Align C4-dicarboxylate-binding periplasmic protein DctP (characterized, see rationale)
to candidate CCNA_01513 CCNA_01513 C4-dicarboxylate-binding protein
Query= uniprot:I7END8 (333 letters) >FitnessBrowser__Caulo:CCNA_01513 Length = 327 Score = 129 bits (325), Expect = 8e-35 Identities = 92/310 (29%), Positives = 151/310 (48%), Gaps = 16/310 (5%) Query: 13 LTMSAGTAMAAC--DDGEIVVKFSHVTNTDKHPKGI----AASLLEKRINEEMNGTMCLE 66 +T + +AAC + GE ++ D HP G A + I++ NG + L+ Sbjct: 9 ITTALAAPLAACVQEIGERPLR-----GADSHPAGYPTVEAVNHFGALISQRTNGRLRLQ 63 Query: 67 VYPNSTLYNDNKVLEAMLQGDVQLAAPSLSKFEKFTKQFRLFDLPFMFKNIDAVDAFQGS 126 Y L + LE + G + + +L+ + LPF+F++ D + Sbjct: 64 NYAGGQLGEEKDTLEITVFGGLDINRVNLAPLNPIEPLTLVPSLPFLFQSTDHMRRSLDG 123 Query: 127 ENGQAMLDSMQRRGLQGLSYWHNGMKQM-SANKPLINPSDANGLKFRVQSSDVLVAQMEA 185 G+ +L+S++R GL GL+++ +G + + P+ P+D GLK RVQ+S++ +A ++A Sbjct: 124 APGRTILNSLERHGLIGLAFYDSGERSFYNTRGPIRTPADMRGLKLRVQTSNLPIAMVQA 183 Query: 186 IGGSPQKMAFSEVYGALQQGVVDGQENTWSNIYGKKFFEVQDGVTETNHGALDYLVVTSV 245 +G SP M++ EV+ AL QGV+DG EN W + + FEV + T H ++V S Sbjct: 184 LGASPIPMSYGEVFQALVQGVIDGAENNWPSYQDSRHFEVARFYSVTRHVMAPEVLVASA 243 Query: 246 DWLDSLDPAVREQFLTILGEVTATRNSESTKVNAEARQSIIDAG-GVVRELTPEQRAAWV 304 L + RE E ARQ++IDAG VV +L R+A+ Sbjct: 244 RTWAKLSSSDREIIRDAATESVPFMRRLWEARETSARQAMIDAGVEVVEDL---DRSAFQ 300 Query: 305 EAMKPVWEQF 314 AM PVW++F Sbjct: 301 AAMAPVWDRF 310 Lambda K H 0.316 0.130 0.371 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: 239 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 333 Length of database: 327 Length adjustment: 28 Effective length of query: 305 Effective length of database: 299 Effective search space: 91195 Effective search space used: 91195 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 (21.6 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