Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate 6938088 Sama_2209 C4-dicarboxylate-binding periplasmic protein (RefSeq)
Query= SwissProt::A3QCW5 (336 letters) >FitnessBrowser__SB2B:6938088 Length = 339 Score = 517 bits (1332), Expect = e-151 Identities = 255/322 (79%), Positives = 291/322 (90%) Query: 15 KMTSIAALLGASLNSWAAPTEIKFSHVVAENTPKGQMALKFKQLVEERLPGEYQVNVFPN 74 K + +A +LG S + A P EIKFSHVVAENTPKGQMALKFK+LVE RLPGEY+V+VFPN Sbjct: 17 KASLLATVLGFSFGAVAEPVEIKFSHVVAENTPKGQMALKFKELVESRLPGEYKVSVFPN 76 Query: 75 SQLFGDNNELSALLLNDVQFVAPSLSKFERYTKKLQLFDLPFLFKDMDAVNRFQQSDAGQ 134 SQLFGDNNEL+ALLLNDVQ VAPSLSKFERYTKKLQ+FDLPFLF+DMDAV+RFQQS+AGQ Sbjct: 77 SQLFGDNNELAALLLNDVQLVAPSLSKFERYTKKLQVFDLPFLFEDMDAVDRFQQSEAGQ 136 Query: 135 QLLNSMKRKGVVGLGYLHNGMKQFSASSPLVLPEDAQGKKFRIMASDVLAAQFQAVEAIP 194 QLLNSM RKG+VGLGYLHNGMKQFSA++ L LP DA GKKFRIM SDV+AAQF+AV AIP Sbjct: 137 QLLNSMSRKGLVGLGYLHNGMKQFSANNALSLPGDAAGKKFRIMPSDVIAAQFEAVGAIP 196 Query: 195 VKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQSNITESNHGVLDYMVVTSNTFWKS 254 VKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQ++ITESNHGVLDYM+VTS TFWKS Sbjct: 197 VKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNHGVLDYMLVTSETFWKS 256 Query: 255 LPADKRKVIKASLDEAIAYGNEIAAAKVNKDKQAIIDSKRSEVTYLTPEQRAAWVNAMKP 314 LP DKR++IK S+DEA+A GN++A K N+D+Q I+DSKR E+ LTPEQR AWVNAM+P Sbjct: 257 LPKDKREIIKQSMDEAVALGNKLALEKANEDRQLILDSKRVELVTLTPEQRQAWVNAMRP 316 Query: 315 VWAQFEDKIGKDLIDAAVASNE 336 VW+QFEDKIGKDLI+AA ++N+ Sbjct: 317 VWSQFEDKIGKDLIEAAESANK 338 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: 437 Number of extensions: 5 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: 339 Length adjustment: 28 Effective length of query: 308 Effective length of database: 311 Effective search space: 95788 Effective search space used: 95788 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