Align Citrate/succinate antiporter; Citrate carrier; Citrate transporter (characterized)
to candidate BWI76_RS26550 BWI76_RS26550 transporter, divalent anion:Na+ symporter (DASS) family protein
Query= SwissProt::P0AE74 (487 letters) >FitnessBrowser__Koxy:BWI76_RS26550 Length = 464 Score = 256 bits (653), Expect = 2e-72 Identities = 155/475 (32%), Positives = 239/475 (50%), Gaps = 28/475 (5%) Query: 12 LAPLVVMGVMF-LIPVPDGMPPQAWHYFAVFVAMIVGMILEPIPATAISFIAVTICVIGS 70 L P++ V+F +IP P+G+ WH +++AM+ G++L P I I ++G Sbjct: 6 LLPIIFFPVLFWIIPHPEGVAAPTWHMVGIYLAMLCGLVLRPFTDAVIMLI-----ILGF 60 Query: 71 NYLLFDAKELADPAFNAQKQALKWGLAGFSSTTVWLVFGAFIFALGYEVSGLGRRIALFL 130 L+ D L AGF S VW + AFI + ++GLG+RIA L Sbjct: 61 ASLVLDPAPL---------------FAGFGSPMVWFIISAFIICKAFVITGLGKRIAYLL 105 Query: 131 VKFMGKRTLTLGYAIVIIDILLAPFTPSNTARTGGTVFPVIKNLPPLFKSFPNDPSARRI 190 +K GK TLTLGY +++ D +LAP T SN +R+GG +P+ +N+ S P+D S R+I Sbjct: 106 LKRYGKNTLTLGYLMMVTDTVLAPATGSNMSRSGGITYPIFRNIAEALGSKPDDGS-RKI 164 Query: 191 GGYLMWMMVISTSLSSSMFVTGAAPNVLGLEFVSKIAGIQISWLQWF-LCFLPVGVILLI 249 G YL +M + + +SS+F+TG A N + + ++I + + W+ WF +P G++LL Sbjct: 165 GAYLTILMYVVSMGTSSLFLTGMATNSITVSLANEIMKVNLEWMTWFKAAVVPAGLVLL- 223 Query: 250 IAPWLSYVLYKPEITHSEEVATWAGDELKTMGALTRREWTLIGLVLLSLGLWVFGSEV-I 308 +APW+ Y +Y PE+ + V A L +G + R E LI +L + W+ GS I Sbjct: 224 LAPWILYKIYAPELKVIDNVNEIAEKGLCELGPVKREEKLLIVFFILGVLGWMTGSITGI 283 Query: 309 NATAVGLLAVSLMLALHVVPWKDITRYNSAWNTLVNLATLVVMANGLTRSGFIDWFAGTM 368 VGL ++ +L V+ W D+ SAW T V A L++ GF + + Sbjct: 284 AFIPVGLAFLACLLLFGVLSWNDVVSEKSAWQTFVWYGAFYGCAVALSKGGFYVFLVDVI 343 Query: 369 STHLEGFSPN--ATVIVLVLVFYFAHYLFASLSAHTATMLPVILAVGKGIPGVPMEQLCI 426 +L+ N + + VLV + Y F S SA + PV+ +G PM + + Sbjct: 344 KNYLDLSHLNEISAIAVLVFISLAVRYFFVSNSAFVVSFYPVLFTLGMTTQAHPM-YVAL 402 Query: 427 LLVLSIGIMGCLTPYATGPGVIIYGCGYVKSKDYWRLGAIFGVIYISMLLLVGWP 481 L S G LT Y G GV + GYV K +W LG I V+ + + L+G P Sbjct: 403 SLAFSAGYGALLTHYGNGAGVFTFSSGYVPQKTFWMLGTIMVVVNVLIFFLIGIP 457 Lambda K H 0.328 0.142 0.453 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: 769 Number of extensions: 49 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 487 Length of database: 464 Length adjustment: 33 Effective length of query: 454 Effective length of database: 431 Effective search space: 195674 Effective search space used: 195674 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 (21.7 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