Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate Pf6N2E2_1301 TRAP-type C4-dicarboxylate transport system, periplasmic component
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1301 Length = 339 Score = 291 bits (744), Expect = 2e-83 Identities = 148/336 (44%), Positives = 223/336 (66%), Gaps = 4/336 (1%) Query: 1 MKLLRSVLLATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRS 60 MK L + ATGL +L V + A +I+ R +RF + + QG+ + F + ++++S Sbjct: 5 MKTLLAGACATGL---LLGSVVSHADEIRERTLRFAFQNVKEHPQGQGAQKFADLLSEKS 61 Query: 61 GGKLKVKGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQE 120 GGK+KV+ F +LG D+Q +AL GG ++ V ++ L D+A+ D PFLFNN +E Sbjct: 62 GGKIKVRLFPGGTLGGDVQTVSALQGGTLDITVLNSGILAAQAPDYAMLDFPFLFNNVEE 121 Query: 121 ADAVFDGPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPV 180 A AV DGP GQKLA +L+ KGLV L YW+ GFRNLTNSK PV K+ED++G+K+RV+Q+P+ Sbjct: 122 AHAVIDGPVGQKLAVQLDSKGLVALGYWDLGFRNLTNSKHPVTKLEDMQGLKIRVIQSPI 181 Query: 181 YIDMFNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSP 240 Y++ F+ GAN VP++F E++T +E T+DGQENP T I+ +KFYEVQKYL+++ H+++P Sbjct: 182 YLETFSALGANPVPMAFPEVYTGLEQHTIDGQENPFTVIEGNKFYEVQKYLSVTGHIFNP 241 Query: 241 WIVLASKRWYDGLSADERKIINEAAVASRDFERKDSREASKQSIAYLKDKGMQINELSDA 300 ++ S++ ++ L+ DE+ +I AA ++ F+R + AS M +NE++ A Sbjct: 242 QSLIISQKTWNRLNDDEKAMIRSAATEAQKFQR-EVTAASMDKAKVTLAGAMTVNEVTPA 300 Query: 301 ELGRMREMVKPAMDKFAADGGADLLNELQGEISKVR 336 E R RE VKP +DKFA ADL+ + EI+KVR Sbjct: 301 EKDRFRERVKPVVDKFAKSLDADLVKTMYEEIAKVR 336 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: 287 Number of extensions: 7 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: 339 Length adjustment: 28 Effective length of query: 309 Effective length of database: 311 Effective search space: 96099 Effective search space used: 96099 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