Align Citrate:H+ symporter (characterized)
to candidate CCNA_01071 CCNA_01071 alpha-ketoglutarate permease
Query= TCDB::P16482 (444 letters) >FitnessBrowser__Caulo:CCNA_01071 Length = 477 Score = 218 bits (555), Expect = 3e-61 Identities = 132/424 (31%), Positives = 205/424 (48%), Gaps = 45/424 (10%) Query: 25 ARIGAILRVTSGNFLEQFDFFLFGFYATYIAHTFFPASSEFASLMMTFAVFGAGFLMRPI 84 AR AIL ++GN +E +D+F + + Y A FFP + L+ AVF GF+ RPI Sbjct: 14 ARARAILGGSAGNLVEWYDWFAYAAFTLYFAPAFFPKGDQTVQLLQAAAVFFLGFVARPI 73 Query: 85 GAIVLGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLLVLIGRLLQGFSA 144 GA ++G Y D GRR L V++S+M G F+I + P +QTIGLWAP ++L R+LQG S Sbjct: 74 GAWIMGLYADHAGRRAALSVSVSLMCAGAFIIAITPDFQTIGLWAPAILLFARVLQGLSV 133 Query: 145 GAELGGVSVYLAEIATPGRKGFYTSWQSGSQQVAIMVAAAMGFALNAVLEPSAISDWGWR 204 G E G + Y++E+A R+GF++S+ + ++A + L L A+ +W WR Sbjct: 134 GGEYGASATYMSEMAGKARRGFWSSFHYVTLIAGQLLALGVLIILQRTLGEEALKEWAWR 193 Query: 205 IPFLFGVLIVPFIFILRRKLEETQEF-------TARRHHLAMRQVFATL-LANWQVVIAG 256 +PF+ G L+ +F +RR LEE+ F T R + F +L +A+ V + G Sbjct: 194 VPFIIGALLAVVVFWIRRGLEESVSFKRPAQSETLSRGQIISAGAFLSLTIASGVVGLMG 253 Query: 257 -------------------------------------MMMVAMTTTAFYLITVYAPTFGK 279 M + A + FY+ T Y F Sbjct: 254 GPLAKAGQYLGAAFLVLFFVSLIVPLIRRHPRESLLIMGLTAGGSLTFYVYTTYMQKFLV 313 Query: 280 KVLMLSASDSLLVTLLVAISNFFWLPVGGALSDRFGRRSVLIAMTLLALATAWPALTMLA 339 S + + ++ L I+ P+ G LSDRFGR+ +LI + T WP +T ++ Sbjct: 314 NTAGFSKAQASEISALSLIAFMLMQPLAGWLSDRFGRKPMLIIAFGGGVLTIWPIMTAIS 373 Query: 340 NAPSFLMMLSVLLWLSFIYGMYNGAMIPALTEIMPAEVRVAGFSLAYSLATAVFGGFTPV 399 S + L+++L Y E+ PAE+R G +L Y+LA +FGG + Sbjct: 374 QTNSVGVALALILVGVAFQSCYTAISAVVKAEMFPAEIRALGVALPYALANVLFGGTAEM 433 Query: 400 ISTA 403 ++ A Sbjct: 434 VALA 437 Lambda K H 0.329 0.139 0.421 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: 535 Number of extensions: 25 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 444 Length of database: 477 Length adjustment: 33 Effective length of query: 411 Effective length of database: 444 Effective search space: 182484 Effective search space used: 182484 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 (21.9 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