Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate HSERO_RS05470 HSERO_RS05470 permease
Query= SwissProt::A0A0H2VAP9 (445 letters) >FitnessBrowser__HerbieS:HSERO_RS05470 Length = 450 Score = 312 bits (799), Expect = 2e-89 Identities = 168/442 (38%), Positives = 259/442 (58%), Gaps = 14/442 (3%) Query: 12 LISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLGFLAAVIG 71 +I+I+ ++L I + + HPF+AL + S +G + GM +V + + G GG LGF+ V+G Sbjct: 15 VIAILALILMITRLRIHPFIALTITSGLLGLISGMPLPKIVKSFQDGFGGVLGFVGIVLG 74 Query: 72 LGTILGKMMEVSGAAERIGLTL------QRCRWLSADVIMVLVGLICGITLFVEVGVVLL 125 LGT+LGK+M SG A++I TL +R W M++ + GI LF E+G VLL Sbjct: 75 LGTMLGKLMAESGGADQIAQTLVRAFGRERVHWA-----MMMGAFLVGIPLFFEIGFVLL 129 Query: 126 IPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIVYGLLV 185 IPL F +A+++ L K+ +P+ +L +H +VPPHP L GADIG I YGLLV Sbjct: 130 IPLVFIVARRSGVPLFKIGMPMLASLSVMHGLVPPHPGPLLAIGIFGADIGKTIFYGLLV 189 Query: 186 GLMASLIGGPLFLKFLGQRLPFKPVPTEFADLKVRDEKT--LPSLGATLFTVLLPIALML 243 GL +I GP+F F+ + + KP A L VR+ +T LP TL TVL P+ LML Sbjct: 190 GLPTVIIAGPMFGAFISRYVDIKPSEELMAQL-VREPQTTKLPGFATTLITVLAPVFLML 248 Query: 244 VKTIAELNMARESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMGTMLTHTENGFG 303 +KT+ ++ + + L++FIGNPI A A+ +A + GI + + +L + Sbjct: 249 LKTLVDVTLPEGHAMRDLMDFIGNPIVALLAALLLAIWTFGIARGFTRQQVLKFVDQSLA 308 Query: 304 SIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSATVA 363 A I+LIIGAGG F +L +S + + + + + P+LLAW VA ++ A GSATVA Sbjct: 309 PTAAIVLIIGAGGGFKQMLVNSGVGTAIGQLAVHAQISPLLLAWFVAGVIRVATGSATVA 368 Query: 364 MMGATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNETFKYY 423 + IVAP++ L P + E++ +A G+G++ + V D+ FWLVK+Y ++ ETFK + Sbjct: 369 TITGAGIVAPLVALIPGTNKELLVLATGAGSLILSHVNDAGFWLVKEYFNMSVGETFKTW 428 Query: 424 TTATFIASVIALAGTFLLSFII 445 T + SV+A+ LL+ ++ Sbjct: 429 TVMETLISVVAIIFIMLLNLVV 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: 564 Number of extensions: 45 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: 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