Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate Ac3H11_1949 TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding protein
Query= SwissProt::A3QCW5 (336 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1949 Length = 345 Score = 131 bits (329), Expect = 3e-35 Identities = 103/335 (30%), Positives = 162/335 (48%), Gaps = 14/335 (4%) Query: 8 TFIKQIVKMTSIAALLG-ASLNSWAAPTEIKFSHVVAENTPKGQMALKFKQLVEERLPGE 66 TF+ V + A A++ +E + S V+ P G+ + V ER G Sbjct: 5 TFLTSAVAAAAALAFTAPAAIAQTTYKSEYRMSLVLGTAFPWGKGGELWANKVRERTQGR 64 Query: 67 YQVNVFPNSQLF-GDNN-ELSALLLNDVQFVAPSLSKFERYTKKLQLFDLPFLFKDMDAV 124 + ++P L GD E SAL + S + K+L LF LPFLF D AV Sbjct: 65 INIKLYPGVSLIQGDQTREFSALRQGVIDMAVGSTINWSPQVKQLNLFSLPFLFPDYAAV 124 Query: 125 NRFQQSDAGQQLLNSMKRKGVVGLGYLHNGMKQFSASSPLV-LPEDAQGKKFRIMASDVL 183 + Q D G+ + ++ + GVV L + NG ++ S S + PED +G K R++ S + Sbjct: 125 DAVTQGDVGKSIFATLDKAGVVPLAWGENGYREISNSKKAIKTPEDLKGLKIRVVGSPLF 184 Query: 184 AAQFQAVEAIPVKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEV-QSNITESNHGVLD 242 F A+ A P + +++ + A+DGQEN S + K + V Q NIT + Sbjct: 185 LDTFTALGANPTQMSWADAQPAFASGAVDGQENPLSIFTAAKLHSVAQKNITLWGYVNDP 244 Query: 243 YMVVTSNTFWKS-LPADKRKVIKASLDEAIAYGNEIAAAK---VNKDKQAI--IDSKRSE 296 + V + W S PAD+ V +A++D A EIA A+ V DK + I + Sbjct: 245 LIFVVNKEIWNSWTPADREIVKQAAID---AGKEEIAIARKGVVEADKPLLKDISALGVT 301 Query: 297 VTYLTPEQRAAWVNAMKPVWAQFEDKIGKDLIDAA 331 VT L+P +RAA+V +PV+ +++ +IG DL++ A Sbjct: 302 VTQLSPAERAAFVKVTRPVYDKWKGQIGADLVNMA 336 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: 295 Number of extensions: 16 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: 345 Length adjustment: 28 Effective length of query: 308 Effective length of database: 317 Effective search space: 97636 Effective search space used: 97636 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