Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate WP_092483299.1 BM299_RS09265 TRAP transporter substrate-binding protein
Query= SwissProt::A3QCW5 (336 letters) >NCBI__GCF_900115975.1:WP_092483299.1 Length = 343 Score = 142 bits (357), Expect = 2e-38 Identities = 90/294 (30%), Positives = 144/294 (48%), Gaps = 5/294 (1%) Query: 36 IKFSHVVAENTPKGQMALKFKQLVEERLPGEYQVNVFPNSQLFGDNNELSALLLNDVQFV 95 +K H VAE+ P KFKQ+VEE+ G+ Q++++ N + + + + L L + V Sbjct: 43 LKAGHAVAESHPYHLGLEKFKQIVEEKTGGQVQIDIYANGTIGSERDMIEGLQLGTIDLV 102 Query: 96 APSLSKFERYTKKLQLFDLPFLFKDMDAVNRFQQSDAGQQLLNSMKRKGVVGLGYLHNGM 155 S + ++ + DLPFLF + + + GQ LL G+VGL + NG Sbjct: 103 LTSTGPVINFVPEMGVVDLPFLFSSREHAYQVLDGEIGQDLLEQFGDIGIVGLAFWENGF 162 Query: 156 KQFSASS-PLVLPEDAQGKKFRIMASDVLAAQFQAVEAIPVKKPFSEVFTLLQTRAIDGQ 214 + + S P+ ED QG K R M ++V A F+ + A P + EV+T LQ + IDGQ Sbjct: 163 RNLTNSERPINSVEDIQGLKIRTMENEVHQAAFKELGADPTPMAWGEVYTALQQKTIDGQ 222 Query: 215 ENTWSNIYSKKFYEVQSNITESNHGVLDYMVVTSNTFWKSLPADKRKVIKASLDEAIAYG 274 EN IY+ K YEVQ + + H +++ L +++ +IK + EA Y Sbjct: 223 ENPIPIIYNMKIYEVQKYLALTGHFYSPALLLIGQKSLDKLSPEQQNIIKKAAVEAATYE 282 Query: 275 NEIAAAKVNKDKQAIIDSKRSEVTYLTPEQRAAWVNAMKPVWAQFEDKIGKDLI 328 E KV +D+Q ++ V +T + A A V+ ++E + GKD I Sbjct: 283 RE--QIKVQEDEQLAKLEEKGMV--ITRPDKNALREATMAVYEKYEGRFGKDTI 332 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: 248 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: 336 Length of database: 343 Length adjustment: 28 Effective length of query: 308 Effective length of database: 315 Effective search space: 97020 Effective search space used: 97020 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 Apr 09 2024. 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