Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate WP_007474712.1 CMTB2_RS05780 C4-dicarboxylate ABC transporter
Query= SwissProt::P37735 (333 letters) >NCBI__GCF_000170735.1:WP_007474712.1 Length = 329 Score = 280 bits (715), Expect = 5e-80 Identities = 152/317 (47%), Positives = 205/317 (64%), Gaps = 9/317 (2%) Query: 13 ATALSLALSVPALAEPIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVDVEVYPNSQL 72 +TAL ++LSV A VIKFSHVV+P+TPKGK A F + E+ + G + VEVYPN+QL Sbjct: 9 STALIVSLSVAA---DYVIKFSHVVSPNTPKGKAADYFAKRVEELSKGRIKVEVYPNAQL 65 Query: 73 YKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEALHKVTQGEAGKML 132 KDK L ++ AVQM APS +KF L V +FDLP++FKD LH+V G+ G+ L Sbjct: 66 GKDKVILRKMKFNAVQMAAPSFSKFTGL-VPQLGLFDLPFLFKDENHLHRVLDGKVGQKL 124 Query: 133 LSKLEAKGITGLAFWDNGFK-IMSANTPLTMPDDFLGLKMRIQSSKVLEAEMNALGAVPQ 191 L + KG LA+WDNGFK + + PL PDD GLK R+ SSKVL + ALGA+P Sbjct: 125 LDMVTKKGYVALAYWDNGFKQLTDSKRPLIKPDDCKGLKFRVMSSKVLIEQFKALGAIPV 184 Query: 192 VMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGYAVIVNKQFWDGL 251 V+ FSEVY ALQ GVVDG EN SN++T+K EVQ++ T++NHGYLGY V+++K+FWD L Sbjct: 185 VLPFSEVYSALQQGVVDGQENTISNIYTKKFYEVQRYMTMTNHGYLGYLVVMSKKFWDKL 244 Query: 252 PADVRTGLEKAMAESTDYANGIAKEENEKALQAMKD----AGTTEFHELTAEERAAWEEV 307 P D++ +++AM E+T AKE NE L +K+ G E LT ++R WE+ Sbjct: 245 PNDLKAVIKQAMKETTAKERVWAKELNEAQLNKIKEYAKKTGKLEIDYLTPQQRLVWEKK 304 Query: 308 LTPVHDEMAERIGAETI 324 L ++ + IG + I Sbjct: 305 LRTIYPKFYNTIGKDLI 321 Lambda K H 0.314 0.130 0.364 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: 277 Number of extensions: 8 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: 333 Length of database: 329 Length adjustment: 28 Effective length of query: 305 Effective length of database: 301 Effective search space: 91805 Effective search space used: 91805 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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