Align citrate transporter (characterized)
to candidate Pf6N2E2_2276 Permeases of the major facilitator superfamily
Query= CharProtDB::CH_014606 (431 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2276 Length = 432 Score = 539 bits (1388), Expect = e-158 Identities = 258/405 (63%), Positives = 321/405 (79%) Query: 13 AILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGSGFLMRPIGAVV 72 AI RV SGNFLE FDF ++GFYAT IAKTFFPA+S FA+LML+ A FG+GFLMRP+GA+ Sbjct: 10 AIFRVVSGNFLEMFDFMVYGFYATAIAKTFFPADSAFASLMLSLATFGAGFLMRPLGAIF 69 Query: 73 LGAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGRLLQGFSAGVEL 132 LGAYIDR GRRKGL+ITLA+M GT+LIA VPGY T+G+ AP+LVL+GRLLQGFSAGVEL Sbjct: 70 LGAYIDRHGRRKGLIITLAMMAAGTVLIACVPGYATLGVAAPLLVLLGRLLQGFSAGVEL 129 Query: 133 GGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDEISEWGWRIPFF 192 GGVSVYL+EI+TPG KGF+ SWQSASQQ A+V A L+G GLN L E+ EWGWR+PF Sbjct: 130 GGVSVYLAEISTPGRKGFFVSWQSASQQAAVVFAGLLGVGLNHWLSPQEMGEWGWRVPFL 189 Query: 193 IGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIAKNWRIITAGTLLVAMTTTTFY 252 +GCMI+P IFV+RRSL+ET F RKHRP EI +I +N+ I+ AG LV MTT +FY Sbjct: 190 VGCMIVPAIFVIRRSLEETPEFQARKHRPSLSEIVRSIGQNFGIVLAGMALVVMTTVSFY 249 Query: 253 FITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGRRPVLMGITLLAL 312 IT YTPT+G+ LNLS D+L+VT+ +G+SNF WLP+ GA+SD++GR+P+L+G T+LA+ Sbjct: 250 LITAYTPTFGKAELNLSDLDALLVTVCIGLSNFFWLPVMGALSDKVGRKPLLLGATVLAI 309 Query: 313 VTTLPVMNWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVYVRTVGFSLAFSL 372 +T P ++WL A P F+ + +V LW SF +G YNGAMV ALTE+MPV VRT GFSLA+SL Sbjct: 310 LTAYPALSWLVANPSFSHLLIVELWLSFLYGSYNGAMVVALTEIMPVEVRTTGFSLAYSL 369 Query: 373 ATAIFGGLTPAISTALVQLTGDKSSPGWWLMCAALCGLAATTMLF 417 ATA FGG TPA T L+ + +K++PG WL AA+ GL AT +LF Sbjct: 370 ATATFGGFTPAACTYLIHVLDNKAAPGIWLSGAAVLGLIATLVLF 414 Lambda K H 0.328 0.141 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: 601 Number of extensions: 20 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: 431 Length of database: 432 Length adjustment: 32 Effective length of query: 399 Effective length of database: 400 Effective search space: 159600 Effective search space used: 159600 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