Align TRAP dicarboxylate transporter DctP subunit; Flags: Precursor (characterized, see rationale)
to candidate SMc00271 SMc00271 periplasmic binding protein
Query= uniprot:Q2IUT5 (332 letters) >FitnessBrowser__Smeli:SMc00271 Length = 325 Score = 152 bits (384), Expect = 1e-41 Identities = 100/317 (31%), Positives = 166/317 (52%), Gaps = 10/317 (3%) Query: 12 AALAL-VGPAAAQQPIVVKFSHVVADNTPKGQAAIKFKELAEKYTNGKVKVEVYPNSQLF 70 A L+L GPAAAQ + SH A PK A++KF EL E+ + G++K++V ++Q Sbjct: 10 AVLSLCAGPAAAQ---TYQLSHNAAAGNPKDVASLKFAELVEQKSEGRLKIDVGGSAQFG 66 Query: 71 GDAKEMEAVALGDVQFIAPSLSKFDKFTKQIQVFDLPFLFNDIAAVDRFQAGKQGQALLR 130 DA+ + + LG + F A S +I + LPFLF D+ + G G + Sbjct: 67 DDAETITNMRLGTIAFSANSQGTTSAVVPEIALLGLPFLFQDLKQAEAVMDGPVGDKIAA 126 Query: 131 SMESKNFLGLAYWHNGMKQIS-ANRPLLKPEDAKGLKFRIQASDILAAQFQGLNATPQKL 189 + E + + LA+W+NG+++ S + R + P D G+K R + F L A+P + Sbjct: 127 AAEQQGLVVLAWWNNGIRETSNSKRQITAPSDLAGMKIRTPPDQMTVDIFTALGASPTPM 186 Query: 190 AFSEVYQALQVGTVDGQENTWSNIFSQKFYEVQKDITESDHGVIDYMVVVNAKWWNGLSK 249 AFSE+Y ALQ G VDGQEN NI S K +EVQ I+ ++H + + ++ L Sbjct: 187 AFSELYIALQQGVVDGQENPLINIHSSKLHEVQPYISMTNHKYESTPFLASKIVFDALLP 246 Query: 250 DLQDAMKKAMDEATKVNNDVAGKLNDEAKQKIASSGASKIHQLTPEQRKQWVEAMKPVWA 309 + Q ++ A EA ++N + G+ + ++ ++G KI+ + P +V+A + V+ Sbjct: 247 EDQQIIRDAAREAGQLNRQMVGEQTTRLRGELEAAGV-KINDVDP---APFVQATQSVYD 302 Query: 310 KFESAIGKDLIDAAVAS 326 K+ + DL+D V + Sbjct: 303 KWRAQY-PDLVDELVGA 318 Lambda K H 0.316 0.129 0.367 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: 240 Number of extensions: 10 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: 332 Length of database: 325 Length adjustment: 28 Effective length of query: 304 Effective length of database: 297 Effective search space: 90288 Effective search space used: 90288 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 (21.6 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