Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate GFF4613 PS417_23605 permease DsdX
Query= SwissProt::A0A0H2VAP9 (445 letters) >FitnessBrowser__WCS417:GFF4613 Length = 467 Score = 288 bits (737), Expect = 3e-82 Identities = 153/437 (35%), Positives = 254/437 (58%), Gaps = 6/437 (1%) Query: 13 ISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLGFLAAVIGL 72 I+I+ +++ I +++ +PF+ + L S + M GM ++ + E+G+G TLG +A V+ L Sbjct: 33 IAIIALIVLIARYRLNPFIVITLVSIGLALMAGMPADTIMGSYEAGVGKTLGHIALVVAL 92 Query: 73 GTILGKMMEVSGAAERIGLTL-QRCRWLSADVIMVLVGLICGITLFVEVGVVLLIPLAFS 131 GT+LGKMM SG AE++ TL R +A MV + + G+ LF EVG VLL+P+AF+ Sbjct: 93 GTMLGKMMAESGGAEQVARTLINRFGERNAHWAMVCIAFLVGLPLFFEVGFVLLVPIAFT 152 Query: 132 IAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIVYGLLVGLMASL 191 +A++ S+L + +P+ L VH +VPPHPAA+ A +G ++Y +L+G+ ++ Sbjct: 153 VARRVGVSILMVGLPMVAGLSVVHALVPPHPAAMMAVLAYNASVGQTVLYAILIGIPTAI 212 Query: 192 IGGPLFLKFLGQRLPF---KPVPTEFADLKVRDEKTLPSLGATLFTVLLPIALMLVKTIA 248 I GP++ KF+ R+ P+ +F D + R LPS T+ T+LLP+ LM++ A Sbjct: 213 IAGPVYAKFIVPRIHLPAENPLERQFIDREPRTR--LPSFTLTMGTILLPVVLMMIGGWA 270 Query: 249 ELNMARESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMGTMLTHTENGFGSIANI 308 + + S L FIGN + A +A V+++ LGI Q + ++L T A+I Sbjct: 271 NVISSPGSAFNQFLLFIGNSVIALLVATLVSFWTLGIAQGFNRESILKFTNECLAPTASI 330 Query: 309 LLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSATVAMMGAT 368 L++GAGG N IL + + + + + + P+++ WL A ++ A GSATVAM A+ Sbjct: 331 TLLVGAGGGLNRILVDAGVTNEILGLAHAFQLSPLVMGWLFAALMRIATGSATVAMTTAS 390 Query: 369 AIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNETFKYYTTATF 428 +VAP+ PE++ +A G+G++ + V D FWL+K+Y T+ +TFK +T Sbjct: 391 GVVAPVAMGLGYPHPELLVLATGAGSVIFSHVNDGGFWLIKEYFNMTVIQTFKTWTVLET 450 Query: 429 IASVIALAGTFLLSFII 445 + SV+A T+ LS I+ Sbjct: 451 LISVVAFGLTYGLSCIL 467 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: 549 Number of extensions: 36 Number of successful extensions: 4 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: 467 Length adjustment: 33 Effective length of query: 412 Effective length of database: 434 Effective search space: 178808 Effective search space used: 178808 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