Align citrate transporter (characterized)
to candidate CA265_RS22390 CA265_RS22390 alpha-ketoglutarate transporter
Query= CharProtDB::CH_014606 (431 letters) >FitnessBrowser__Pedo557:CA265_RS22390 Length = 428 Score = 221 bits (563), Expect = 3e-62 Identities = 120/365 (32%), Positives = 200/365 (54%), Gaps = 10/365 (2%) Query: 20 GNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGSGFLMRPIGAVVLGAYIDR 79 GN +E +D++ + +A Y + FFP + A L+ T +F GFLMRPIG + G+ D+ Sbjct: 22 GNLVEWYDWYTYSAFALYFSPAFFPNSNPTAQLLDTAGIFAVGFLMRPIGGWLFGSIADK 81 Query: 80 IGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGRLLQGFSAGVELGGVSVYL 139 +GR++ + +++ IM G+L+I L PGY+ IG+ AP+L++ RL+QG S G E G + YL Sbjct: 82 LGRKRSMTLSVLIMAIGSLIIGLTPGYKQIGIAAPLLLIFARLIQGLSTGGEYGTSATYL 141 Query: 140 SEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGH-----DEISEWGWRIPFFIG 194 SE+AT ++GFY+S+ Q V ++ L+ G+ + L + E+ EWGWRIPFFIG Sbjct: 142 SEMATKKHRGFYSSF----QYVTLIGGQLLALGIQLILQNWLLTPAELHEWGWRIPFFIG 197 Query: 195 CMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIAKNWRIITAGTLLVAMTTTTFYFI 254 ++ + LRR + ET AF + K+ D + + K + + L T FY Sbjct: 198 AILSFIALYLRRHIDETSAF-KSKNTADKKGGIAVLMKYPKEVFTVVGLTLGGTIAFYTF 256 Query: 255 TVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGRRPVLMGITLLALVT 314 + Y + ++LS S ++ + + + P+ G +SD+IGR+P+L+G +L + Sbjct: 257 STYMQKFLVNTVHLSKETSTTLSFISLLVFVVLQPLFGLLSDKIGRKPLLIGFGVLGTLC 316 Query: 315 TLPVMNWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVYVRTVGFSLAFSLAT 374 T P++ L + T + L+++ Y E+ P +R +G L ++L Sbjct: 317 TYPILTGLAGESNTTIIFLLMIGALIIVSGYTSINAVVKAELFPAEIRALGVGLPYALTV 376 Query: 375 AIFGG 379 AIFGG Sbjct: 377 AIFGG 381 Lambda K H 0.328 0.141 0.432 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: 522 Number of extensions: 27 Number of successful extensions: 4 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: 431 Length of database: 428 Length adjustment: 32 Effective length of query: 399 Effective length of database: 396 Effective search space: 158004 Effective search space used: 158004 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 (21.8 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