Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate CA265_RS01125 CA265_RS01125 gluconate permease
Query= SwissProt::A0A0H2VAP9 (445 letters) >FitnessBrowser__Pedo557:CA265_RS01125 Length = 429 Score = 248 bits (632), Expect = 3e-70 Identities = 147/438 (33%), Positives = 242/438 (55%), Gaps = 23/438 (5%) Query: 11 LLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLGFLAAVI 70 LL I+L+ + I+K K +P +AL+ + G ++GM ++ +I +GIG TLG + V+ Sbjct: 6 LLFGILLLFVLILK-KINPMIALIAVAIITGLLLGMPATKVMASISNGIGSTLGSMVMVL 64 Query: 71 GLGTILGKMMEVSGAAERIGLTL------QRCRWLSADVIMVLVGLICGITLFVEVGVVL 124 LG ++GK++E SG+A++I L + +W ++L GL+ GI LF G V+ Sbjct: 65 ALGAMMGKLIEDSGSAKKIVFILIGAFGKKNIQWA-----VLLTGLLVGIPLFYNAGFVV 119 Query: 125 LIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIVYGLL 184 LIPL F+I+ T S L + IP+ TAL H +PPHP + +A ADIG ++YGL Sbjct: 120 LIPLVFAISATTGLSKLYIGIPMATALSVTHGFLPPHPGPVALAGIFHADIGKTLIYGLT 179 Query: 185 VGLMASLIGGPLFLKFLGQRLPFKPVPTEFADLKVRDEKTLPSLGATLFTVLLPIALMLV 244 + + ++I G F + + +R + +E+ LPS + T LLP+ L++ Sbjct: 180 LSVPIAVIAGIYFPRLILKR----DQSVTVQHFSISEEENLPSASRSFITALLPVFLIIA 235 Query: 245 KTIAELNMARESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMGTMLTHTENGFGS 304 TI + + L F+ +P A I+V +A V Q S+ + G S Sbjct: 236 GTIGS-SFKIDYICKPLFIFLADPTAALLISVIIALVV----QKTSITKAMESCAEGVKS 290 Query: 305 IANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSATVAM 364 IA I+LII AGGAF IL S + +T+ + +++ P+LLAWL+ L +GSATVA Sbjct: 291 IAMIILIIAAGGAFKQILIDSGMGETVKQLTGGLNLSPLLLAWLITASLRVTLGSATVAA 350 Query: 365 MGATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNETFKYYT 424 + A+ +V P++ P PE++ +++G+G++ + V D+ FW+ K+Y +L ETF+ +T Sbjct: 351 LTASGMVLPLIG--PGTPPELMVLSVGAGSLMFSHVNDTGFWMFKEYFNLSLKETFRTWT 408 Query: 425 TATFIASVIALAGTFLLS 442 + SV+ L G +L+ Sbjct: 409 MMESLVSVLGLVGVLVLN 426 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: 504 Number of extensions: 29 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 445 Length of database: 429 Length adjustment: 32 Effective length of query: 413 Effective length of database: 397 Effective search space: 163961 Effective search space used: 163961 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