Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate 208331 DVU2822 TRAP dicarboxylate family transporter
Query= uniprot:G8AR24 (337 letters) >MicrobesOnline__882:208331 Length = 336 Score = 170 bits (431), Expect = 4e-47 Identities = 100/332 (30%), Positives = 182/332 (54%), Gaps = 6/332 (1%) Query: 4 LRSVLLATGLAA-AILAPVAAS--AQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRS 60 +R+ A +AA A +A +AA A+ K IR + ++ +N + F E + +S Sbjct: 1 MRNFFKANAIAAIACIAMLAAGSYAEAAKRITIRLAHPMAPGNNVTLGYEKFKEIVEAKS 60 Query: 61 GGKLKVKGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQE 120 GK++++ F + LGSD A G EM S+ + K+ VFDLP++ + E + Sbjct: 61 NGKVRIQLFGNCMLGSDRVTMEATQRGTLEMASSSSPNMTNFSKEMMVFDLPYITSPEHQ 120 Query: 121 AD---AVFDGPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQ 177 A+ +G G++L A GL ++Y E G+RN +K+P++ +DLK +K+R Sbjct: 121 EKLYKALDEGALGERLDAIAAGIGLKPIMYSEYGYRNFATTKKPIKTADDLKNLKVRTTD 180 Query: 178 NPVYIDMFNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHV 237 +P+ + + + G N P+S+ E +TA++ GTVDG+ N + +K EV ++ S H Sbjct: 181 SPIEVAVASALGMNPTPVSWGETYTALQQGTVDGEGNTFGLLNDAKHTEVLRHAMDSAHN 240 Query: 238 YSPWIVLASKRWYDGLSADERKIINEAAVASRDFERKDSREASKQSIAYLKDKGMQINEL 297 YS +++ +K ++D L AD ++I+ ++ + ++R S + K++ ++G+ I +L Sbjct: 241 YSMHLLMINKAYFDKLPADVQQILVDSGKEALAYQRAISNDLEKKAEQAFVERGIVITKL 300 Query: 298 SDAELGRMREMVKPAMDKFAADGGADLLNELQ 329 + E +MRE+ +P DKF+ D ADL+ +Q Sbjct: 301 APEERAKMRELTRPVWDKFSNDIPADLVKLVQ 332 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: 235 Number of extensions: 9 Number of successful extensions: 2 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: 336 Length adjustment: 28 Effective length of query: 309 Effective length of database: 308 Effective search space: 95172 Effective search space used: 95172 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