Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate 5208721 Shew_1224 sodium:dicarboxylate symporter (RefSeq)
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__PV4:5208721 Length = 416 Score = 228 bits (581), Expect = 3e-64 Identities = 131/411 (31%), Positives = 224/411 (54%), Gaps = 22/411 (5%) Query: 6 PLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAG 65 P ++ + I+ + +G++LG + LKPLGD FI IKM++AP+IFC +V I Sbjct: 9 PFWQKVLAGFILGVGLGVVLG----EQATQLKPLGDLFIAAIKMLVAPLIFCAIVVSITS 64 Query: 66 MQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTA 125 + N S+ + L F + TIA LIGL + +++ G + + + + Sbjct: 65 LGNDVSLKRLSIKTLAMFMLTGTIASLIGLAIGSLIDMGGSLELATTEV----------- 113 Query: 126 GKDQSIVGF---ILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDR 182 +++++ GF +L++IP + A G +LQ+++F+ + G A++++G +P+ I+ Sbjct: 114 -RERNVPGFAQVLLDMIPVNPFASLAEGKVLQIIVFAALVGIAINKIGEKAEPLKRTIEA 172 Query: 183 FAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGA 242 A VMF + M+++L PIG G MA+ +G YG+ +L+ LG+ + YI ++ ++ V G Sbjct: 173 GAEVMFQLTRMVLQLTPIGVFGLMAWVVGEYGLSTLLPLGKFIGAIYIAALIHMVFVYGG 232 Query: 243 ICR-AHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYS 301 + R G S ++ R L+ T+SS LP E +G K V+P G + Sbjct: 233 LVRFGAGLSAVQFFRKAMPAQLVAFTTASSFGTLPASTRATETMGVSKKYGAFVLPLGAT 292 Query: 302 FNLDGT-SIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATL 360 N+DG IY +AA+FIAQ +++T + + + ++S G AGV GS ++L+ TL Sbjct: 293 MNMDGCGGIYPAIAAIFIAQIYGIPLEMTDYMLIAVTATVASVGTAGVPGSAMVMLSVTL 352 Query: 361 SAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQ 411 VG LP+ G+A I IDR + R TN+ G+ + VVV K +LD++Q Sbjct: 353 GVVG-LPLEGIAFIASIDRVIDMIRTATNVTGDMMTAVVVGKSEGQLDQEQ 402 Lambda K H 0.326 0.142 0.402 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: 430 Number of extensions: 31 Number of successful extensions: 5 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: 444 Length of database: 416 Length adjustment: 32 Effective length of query: 412 Effective length of database: 384 Effective search space: 158208 Effective search space used: 158208 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 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