Align Citrate/succinate antiporter; Citrate carrier; Citrate transporter (characterized)
to candidate BWI76_RS16110 BWI76_RS16110 L-tartrate/succinate antiporter
Query= SwissProt::P0AE74 (487 letters) >FitnessBrowser__Koxy:BWI76_RS16110 Length = 501 Score = 512 bits (1319), Expect = e-149 Identities = 233/472 (49%), Positives = 325/472 (68%) Query: 14 PLVVMGVMFLIPVPDGMPPQAWHYFAVFVAMIVGMILEPIPATAISFIAVTICVIGSNYL 73 P++V ++ +PVP+G+PP AWHYFA+FV +IVG+I EP+P I V + + S +L Sbjct: 28 PIIVAVLLLFVPVPEGLPPYAWHYFAIFVGVIVGLIFEPLPGAVIGITGVVVIALCSQWL 87 Query: 74 LFDAKELADPAFNAQKQALKWGLAGFSSTTVWLVFGAFIFALGYEVSGLGRRIALFLVKF 133 LF ++LA P F + KW ++GF ++TVWL+FGAF+FA GY+ + GRR+AL LVK+ Sbjct: 88 LFSPEQLAAPNFKLAGASFKWAVSGFGNSTVWLIFGAFMFAAGYDKTQFGRRLALILVKY 147 Query: 134 MGKRTLTLGYAIVIIDILLAPFTPSNTARTGGTVFPVIKNLPPLFKSFPNDPSARRIGGY 193 +G+R+LTLGYAI D+LLAPFTPSNTAR+GGT++P+I NLPPL+ S PNDPSARRIG Y Sbjct: 148 LGRRSLTLGYAITFADLLLAPFTPSNTARSGGTIYPIIANLPPLYGSKPNDPSARRIGSY 207 Query: 194 LMWMMVISTSLSSSMFVTGAAPNVLGLEFVSKIAGIQISWLQWFLCFLPVGVILLIIAPW 253 LMW+ + + ++SSMF++ APN+L L V I GI ISW WF+ FLP+G++L++ P Sbjct: 208 LMWVAITAACITSSMFLSALAPNLLALALVKSIVGINISWGTWFIAFLPLGILLILTMPL 267 Query: 254 LSYVLYKPEITHSEEVATWAGDELKTMGALTRREWTLIGLVLLSLGLWVFGSEVINATAV 313 L+Y Y PE+ ++EV WA EL+ +G L+R E L+ V +L +W+F +E I Sbjct: 268 LAYWFYPPEVKVNDEVPLWAARELEKLGRLSRNEILLLVFVCFALMMWIFAAEWIEPALA 327 Query: 314 GLLAVSLMLALHVVPWKDITRYNSAWNTLVNLATLVVMANGLTRSGFIDWFAGTMSTHLE 373 LL + LML V+ W DIT +AWNT ATLV +A+GL+ +GFI W + Sbjct: 328 ALLVIVLMLWTGVLSWNDITSNKAAWNTFAWFATLVALADGLSSTGFIAWLGKEGGALMS 387 Query: 374 GFSPNATVIVLVLVFYFAHYLFASLSAHTATMLPVILAVGKGIPGVPMEQLCILLVLSIG 433 G SP +VL+L FY HYLFAS +AHT +LP +L + IPG+ M+ +L+V S+G Sbjct: 388 GISPGVATVVLLLAFYLLHYLFASTTAHTTALLPAMLTIASTIPGMNMQVFVLLMVTSLG 447 Query: 434 IMGCLTPYATGPGVIIYGCGYVKSKDYWRLGAIFGVIYISMLLLVGWPILAM 485 +MG +TPY TGP I YG GY+ +KDYWRLG IFG I+++ LLL+G+P ++M Sbjct: 448 VMGIITPYGTGPSPIYYGSGYLPTKDYWRLGTIFGAIFLAALLLIGYPWMSM 499 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: 959 Number of extensions: 44 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: 487 Length of database: 501 Length adjustment: 34 Effective length of query: 453 Effective length of database: 467 Effective search space: 211551 Effective search space used: 211551 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: 52 (24.6 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