Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate Pf6N2E2_3238 TRAP-type C4-dicarboxylate transport system, periplasmic component
Query= SwissProt::A3QCW5 (336 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3238 Length = 331 Score = 343 bits (880), Expect = 3e-99 Identities = 180/328 (54%), Positives = 229/328 (69%), Gaps = 1/328 (0%) Query: 10 IKQIVKMTSIAALLGASLNSWAA-PTEIKFSHVVAENTPKGQMALKFKQLVEERLPGEYQ 68 +K I K L A N+ AA P IKFSHVV E TPKGQ AL FK+L EERLPG+ + Sbjct: 2 LKPIWKTLLCTLALSAGGNALAAEPIVIKFSHVVGEQTPKGQGALMFKKLAEERLPGKVK 61 Query: 69 VNVFPNSQLFGDNNELSALLLNDVQFVAPSLSKFERYTKKLQLFDLPFLFKDMDAVNRFQ 128 V V+PNS L+GD+ E+ ALLL +VQ +A SL+KFE+YTK +QLFDLPFLF D+ AV+RFQ Sbjct: 62 VEVYPNSTLYGDDKEMEALLLGEVQIIARSLAKFEQYTKSVQLFDLPFLFDDIPAVDRFQ 121 Query: 129 QSDAGQQLLNSMKRKGVVGLGYLHNGMKQFSASSPLVLPEDAQGKKFRIMASDVLAAQFQ 188 QS GQ+LL SM+ K + GL Y HNGMKQ SA+ PL PEDA+ FRI S VL QF+ Sbjct: 122 QSPEGQKLLKSMESKNITGLAYWHNGMKQLSANKPLRTPEDARDLTFRIQTSAVLEEQFK 181 Query: 189 AVEAIPVKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQSNITESNHGVLDYMVVTS 248 AV+A FS V+ L+T ++G ENT+SN Y++K EVQ +TESNHG+LDYM++T+ Sbjct: 182 AVDAKAKPMIFSVVYQGLRTGLVNGTENTYSNFYNQKLNEVQKYVTESNHGILDYMLITT 241 Query: 249 NTFWKSLPADKRKVIKASLDEAIAYGNEIAAAKVNKDKQAIIDSKRSEVTYLTPEQRAAW 308 + FWK LP D R + + E+ AY N+ A +DKQ ++D+K +E+ LTPEQR AW Sbjct: 242 SDFWKGLPPDIRSELDKIVVESTAYANQEAERFNQQDKQHVLDAKTTEIITLTPEQRNAW 301 Query: 309 VNAMKPVWAQFEDKIGKDLIDAAVASNE 336 MKPVWA+FE +IG DLI AA ASN+ Sbjct: 302 REKMKPVWAKFEQEIGPDLIKAAQASNK 329 Lambda K H 0.317 0.130 0.368 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: 321 Number of extensions: 4 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: 336 Length of database: 331 Length adjustment: 28 Effective length of query: 308 Effective length of database: 303 Effective search space: 93324 Effective search space used: 93324 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