLAAADRFQSGP 123 Query: 129 FGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDMFNGF 188 G+ L + DK + GL YW NG + L+ +K P+ + +D +G+K RV + V + F Sbjct: 124 QGKALLRAMEDKNITGLAYWHNGMKQLSANK-PLREPKDARGLKFRVQASAVLDEQFKAV 182 Query: 189 GANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVLASKR 248 AN +SF+E++ ++TG V+G EN + +S K +EVQ Y+T S H ++V+ + + Sbjct: 183 RANPRKMSFAEVYQGLQTGVVNGTENTWSNYESQKVHEVQPYMTASDHGLIDYMVITNTK 242 Query: 249 WYDGLSAD---ERKIINEAAVASRDFERKDSREASKQSIAYLKDKGMQINELSDAELGRM 305 +++GL D E + I E A + + D + ++Q+IA +I EL+ + + Sbjct: 243 FWNGLPEDLRGELETIMEEVTAEVNRQADDLNQQARQAIA--ASGKTEIIELTPEQRAQW 300 Query: 306 REMVKPAMDKFAADGGADLLNELQ 329 RE +KP KF + GA+L+ Q Sbjct: 301 REAMKPVWKKFENEIGAELIEAAQ 324 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: 222 Number of extensions: 11 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: 329 Length adjustment: 28 Effective length of query: 309 Effective length of database: 301 Effective search space: 93009 Effective search space used: 93009 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