Align Citrate-proton symporter; Citrate carrier protein; Citrate transporter; Citrate utilization determinant; Citrate utilization protein A (characterized)
to candidate GFF2854 PS417_14575 MFS transporter
Query= SwissProt::P0A2G3 (434 letters) >FitnessBrowser__WCS417:GFF2854 Length = 445 Score = 240 bits (613), Expect = 6e-68 Identities = 153/437 (35%), Positives = 229/437 (52%), Gaps = 11/437 (2%) Query: 3 QHTPATSRAGTFGAILRVTSGNFLEQFDFFLFGFYATYIARTFFPAESEFASLMLTFAVF 62 Q +P T R I+ GNF+E FDF ++GF AT IA+ FFP+ A+L+ TFAVF Sbjct: 8 QVSPQTLRK----VIIAAGIGNFVEWFDFAVYGFLATTIAQQFFPSGDASAALLKTFAVF 63 Query: 63 GSGFLMRPVGAIVLGAYIDRIGRRKGLMVTLAIMGCGTLLIALVPGYQTIGLAAPALVLL 122 F RP+G I G DRIGR++ L +T+ +M T LI L+P Y IG+AAP L+ L Sbjct: 64 AVAFAFRPLGGIFFGMLGDRIGRKRTLAMTILLMAGATTLIGLLPTYAAIGVAAPILLSL 123 Query: 123 GRLLQGFSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYSLNITLGH 182 R QGFSAG E G YL E A + +Y S+ S A AA++ Y+L +L Sbjct: 124 IRCAQGFSAGGEYAGACAYLMEHAPSDKRAWYGSFVPVSTFSAFAAAAVVAYALEASLSA 183 Query: 183 DAISEWGWRIPFFIGCMIIPLIFVLRRSLQETEAF--LQRKHRPDTREIFATIAKNWRII 240 +A+ WGWR+PF I + + LR L ET AF ++ +H + T+ + I Sbjct: 184 EAMGSWGWRLPFLIAAPLGLVGLYLRWKLDETPAFQAVKEEHTVAHSPLKETLRNHGAAI 243 Query: 241 TAGTLLVAMTTTTFYFITVYTPTYGRTVLNLSARDSLIVTMLVGVSNFIWLPIGGAISDR 300 + V++T +FY T Y TY + LS +L+V+++ + P+ G SDR Sbjct: 244 SCLGAFVSLTALSFYMFTTYFATYLQVAGGLSRAMALLVSLIALIFAAAICPLAGLYSDR 303 Query: 301 IGRRAVLMGITLLALITTWPVMQWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAA-LTEV 359 +GRRA +M +L ++ +P +L A+ ++V + + G + AA L+E Sbjct: 304 VGRRATVMTACVLLMVVVYP--SFLMASSGSFAASIVGVMLLAVGAVLCGVVTAALLSET 361 Query: 360 MPVYVRTVGFSLAFSLATAIFGGLTPAISTALVKLTGDKSSPGWWLMCAALCGLAATAML 419 P R ++ ++LA IFGG P ++T L+ TG SP ++L+ AL LA L Sbjct: 362 FPTRTRYTASAITYNLAYTIFGGTAPLMATWLISTTGSNLSPAFYLIAVALLALAGGLAL 421 Query: 420 --FVRLSRGYIAAENKA 434 R+S + AE+K+ Sbjct: 422 PETSRISLHDVGAEDKS 438 Lambda K H 0.329 0.140 0.432 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: 496 Number of extensions: 17 Number of successful extensions: 5 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: 434 Length of database: 445 Length adjustment: 32 Effective length of query: 402 Effective length of database: 413 Effective search space: 166026 Effective search space used: 166026 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