Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate CCNA_00664 CCNA_00664 C4-dicarboxylate transport protein
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__Caulo:CCNA_00664 Length = 417 Score = 513 bits (1322), Expect = e-150 Identities = 252/409 (61%), Positives = 334/409 (81%), Gaps = 1/409 (0%) Query: 7 KSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMES 66 KS+Y QVL AI +G+L+G +P+IG +KPLGDGF+KLIK++IAPVIFCTV GIA M Sbjct: 2 KSIYVQVLIAIVLGVLVGAIWPQIGVALKPLGDGFIKLIKLVIAPVIFCTVAGGIARMGD 61 Query: 67 MKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKD 126 MKA GR G AL+YFE+VST+AL+IGL++ ++QPGAG N+DPATLDA A Y ++A+ Sbjct: 62 MKAFGRVGVKALIYFEVVSTLALVIGLVVGRLIQPGAGFNIDPATLDASIAAGYVEKAQH 121 Query: 127 -QGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVI 185 +G+VA+++ +IP + IGAFA GN+LQVL+ A+L GFA R+G G+ + +V++ S++ Sbjct: 122 GEGMVAYLLHLIPDTFIGAFADGNLLQVLVIAILTGFACVRMGDFGEKVAHVLDETSKLF 181 Query: 186 FGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKAT 245 FGII++++RLAPIGAFGAM FTIGKYGV LVQLG L+ FY+T +LFV++VLG IA + Sbjct: 182 FGIIHIVVRLAPIGAFGAMGFTIGKYGVEALVQLGALVATFYVTSLLFVLVVLGGIAWVS 241 Query: 246 GFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGT 305 GFSIF+F+ YIREELLIVLGTSSSES LP+M++K+E G R+SVVGLVIPTGYSFNLDGT Sbjct: 242 GFSIFRFLAYIREELLIVLGTSSSESVLPQMMEKLENAGARRSVVGLVIPTGYSFNLDGT 301 Query: 306 SIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLP 365 +IY+T+A +F+AQATN+ + + ++ LL V +L+SKGA+GVTG+GFI LAATL+ V +P Sbjct: 302 NIYMTLATLFLAQATNTPLSLGQELALLGVAMLTSKGASGVTGAGFITLAATLAVVPDIP 361 Query: 366 VAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVL 414 +A LA+++G+DRFMSE RALTNLVGNGVAT+VVA+W LD ++LD VL Sbjct: 362 IAALAILVGVDRFMSECRALTNLVGNGVATLVVARWEGALDRQRLDRVL 410 Lambda K H 0.327 0.142 0.401 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: 611 Number of extensions: 30 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: 428 Length of database: 417 Length adjustment: 32 Effective length of query: 396 Effective length of database: 385 Effective search space: 152460 Effective search space used: 152460 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 (21.7 bits) S2: 50 (23.9 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