Align Citrate:H+ symporter (characterized)
to candidate N515DRAFT_0974 N515DRAFT_0974 MFS transporter, MHS family, proline/betaine transporter
Query= TCDB::P16482 (444 letters) >FitnessBrowser__Dyella79:N515DRAFT_0974 Length = 433 Score = 203 bits (516), Expect = 1e-56 Identities = 120/398 (30%), Positives = 202/398 (50%), Gaps = 5/398 (1%) Query: 28 GAILRVTSGNFLEQFDFFLFGFYATYIAHTFFPASSEFASLMMTFAVFGAGFLMRPIGAI 87 G++ +E +DF L+ ++AT ++ FF +SL+ T A F + MRP+GA+ Sbjct: 13 GSMAVAALSTVVEWYDFTLYLYFATVLSRVFFGGGE--SSLLATLAGFAISYAMRPLGAV 70 Query: 88 VLGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLLVLIGRLLQGFSAGAE 147 V G D++GRR+ L++++ +M L+PS+ G A L+L+ R FS G E Sbjct: 71 VFGHIGDRIGRRRTLLLSMMLMTLAMLATALLPSHAVAGPAAGALLLLLRCFMAFSVGGE 130 Query: 148 LGGVSVYLAEIATPGRKGFYTSWQSGSQQVAIMVAAAMGFALNAVLEPSAISDWGWRIPF 207 GV YL E A R+G TS S + ++ ++A + + + + + WGWRIPF Sbjct: 131 YTGVVAYLLEGARKDRRGLITSLASAASEIGALLAVGVSALTVSAMSTAQLDSWGWRIPF 190 Query: 208 LFGVLIVPFIFILRRKLEETQEFTAR-RHHLAMRQVFATLLANWQVVIAGMMMV-AMTTT 265 G + ++I R +EE+ +F + H +LAN + + + A+ + Sbjct: 191 FVGAALAGCVWIARSTMEESPDFVRQVEQHTVPDSPLGHMLANHRPALFRTFAISALGSI 250 Query: 266 AFYLITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVGGALSDRFGRRSVLIAMTL 325 +Y+ Y P F +L+ SL ++ L A++ P+ GALSDR GRR VL+ + + Sbjct: 251 TYYVGITYVPAFLSSSGILAEERSLWLSTLAAVAVILVTPLAGALSDRVGRRPVLVWLAV 310 Query: 326 LALATAWPALTMLANAPSFLMMLSVLLWLSFIYGMYNGAMIPALTEIMPAEVRVAGFSLA 385 ++ ++A A + L ++ L+ + G + PA E P E R++G +L Sbjct: 311 ASVLLPLAMFQLMARAMELNIALGAIV-LACLAGGVSAVGAPATAEQFPGEGRLSGLALG 369 Query: 386 YSLATAVFGGFTPVISTALIEYTGDKASPGYWMSFAAI 423 ++ATA+FGG TP ++ LI+ TG A PG + AI Sbjct: 370 VTMATAIFGGLTPFLAELLIKMTGWHAVPGAMIGLVAI 407 Lambda K H 0.329 0.139 0.421 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: 510 Number of extensions: 28 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: 444 Length of database: 433 Length adjustment: 32 Effective length of query: 412 Effective length of database: 401 Effective search space: 165212 Effective search space used: 165212 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 (21.9 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