Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate BPHYT_RS16725 BPHYT_RS16725 permease
Query= SwissProt::A0A0H2VAP9 (445 letters) >FitnessBrowser__BFirm:BPHYT_RS16725 Length = 465 Score = 306 bits (784), Expect = 9e-88 Identities = 179/464 (38%), Positives = 265/464 (57%), Gaps = 32/464 (6%) Query: 9 STLL----ISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLG 64 STLL I+I L++L I ++K +PFL L++ S +G GM +V + E+G G TLG Sbjct: 7 STLLVFAVIAIALLILLITRYKVYPFLVLIIVSLLLGLASGMPMATIVKSFETGNGNTLG 66 Query: 65 FLAAVIGLGTILGKMMEVSGAAERIGLTL------QRCRWLSADVIMVLVGLICGITLFV 118 +A V+GLGT+LGKMM SG AERI TL + W M++V +I G+ +F Sbjct: 67 HIAIVVGLGTMLGKMMAESGGAERIATTLIDFFGEKNIHWA-----MMIVAIIVGLPVFF 121 Query: 119 EVGVVLLIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSV 178 EVG VLLIP+AF++AK+TN SLL + +P+ L VH ++PPHPAA+ ADIG Sbjct: 122 EVGFVLLIPIAFNVAKRTNKSLLLVGLPMVAGLSVVHGLLPPHPAAMLAVQAYHADIGRT 181 Query: 179 IVYGLLVGLMASLIGGPLFLKFLGQ--RLPFKPV--------------PTEFADLKVRDE 222 I YGL+VG+ +++ GPLF + + +LP + + A V + Sbjct: 182 IAYGLIVGVPTAIVAGPLFALMISRYIKLPKENALAAQFLGHGDETKNGAQTAAQNVAPK 241 Query: 223 KTLPSLGATLFTVLLPIALMLVKTIAELNMARESGLYTLLEFIGNPITATFIAVFVAYYV 282 + LPS G TL T+LLP+ LMLV + A+L ++ LL F GN A IAV V+++ Sbjct: 242 RELPSFGITLLTILLPVILMLVGSWADLFTTPKTLPNDLLHFAGNSDVALLIAVLVSFWT 301 Query: 283 LGIRQHMSMGTMLTHTENGFGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHP 342 G + + + + IA I LI+GAGG F +L S ++ + + + MH+ P Sbjct: 302 FGASRGFTREQIQKFCGDCLAPIAGITLIVGAGGGFGRVLMDSGISKEIVNVATAMHLSP 361 Query: 343 ILLAWLVALILHAAVGSATVAMMGATAIVAPMLPLY-PDISPEIIAIAIGSGAIGCTIVT 401 +L WLVA ++ A GSATVAM A IVAP+ + PE++ +A GSG++ + V Sbjct: 362 LLFGWLVAALIRLATGSATVAMTTACGIVAPIASASGVHVEPELLVLATGSGSLIFSHVN 421 Query: 402 DSLFWLVKQYCGATLNETFKYYTTATFIASVIALAGTFLLSFII 445 D FWL+K+Y G T+ +TFK ++ I S++ L TF L+ ++ Sbjct: 422 DGGFWLIKEYFGMTVGQTFKTWSLLETIISLMGLGLTFALAAVV 465 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: 558 Number of extensions: 39 Number of successful extensions: 6 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: 465 Length adjustment: 33 Effective length of query: 412 Effective length of database: 432 Effective search space: 177984 Effective search space used: 177984 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