Align D-serine transporter DsdX (characterized)
to candidate PP_0652 PP_0652 Gluconate transporter
Query= SwissProt::P08555 (445 letters) >FitnessBrowser__Putida:PP_0652 Length = 461 Score = 248 bits (632), Expect = 4e-70 Identities = 141/450 (31%), Positives = 244/450 (54%), Gaps = 11/450 (2%) Query: 7 VVSTLLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLGFL 66 +++ L +VL+ L + + K HP LALL+ S VG M P +V+ + +G G TLG + Sbjct: 9 LLTALASVLVLVALIVSRLKMHPLLALLVVSIGVGFATHMAPGSIVSHLLTGAGKTLGAV 68 Query: 67 AAVIGLGTILGKMMEVSGAAERIG-LTLQRCRWLSVDVIMVLVGLICGITLFVEVGVVLL 125 VI LG +LGK++ +G E++ + L+R + M+LV + GI +F EVG+V++ Sbjct: 69 GVVIALGAMLGKILADAGVTEQVADVILKRTPDRMIPWAMMLVAFVIGIPMFFEVGLVIM 128 Query: 126 IPLAFSIAKKTNT-------SLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSV 178 +PL FS+A+K + + + + +P+ +AL A+H +VPPHP L L +G Sbjct: 129 LPLIFSVARKLESKARFKGSAYVYVGVPVISALAAMHGMVPPHPGPLTAIAVLKTSVGPT 188 Query: 179 IVYGLLVGLMASLIGGPLFLKFLGQRLPFKP---VPTEFADLKVRDEKTLPSLGATLFTI 235 ++YG L + A ++GGPL+ F+ R+ +P + +F + D + P + + Sbjct: 189 MLYGFLAAIPAMILGGPLYGMFISPRMNTRPDQALLDQFTLAEKADGQPRPGVMVGMLAA 248 Query: 236 LLPIALMLVKTIAELNMARESGLYILVEFIGNPITAMFIAVFVAYYVLGIRQHMSMGTML 295 LLP LMLV +AE+ + + + L + F+GNP+ AM + V A L + + + Sbjct: 249 LLPAILMLVHAVAEMLLPKGNALLEMASFLGNPLIAMLLGVLFAGASLVLARGGDAEQLR 308 Query: 296 THTENGFGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHA 355 IA+I++II GGAF +L S+ + D + + P++L WL+A++L Sbjct: 309 DALGKSLKPIASIIMIIAGGGAFQEMLTSAKVGDAIVHLTQQSAFPPLILGWLIAMLLSV 368 Query: 356 AVGSATVAMMGATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGAT 415 + GSATV ++GA ++AP+ P ++ ++A++IG G++ + FW+VK+ G T Sbjct: 369 STGSATVGIVGAAGLLAPLAGADPSLNLPLLALSIGCGSLFFNYANHAGFWMVKESFGMT 428 Query: 416 LNETFKYYTTATFIASVVALAGTFLLSFII 445 + E K + I +VV L +L+ I Sbjct: 429 MGEATKTISVVQSIVAVVGLMVVLMLNAAI 458 Lambda K H 0.329 0.143 0.418 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: 581 Number of extensions: 44 Number of successful extensions: 8 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: 445 Length of database: 461 Length adjustment: 33 Effective length of query: 412 Effective length of database: 428 Effective search space: 176336 Effective search space used: 176336 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