Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate Ac3H11_3524 TRAP-type C4-dicarboxylate transport system, periplasmic component
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3524 Length = 335 Score = 331 bits (848), Expect = 2e-95 Identities = 163/332 (49%), Positives = 230/332 (69%), Gaps = 3/332 (0%) Query: 5 RSVLLATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKL 64 +++ LA L AA+ APVAA +K + G GLS+ Q +AV+ F E + +SGGK+ Sbjct: 4 KTLALAATLLAALAAPVAAQ---VKEHTFKVGIGLSDDHPQAQAVRHFAERLQAKSGGKM 60 Query: 65 KVKGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQEADAV 124 K FA +LG+D+ M +AL GG EM + ++TL+ ++K F V +LP FN E EADA+ Sbjct: 61 NAKLFASGALGNDVSMTSALRGGTLEMTIPDSSTLMSLIKPFGVLNLPLTFNTEAEADAL 120 Query: 125 FDGPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDM 184 DGPFGQKL A L DKGL+GL +WENGFR++TNS+R + +DL G+KLRV+Q+P+++D Sbjct: 121 LDGPFGQKLLAMLPDKGLIGLGFWENGFRHVTNSRRAINTADDLAGLKLRVIQSPLFLDT 180 Query: 185 FNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVL 244 F+ G NA P+ F+EL+TAME VDGQENP TI +SKFYEVQK+L +S+H+YS W++L Sbjct: 181 FSALGTNATPMPFTELYTAMEQKAVDGQENPPATILASKFYEVQKHLVLSRHMYSAWVLL 240 Query: 245 ASKRWYDGLSADERKIINEAAVASRDFERKDSREASKQSIAYLKDKGMQINELSDAELGR 304 SK+ +DGLSADERKI+ EAA + FERK R S+ ++ LK GMQI EL AE + Sbjct: 241 ISKKTWDGLSADERKIVQEAAREATLFERKTIRAFSQTALGELKKAGMQITELPAAEQAK 300 Query: 305 MREMVKPAMDKFAADGGADLLNELQGEISKVR 336 +R ++P + K+ + G + +E+ GE++K R Sbjct: 301 LRTKLQPVLAKYGKEFGEETTSEMMGELAKAR 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: 286 Number of extensions: 10 Number of successful extensions: 1 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: 335 Length adjustment: 28 Effective length of query: 309 Effective length of database: 307 Effective search space: 94863 Effective search space used: 94863 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