Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate CCNA_00664 CCNA_00664 C4-dicarboxylate transport protein
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Caulo:CCNA_00664 Length = 417 Score = 481 bits (1238), Expect = e-140 Identities = 241/409 (58%), Positives = 323/409 (78%), Gaps = 1/409 (0%) Query: 9 KSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQN 68 KS+Y QV++AI +G+L+G +PQ GVALKPLGDGFIKLIK+VIAP+IFCTV GIA M + Sbjct: 2 KSIYVQVLIAIVLGVLVGAIWPQIGVALKPLGDGFIKLIKLVIAPVIFCTVAGGIARMGD 61 Query: 69 MKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVT-AGK 127 MK+ G+ G AL+YFE+VST+AL+IGLVV ++QPG G +ID +TLDAS A YV A Sbjct: 62 MKAFGRVGVKALIYFEVVSTLALVIGLVVGRLIQPGAGFNIDPATLDASIAAGYVEKAQH 121 Query: 128 DQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHVM 187 + +V ++L++IP+T +GAFA+G++LQVL+ +++ GFA R+G +G+ V +D + + Sbjct: 122 GEGMVAYLLHLIPDTFIGAFADGNLLQVLVIAILTGFACVRMGDFGEKVAHVLDETSKLF 181 Query: 188 FNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICRAH 247 F II+++++LAPIGA GAM FTIG YGV +LVQLG L+ FY+T +LFVLVVLG I Sbjct: 182 FGIIHIVVRLAPIGAFGAMGFTIGKYGVEALVQLGALVATFYVTSLLFVLVVLGGIAWVS 241 Query: 248 GFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDGT 307 GFS+ + + YIREELLIVLGTSSSES LP+M+ K+E GA++SVVGLVIPTGYSFNLDGT Sbjct: 242 GFSIFRFLAYIREELLIVLGTSSSESVLPQMMEKLENAGARRSVVGLVIPTGYSFNLDGT 301 Query: 308 SIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHLP 367 +IY+T+A +F+AQAT+T + + ++ LL V +L+SKGA+GVTG+GFI LAATL+ V +P Sbjct: 302 NIYMTLATLFLAQATNTPLSLGQELALLGVAMLTSKGASGVTGAGFITLAATLAVVPDIP 361 Query: 368 VAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAEL 416 +A LA+++G+DRFMSE RALTNLVGN VAT+VVA+W LD +L L Sbjct: 362 IAALAILVGVDRFMSECRALTNLVGNGVATLVVARWEGALDRQRLDRVL 410 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: 656 Number of extensions: 29 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: 444 Length of database: 417 Length adjustment: 32 Effective length of query: 412 Effective length of database: 385 Effective search space: 158620 Effective search space used: 158620 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