Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate Pf1N1B4_556 Gluconate permease
Query= SwissProt::A0A0H2VAP9 (445 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_556 Length = 450 Score = 333 bits (853), Expect = 9e-96 Identities = 180/450 (40%), Positives = 269/450 (59%), Gaps = 8/450 (1%) Query: 1 MHSQIWVVSTLLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIG 60 M + +++ +++++ +++ I KFK HPFLAL++A+ F+G GM ++ A + G G Sbjct: 4 MSHESFLLLDAVVTVIGLIVLITKFKLHPFLALIIAAAFLGLTSGMPIGTIIKAFQDGFG 63 Query: 61 GTLGFLAAVIGLGTILGKMMEVSGAAERIGLTLQRCRWLSADVI---MVLVGLICGITLF 117 G LGF+ ++ LGT+LGKMM SG A++I TL R D + M+ + GI LF Sbjct: 64 GVLGFVGIILALGTMLGKMMAESGGADQIAQTLIRA--FGKDKVQWAMMFAAFLVGIPLF 121 Query: 118 VEVGVVLLIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGS 177 E+G VLLIPL F +A++T S++K+ IPL L AVH +VPPHP L GADIG Sbjct: 122 FEIGFVLLIPLVFIVARRTGVSIIKIGIPLLAGLSAVHGLVPPHPGPLLAIGVFGADIGK 181 Query: 178 VIVYGLLVGLMASLIGGPLFLKFLGQRLPFKPVPTEFADLKVR--DEKTLPSLGATLFTV 235 I+YGL+V L ++I GP+F F+ + +P P E D R D LPS G TL TV Sbjct: 182 TILYGLIVALPTAIIAGPIFGTFIAKHIPGHP-NQELVDQLSRETDSAELPSFGITLVTV 240 Query: 236 LLPIALMLVKTIAELNMARESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMGTML 295 LLP+ LML+KT A++ + + T ++ IG+PI+A +A+ ++ Y G +Q + M+ Sbjct: 241 LLPVFLMLLKTFADVVLPDGNIFRTFMDLIGHPISALLLALLLSLYTFGYKQGIGSSQMM 300 Query: 296 THTENGFGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHA 355 + A I+LIIGAGG F +L +S + D + + N + PILLAWLVA ++ Sbjct: 301 KWLDASLAPTAAIILIIGAGGGFKQMLVTSGVGDVIGHMAVNAQISPILLAWLVAAVIRI 360 Query: 356 AVGSATVAMMGATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGAT 415 A GSATVA + IV P++ + P ++ E++ +A G+G++ + V D+ FWLVKQY T Sbjct: 361 ATGSATVATITGAGIVVPVVGMIPGVNRELLVLATGAGSLILSHVNDAGFWLVKQYFNMT 420 Query: 416 LNETFKYYTTATFIASVIALAGTFLLSFII 445 + ETFK +T I SV+ L LLS + Sbjct: 421 VAETFKTWTAMETILSVVGLGFILLLSLFV 450 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: 634 Number of extensions: 38 Number of successful extensions: 5 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: 450 Length adjustment: 33 Effective length of query: 412 Effective length of database: 417 Effective search space: 171804 Effective search space used: 171804 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