Align D-serine transporter DsdX (characterized)
to candidate 18320 b4296 KpLE2 phage-like element; predicted transporter (NCBI)
Query= SwissProt::P08555 (445 letters) >FitnessBrowser__Keio:18320 Length = 449 Score = 277 bits (709), Expect = 4e-79 Identities = 148/444 (33%), Positives = 255/444 (57%), Gaps = 9/444 (2%) Query: 11 LLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLGFLAAVI 70 ++ I L++L +K K + F++L++ S V GM +V ++ESG+GGTLG + + Sbjct: 6 VVAGIALLLLLTIKIKLNTFVSLIIVSIAVAIASGMDLSKVVTSVESGLGGTLGHIGLIF 65 Query: 71 GLGTILGKMMEVSGAAERIGLTLQRCRWLS-VDVIMVLVGLICGITLFVEVGVVLLIPLA 129 G G +LG+++ +G A+RI LT+ + +D +V I GI LF EVG++LL+P+ Sbjct: 66 GFGVMLGRLLADAGGAQRIALTMLNYFGKNKLDWAVVCSAFIVGIALFFEVGLILLVPIL 125 Query: 130 FSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIVYGLLVGLMA 189 F+IA++ S + + +P+ + L+ H +PPHP +A + GAD+G V++YG++VG+ Sbjct: 126 FAIAREAKISPMFMCVPMLSGLLVAHGFLPPHPGPTVIAREYGADVGLVLIYGIIVGIPT 185 Query: 190 SLIGGPLFLKFLGQRLP--FKPVPT--EFADLKVRDEKTLPSLGATLFTILLPIALMLVK 245 ++ GP+ KF + +P FK + E +P G + T +LP+ LM V Sbjct: 186 FILCGPVLNKFCQRIIPDAFKKEGNIASLGATRRFSESEMPGFGISFLTAMLPVILMAVV 245 Query: 246 TIAELNMAR---ESGL-YILVEFIGNPITAMFIAVFVAYYVLGIRQHMSMGTMLTHTENG 301 TI ++ A+ +SGL Y ++ F+GN AM I++ A Y +G+ + ++ ++ Sbjct: 246 TIIQMTHAKSAADSGLFYNVILFLGNSTIAMLISLLFAIYTMGLGRGKTIPDLMDSCGKA 305 Query: 302 FGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSAT 361 IA +LLIIG GGAF +L S + ++ ++S M ++PIL+AW VA L +GSAT Sbjct: 306 IAGIAGLLLIIGGGGAFKQVLIDSGVGQYISTLVSGMDINPILMAWGVAAFLRICLGSAT 365 Query: 362 VAMMGATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNETFK 421 VA + +V P+L ++P+ + +I +A G+G+ C+ V D+ FW++K + G T ET Sbjct: 366 VAAISTAGLVIPLLAVHPNTNLALITLATGAGSCICSHVNDASFWMIKDFFGLTTKETLL 425 Query: 422 YYTTATFIASVVALAGTFLLSFII 445 +T + + S+ L L S ++ Sbjct: 426 SWTLMSTLLSISGLIFILLASLVL 449 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: 561 Number of extensions: 28 Number of successful extensions: 3 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: 449 Length adjustment: 33 Effective length of query: 412 Effective length of database: 416 Effective search space: 171392 Effective search space used: 171392 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