Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate BWI76_RS26235 BWI76_RS26235 gluconate transporter
Query= SwissProt::A0A0H2VAP9 (445 letters) >FitnessBrowser__Koxy:BWI76_RS26235 Length = 446 Score = 245 bits (625), Expect = 2e-69 Identities = 154/447 (34%), Positives = 250/447 (55%), Gaps = 8/447 (1%) Query: 3 SQIWVVSTLLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNA-IESGIGG 61 S + +V T + S++L++ ++K + H F+AL++ S G GM PLD + A +E G+GG Sbjct: 2 STLTLVLTAVGSVLLLLFLVMKARMHAFVALMVVSIGAGLFSGM-PLDKIAATMEKGMGG 60 Query: 62 TLGFLAAVIGLGTILGKMMEVSGAAERIGLTLQRCRWLS-ADVIMVLVGLICGITLFVEV 120 TLGFLA V+ LG + GK++ +GA ++I + + + S A + L GLIC + LF EV Sbjct: 61 TLGFLAIVVALGAMFGKILHETGAVDQIAVKMLKSFGHSRAHYAIGLAGLICALPLFFEV 120 Query: 121 GVVLLIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIV 180 +VLLI +AFS+A+ T T+L+KL IPL + A + P PA + +A+++ AD G +I+ Sbjct: 121 AIVLLISVAFSMARHTGTNLVKLVIPLFAGVAAAAAFLLPGPAPMLLASQMHADFGWMIL 180 Query: 181 YGLLVGLMASLIGGPLFLKFLGQRLPFKPVPTEFADLKVRDEKTLPSLGATLFTVLLPIA 240 GL + +I GPL+ F+ + + P + ++ + + K +PS G +L +LLP+ Sbjct: 181 IGLCAAIPGMIIAGPLWGNFISRYVELH-TPDDISEPHLGEGK-MPSFGFSLALILLPLV 238 Query: 241 LMLVKTIAELNMARESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMGTMLTHTEN 300 L+ +KTIA + S Y EFIG+P TA +A VA Y L +RQ M+ ++ + Sbjct: 239 LVGLKTIAARFVPEGSTAYEWFEFIGHPFTAILVACLVAIYGLAVRQGMAKDRVMEICGH 298 Query: 301 GFGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSA 360 ILL+IGAGG F +L S + L L+ M + + +++A + GSA Sbjct: 299 ALQPAGIILLVIGAGGVFKQVLVDSGVGPALGEALTGMGLPIAITCFVLAAAVRIIQGSA 358 Query: 361 TVAMMGATAIVAPMLPL--YPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNE 418 TVA + A +V P++ Y ++I I G+I + V D+ FWL ++ GAT + Sbjct: 359 TVACLTAVGLVMPVIEQLHYSGAQMAALSICIAGGSIVVSHVNDAGFWLFGKFTGATEAQ 418 Query: 419 TFKYYT-TATFIASVIALAGTFLLSFI 444 T K +T T + +V A+ G + + Sbjct: 419 TLKTWTMMETILGTVGAIVGMIAFTLL 445 Lambda K H 0.328 0.142 0.417 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: 537 Number of extensions: 44 Number of successful extensions: 6 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: 446 Length adjustment: 32 Effective length of query: 413 Effective length of database: 414 Effective search space: 170982 Effective search space used: 170982 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