Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate 1937013 b3415 gluconate transporter, high-affinity GNT I system (NCBI)
Query= SwissProt::A0A0H2VAP9 (445 letters) >FitnessBrowser__Keio:1937013 Length = 438 Score = 298 bits (762), Expect = 3e-85 Identities = 162/440 (36%), Positives = 259/440 (58%), Gaps = 16/440 (3%) Query: 13 ISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLD-MVNAIESGIGGTLGFLAAVIG 71 I ++L++L +++FK + F+AL+L + VG M GM PLD ++ +I++G+GGTLG LA ++G Sbjct: 8 IGVILLLLLMIRFKMNGFIALVLVALAVGLMQGM-PLDKVIGSIKAGVGGTLGSLALIMG 66 Query: 72 LGTILGKMMEVSGAAERIGLTL------QRCRWLSADVIMVLVGLICGITLFVEVGVVLL 125 G +LGKM+ G A+RI TL + +W +VL G G LF EVG VL+ Sbjct: 67 FGAMLGKMLADCGGAQRIATTLIAKFGKKHIQWA-----VVLTGFTVGFALFYEVGFVLM 121 Query: 126 IPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIVYGLLV 185 +PL F+IA N LL + +P+ AL H +PPHP +A AD+G ++YG ++ Sbjct: 122 LPLVFTIAASANIPLLYVGVPMAAALSVTHGFLPPHPGPTAIATIFNADMGKTLLYGTIL 181 Query: 186 GLMASLIGGPLFLKFLGQRLPFKPVPTEFADLKVRDEKTLPSLGATLFTVLLPIALMLVK 245 + ++ GP++ + L + KP+P K E+ +PS G +++T L+P+ LM ++ Sbjct: 182 AIPTVILAGPVYARVL--KGIDKPIPEGLYSAKTFSEEEMPSFGVSVWTSLVPVVLMAMR 239 Query: 246 TIAELNMARESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMGTMLTHTENGFGSI 305 IAE+ + + + EF+G+P+ AT IAV +A + G+ + SM + + I Sbjct: 240 AIAEMILPKGHAFLPVAEFLGDPVMATLIAVLIAMFTFGLNRGRSMDQINDTLVSSIKII 299 Query: 306 ANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSATVAMM 365 A +LLIIG GGAF +L S + +A ++ ++ P+L+AW +A +L A+GSATVA + Sbjct: 300 AMMLLIIGGGGAFKQVLVDSGVDKYIASMMHETNISPLLMAWSIAAVLRIALGSATVAAI 359 Query: 366 GATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNETFKYYTT 425 A I AP++ +SPE++ IA+GSG++ + V D FWL K+Y T+ ET K ++ Sbjct: 360 TAGGIAAPLIAT-TGVSPELMVIAVGSGSVIFSHVNDPGFWLFKEYFNLTIGETIKSWSM 418 Query: 426 ATFIASVIALAGTFLLSFII 445 I SV L G LL+ +I Sbjct: 419 LETIISVCGLVGCLLLNMVI 438 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: 27 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: 438 Length adjustment: 32 Effective length of query: 413 Effective length of database: 406 Effective search space: 167678 Effective search space used: 167678 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