Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate Pf6N2E2_3238 TRAP-type C4-dicarboxylate transport system, periplasmic component
Query= SwissProt::Q9HU18 (331 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3238 Length = 331 Score = 467 bits (1202), Expect = e-136 Identities = 230/331 (69%), Positives = 273/331 (82%) Query: 1 MLKHTAKALVCALSLTVAGIVQAADPIVIKFSHVVAEHTPKGQGALLFKKLVEERLPGKV 60 MLK K L+C L+L+ G AA+PIVIKFSHVV E TPKGQGAL+FKKL EERLPGKV Sbjct: 1 MLKPIWKTLLCTLALSAGGNALAAEPIVIKFSHVVGEQTPKGQGALMFKKLAEERLPGKV 60 Query: 61 KVEVYPNSSLFGDGKEMEALLLGDVQIIAPSLAKFEQYTKKLQIFDLPFLFDNIQAVDRF 120 KVEVYPNS+L+GD KEMEALLLG+VQIIA SLAKFEQYTK +Q+FDLPFLFD+I AVDRF Sbjct: 61 KVEVYPNSTLYGDDKEMEALLLGEVQIIARSLAKFEQYTKSVQLFDLPFLFDDIPAVDRF 120 Query: 121 QQSPQGKELLTSMQDKGITGLGYWHNGMKQLSANKPLREPKDARGLKFRVQASKVLEEQF 180 QQSP+G++LL SM+ K ITGL YWHNGMKQLSANKPLR P+DAR L FR+Q S VLEEQF Sbjct: 121 QQSPEGQKLLKSMESKNITGLAYWHNGMKQLSANKPLRTPEDARDLTFRIQTSAVLEEQF 180 Query: 181 KAVRANPRKMSFAEVYQGLQTGVVNGTENPWSNIYSQKMHEVQKYITESDHGVLDYMVIT 240 KAV A + M F+ VYQGL+TG+VNGTEN +SN Y+QK++EVQKY+TES+HG+LDYM+IT Sbjct: 181 KAVDAKAKPMIFSVVYQGLRTGLVNGTENTYSNFYNQKLNEVQKYVTESNHGILDYMLIT 240 Query: 241 NTKFWNGLPEDVRGVLAKTMDEVTVEVNKQAEALNQGDKQRIVEAKTSEIIELTPEQRAE 300 + FW GLP D+R L K + E T N++AE NQ DKQ +++AKT+EII LTPEQR Sbjct: 241 TSDFWKGLPPDIRSELDKIVVESTAYANQEAERFNQQDKQHVLDAKTTEIITLTPEQRNA 300 Query: 301 WRKAMQPVWKKFEGEIGADLIKAAEAANQAQ 331 WR+ M+PVW KFE EIG DLIKAA+A+N+AQ Sbjct: 301 WREKMKPVWAKFEQEIGPDLIKAAQASNKAQ 331 Lambda K H 0.316 0.132 0.376 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: 372 Number of extensions: 13 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: 331 Length of database: 331 Length adjustment: 28 Effective length of query: 303 Effective length of database: 303 Effective search space: 91809 Effective search space used: 91809 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