Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate 7024209 Shewana3_1416 TRAP dicarboxylate transporter, DctP subunit (RefSeq)
Query= SwissProt::A3QCW5 (336 letters) >FitnessBrowser__ANA3:7024209 Length = 340 Score = 523 bits (1346), Expect = e-153 Identities = 255/327 (77%), Positives = 294/327 (89%) Query: 10 IKQIVKMTSIAALLGASLNSWAAPTEIKFSHVVAENTPKGQMALKFKQLVEERLPGEYQV 69 +K + KM ++A++ S N +AAP EIKFSHVVAENTPKGQMALKFK+LVE+RLPGEY V Sbjct: 13 LKTVAKMLALASVFATSFNVFAAPVEIKFSHVVAENTPKGQMALKFKELVEQRLPGEYTV 72 Query: 70 NVFPNSQLFGDNNELSALLLNDVQFVAPSLSKFERYTKKLQLFDLPFLFKDMDAVNRFQQ 129 +VFPNSQLFGDNNEL+ALLLNDVQFVAPSLSKFERYTK+LQ+FDLPFLF DMDAVNRFQQ Sbjct: 73 SVFPNSQLFGDNNELAALLLNDVQFVAPSLSKFERYTKRLQVFDLPFLFNDMDAVNRFQQ 132 Query: 130 SDAGQQLLNSMKRKGVVGLGYLHNGMKQFSASSPLVLPEDAQGKKFRIMASDVLAAQFQA 189 +AGQ LLNSM RKG+VGLGYLHNGMKQFSA++PL P DA+G KFR+MASDVLAAQF A Sbjct: 133 GEAGQALLNSMSRKGIVGLGYLHNGMKQFSANTPLKQPSDAKGLKFRVMASDVLAAQFDA 192 Query: 190 VEAIPVKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQSNITESNHGVLDYMVVTSN 249 V AIPVKKPFSEVFTLLQTRAIDGQENTWSN YS+KFYEVQS ITESNHGVLDYMVVTS+ Sbjct: 193 VGAIPVKKPFSEVFTLLQTRAIDGQENTWSNTYSQKFYEVQSQITESNHGVLDYMVVTSD 252 Query: 250 TFWKSLPADKRKVIKASLDEAIAYGNEIAAAKVNKDKQAIIDSKRSEVTYLTPEQRAAWV 309 FWKSLPADKRKVIK +LDE+IA GN+IAA K N+DKQ I+DSKRS++ LTP++R W+ Sbjct: 253 AFWKSLPADKRKVIKEALDESIALGNKIAAEKDNEDKQLILDSKRSQLVTLTPDERQKWI 312 Query: 310 NAMKPVWAQFEDKIGKDLIDAAVASNE 336 + MKPVWA+FED++GKD+I+AAVA+N+ Sbjct: 313 DVMKPVWAKFEDQVGKDVIEAAVAANK 339 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: 444 Number of extensions: 9 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: 340 Length adjustment: 28 Effective length of query: 308 Effective length of database: 312 Effective search space: 96096 Effective search space used: 96096 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