Align Citrate-proton symporter; Citrate carrier protein; Citrate transporter; Citrate utilization determinant; Citrate utilization protein A (characterized)
to candidate Pf1N1B4_5606 Alpha-ketoglutarate permease
Query= SwissProt::P0A2G3 (434 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5606 Length = 461 Score = 199 bits (507), Expect = 1e-55 Identities = 138/426 (32%), Positives = 226/426 (53%), Gaps = 19/426 (4%) Query: 16 AILRVTSGNFLEQFDFFLFGFYATYIARTFFPAESEFASLMLTFAVFGSGFLMRPVGAIV 75 AI+ SGN +E +DFF++ + A Y A +FFP + L+ T VF GF MRP+G + Sbjct: 29 AIMGACSGNLVEWYDFFIYAYTAIYFAASFFPKGDTTSQLLATAGVFAVGFFMRPLGGWI 88 Query: 76 LGAYIDRIGRRKGLMVTLAIMGCGTLLIALVPGYQTIGLAAPALVLLGRLLQGFSAGVEL 135 G D GR+ +++++ +M G+LLIA++P Y TIG+AAP L+++ RL+QG S G E Sbjct: 89 FGWIADTRGRKVSMIISVFMMCAGSLLIAVMPTYATIGVAAPILLVVARLIQGLSVGAEY 148 Query: 136 GGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYSLNITLGHDAISEWGWRIPFF 195 G + Y+SEIATPG + FY S+Q + ++A + L TL + + EWGWRIPFF Sbjct: 149 GTGATYISEIATPGRRCFYGSFQYFTIIAGQLLALMTVVILQQTLTGEELREWGWRIPFF 208 Query: 196 IGCMIIPLIFVLRRSLQE--TEAFLQRKHRPDTREIFATIAKNWRIITAGTLLVAMTTTT 253 IG + ++ LRR++ E T+ + RK R +F K+ R + L+VA T Sbjct: 209 IGALSSIVVVYLRRAMHETATKKDMNRKDAGSLRGMF----KHKRAV---ALVVAFTIGG 261 Query: 254 FYFITVYTPTYGRTVLNLSA---RDSLIVTMLVGVSNFIWL-PIGGAISDRIGRRAVLMG 309 + +T TY + L +SA +++ M + F++ P+ G ++DRIG +A ++ Sbjct: 262 SLYFYTFT-TYMQKFLVISAGFSPETVSFIMTAALVGFMFCQPLFGLLADRIGIKAHMLM 320 Query: 310 ITLLALITTWPVMQWL-TAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVYVRTVG 368 + LA++ P++ L + + FT LV + +Y E+ P VR +G Sbjct: 321 FSGLAMLLVIPLLYSLQSVSSPFTAFLLVFGGLA-IASLYTPIAGIVKAELFPPAVRALG 379 Query: 369 FSLAFSLATAIFGGLTPAISTALVKLTGDKSSPGWWLMCAALCGLAATAMLFVRLSR-GY 427 +++ A FGG ++ +L + + ++ + A + AML LSR GY Sbjct: 380 VGFPYAVGNAAFGGTAEYVALSL--RSQGVEAYFFFYVAAVVTITFIAAMLMPNLSRYGY 437 Query: 428 IAAENK 433 I+ + Sbjct: 438 ISGSGE 443 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: 493 Number of extensions: 24 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: 434 Length of database: 461 Length adjustment: 33 Effective length of query: 401 Effective length of database: 428 Effective search space: 171628 Effective search space used: 171628 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