Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate AZOBR_RS30130 AZOBR_RS30130 C4-dicarboxylate ABC transporter
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__azobra:AZOBR_RS30130 Length = 319 Score = 172 bits (435), Expect = 1e-47 Identities = 106/311 (34%), Positives = 175/311 (56%), Gaps = 11/311 (3%) Query: 8 LLATGLAAAILAPVAASAQDIKPRLIRFG-YGLSESSNQGRAVKFFVEDMAKRSGGKLKV 66 LLA A A+LA SA+D + I G Y E AVK+ + +++RS GKL V Sbjct: 3 LLAACAAGALLA-APVSARDFRSADIHPGDYPTVE------AVKYMGKLLSERSNGKLGV 55 Query: 67 KGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQEADAVFD 126 K + + +LG++ + G +MM + A L +V + V LPF+F + AV D Sbjct: 56 KVYPNGALGNERDTIEQIKIGGLDMMRINVAPLNNVVPESMVVALPFIFRDTDHMHAVLD 115 Query: 127 GPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDMFN 186 GP G ++ A + +GL+GL ++++G R+L SK+PV + DLKG+K+RV Q+ +++ M Sbjct: 116 GPIGDEILAAMESQGLIGLAFYDSGSRSLY-SKKPVSSLADLKGMKIRVQQSDLFVSMIE 174 Query: 187 GFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVLAS 246 GAN P+ E++T ++TG +D EN + +SS+ +E KY T ++H +P +++ S Sbjct: 175 ALGANPTPMPMGEVYTGLKTGIIDAAENNYPSYESSRHFEAAKYFTRTEHAMAPEVLVFS 234 Query: 247 KRWYDGLSADERKIINEAAVASRDFERKDSREASKQSIAYLKDKGMQINELSDAELGRMR 306 K +D LS D++ I +AA S + RK E + S A ++ G QI+++ + + Sbjct: 235 KVTWDRLSKDDQAAIRKAAKDSVPYMRKLWTEREEASRAIVEKAGSQISDVKNKQ--EFI 292 Query: 307 EMVKPAMDKFA 317 + +KP KFA Sbjct: 293 DAMKPVFAKFA 303 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: 233 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: 337 Length of database: 319 Length adjustment: 28 Effective length of query: 309 Effective length of database: 291 Effective search space: 89919 Effective search space used: 89919 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