Align Citrate-proton symporter; Citrate carrier protein; Citrate transporter; Citrate utilization determinant; Citrate utilization protein A (characterized)
to candidate PP_2411 PP_2411 Major facilitator family transporter
Query= SwissProt::P0A2G3 (434 letters) >FitnessBrowser__Putida:PP_2411 Length = 445 Score = 245 bits (625), Expect = 2e-69 Identities = 150/413 (36%), Positives = 224/413 (54%), Gaps = 10/413 (2%) Query: 5 TPATSRAGTFGAILRVTSGNFLEQFDFFLFGFYATYIARTFFPAESEFASLMLTFAVFGS 64 +PAT R I GNF+E FDF ++GF AT IA FF +E +L+ TFAVF Sbjct: 8 SPATLRR----VIAASAIGNFVEWFDFAVYGFLATLIASQFFASEDASVALLKTFAVFAV 63 Query: 65 GFLMRPVGAIVLGAYIDRIGRRKGLMVTLAIMGCGTLLIALVPGYQTIGLAAPALVLLGR 124 F +RP+G IV GA DR+GR++ L +T+ +M T LI L+P Y +IGLAAPAL+ L R Sbjct: 64 AFALRPLGGIVFGALGDRLGRKRILSLTILLMAGSTTLIGLLPTYASIGLAAPALLTLAR 123 Query: 125 LLQGFSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYSLNITLGHDA 184 LQGFSAG E G YL E A + FY S+ S A AA+I Y L +L +A Sbjct: 124 CLQGFSAGGEYAGACAYLMEHAPDDKRAFYGSFVPVSTFSAFACAAVIAYGLEASLSTEA 183 Query: 185 ISEWGWRIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTRE---IFATIAKNWRIIT 241 ++ WGWRIPF I + + LR ++ET AF + + E + T+ + R+I Sbjct: 184 MNAWGWRIPFLIAAPLGLVGLYLRWRMEETPAFREAVAQGKEHEHSPLKETLRHHGRVIR 243 Query: 242 AGTLLVAMTTTTFYFITVYTPTYGRTVLNLSARDSLIVTMLVGVSNFIWLPIGGAISDRI 301 +++T +FY T Y TY + V NL+ SL+VT + + + P+ GA SDR+ Sbjct: 244 NLGAFISLTALSFYMFTTYFATYLQLVGNLTRAQSLLVTTVALLFAAVGCPLAGAFSDRV 303 Query: 302 GRRAVLMGITLLALITTWPVMQWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAA-LTEVM 360 GRR + L ++ +P WL ++ + L ++ + + +G + AA L+E Sbjct: 304 GRRKTIGFTCLWVMLCVFPA-YWLASSGSMSGALLGVILLA-VGALCSGVVTAALLSESF 361 Query: 361 PVYVRTVGFSLAFSLATAIFGGLTPAISTALVKLTGDKSSPGWWLMCAALCGL 413 P R ++ +++A +FGG P ++T L+ TG +P ++L+ AL L Sbjct: 362 PTRTRYTASAITYNVAYTLFGGTAPLVATWLIAQTGSSLAPAFYLVVIALVAL 414 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: 518 Number of extensions: 24 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