Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate WP_007474712.1 CMTB2_RS05780 C4-dicarboxylate ABC transporter
Query= SwissProt::A3QCW5 (336 letters) >NCBI__GCF_000170735.1:WP_007474712.1 Length = 329 Score = 270 bits (689), Expect = 5e-77 Identities = 148/313 (47%), Positives = 197/313 (62%), Gaps = 5/313 (1%) Query: 29 SWAAPTEIKFSHVVAENTPKGQMALKFKQLVEERLPGEYQVNVFPNSQLFGDNNELSALL 88 S AA IKFSHVV+ NTPKG+ A F + VEE G +V V+PN+QL D L + Sbjct: 17 SVAADYVIKFSHVVSPNTPKGKAADYFAKRVEELSKGRIKVEVYPNAQLGKDKVILRKMK 76 Query: 89 LNDVQFVAPSLSKFERYTKKLQLFDLPFLFKDMDAVNRFQQSDAGQQLLNSMKRKGVVGL 148 N VQ APS SKF +L LFDLPFLFKD + ++R GQ+LL+ + +KG V L Sbjct: 77 FNAVQMAAPSFSKFTGLVPQLGLFDLPFLFKDENHLHRVLDGKVGQKLLDMVTKKGYVAL 136 Query: 149 GYLHNGMKQFSASS-PLVLPEDAQGKKFRIMASDVLAAQFQAVEAIPVKKPFSEVFTLLQ 207 Y NG KQ + S PL+ P+D +G KFR+M+S VL QF+A+ AIPV PFSEV++ LQ Sbjct: 137 AYWDNGFKQLTDSKRPLIKPDDCKGLKFRVMSSKVLIEQFKALGAIPVVLPFSEVYSALQ 196 Query: 208 TRAIDGQENTWSNIYSKKFYEVQSNITESNHGVLDYMVVTSNTFWKSLPADKRKVIKASL 267 +DGQENT SNIY+KKFYEVQ +T +NHG L Y+VV S FW LP D + VIK ++ Sbjct: 197 QGVVDGQENTISNIYTKKFYEVQRYMTMTNHGYLGYLVVMSKKFWDKLPNDLKAVIKQAM 256 Query: 268 DEAIA----YGNEIAAAKVNKDKQAIIDSKRSEVTYLTPEQRAAWVNAMKPVWAQFEDKI 323 E A + E+ A++NK K+ + + E+ YLTP+QR W ++ ++ +F + I Sbjct: 257 KETTAKERVWAKELNEAQLNKIKEYAKKTGKLEIDYLTPQQRLVWEKKLRTIYPKFYNTI 316 Query: 324 GKDLIDAAVASNE 336 GKDLI A+ E Sbjct: 317 GKDLIKEAIKEGE 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: 322 Number of extensions: 13 Number of successful extensions: 3 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: 329 Length adjustment: 28 Effective length of query: 308 Effective length of database: 301 Effective search space: 92708 Effective search space used: 92708 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 24 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