Align Citrate:H+ symporter (characterized)
to candidate BPHYT_RS27415 BPHYT_RS27415 major facilitator transporter
Query= TCDB::P16482 (444 letters) >FitnessBrowser__BFirm:BPHYT_RS27415 Length = 432 Score = 637 bits (1644), Expect = 0.0 Identities = 320/423 (75%), Positives = 362/423 (85%) Query: 21 TAGGARIGAILRVTSGNFLEQFDFFLFGFYATYIAHTFFPASSEFASLMMTFAVFGAGFL 80 T ++ A+ RVT+GNFLEQFDFFLFGFYAT IA+ FFPA+SEFASLMMTFAVFGAGFL Sbjct: 9 TPARSKAAAVFRVTAGNFLEQFDFFLFGFYATQIANVFFPAASEFASLMMTFAVFGAGFL 68 Query: 81 MRPIGAIVLGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLLVLIGRLLQ 140 MRP+GAIVLGAYID VGRRKGLIVTLSIMATGT LI +P Y TIGL AP LVLIGRLLQ Sbjct: 69 MRPLGAIVLGAYIDDVGRRKGLIVTLSIMATGTILIAFVPGYATIGLAAPALVLIGRLLQ 128 Query: 141 GFSAGAELGGVSVYLAEIATPGRKGFYTSWQSGSQQVAIMVAAAMGFALNAVLEPSAISD 200 GFSAGAELGGVSVYLAE+ATPGRKG +TSWQS SQQVAI+VAAA+GFALN L+ + I+ Sbjct: 129 GFSAGAELGGVSVYLAEMATPGRKGLFTSWQSASQQVAIVVAAALGFALNQSLDAATIAA 188 Query: 201 WGWRIPFLFGVLIVPFIFILRRKLEETQEFTARRHHLAMRQVFATLLANWQVVIAGMMMV 260 WGWR+PF G +IVPFIF+LRR L+ET+EF AR+H M++V TL+ NW VVIAGMM+V Sbjct: 189 WGWRVPFFVGCMIVPFIFMLRRNLQETEEFKARQHRPNMKEVLRTLVENWTVVIAGMMLV 248 Query: 261 AMTTTAFYLITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVGGALSDRFGRRSVL 320 AMTT +FYLITVYAPTFGK VL LS +DSLLVTL VA+SNF WLP+GGALSDR GRR +L Sbjct: 249 AMTTASFYLITVYAPTFGKTVLHLSTADSLLVTLCVAVSNFVWLPIGGALSDRIGRRPLL 308 Query: 321 IAMTLLALATAWPALTMLANAPSFLMMLSVLLWLSFIYGMYNGAMIPALTEIMPAEVRVA 380 +AMTLLA+ TA+PAL+ LA+APSF+ ML LLWLSF+YG+YNGAM+ ALTE+MPA+VRVA Sbjct: 309 VAMTLLAILTAYPALSFLAHAPSFVNMLLALLWLSFMYGIYNGAMVVALTEVMPAQVRVA 368 Query: 381 GFSLAYSLATAVFGGFTPVISTALIEYTGDKASPGYWMSFAAICGLLATCYLYRRSAVAL 440 GFSLAYSLATAVFGGFTP ISTALI TGDKA+PGYWMSFAA C LLAT LYRR A L Sbjct: 369 GFSLAYSLATAVFGGFTPAISTALIHMTGDKAAPGYWMSFAAACALLATFALYRRRAATL 428 Query: 441 QTA 443 A Sbjct: 429 TPA 431 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: 681 Number of extensions: 27 Number of successful extensions: 1 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: 432 Length adjustment: 32 Effective length of query: 412 Effective length of database: 400 Effective search space: 164800 Effective search space used: 164800 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