Align citrate transporter (characterized)
to candidate WP_011427276.1 RHE_RS20930 MFS transporter
Query= CharProtDB::CH_014606 (431 letters) >NCBI__GCF_000092045.1:WP_011427276.1 Length = 628 Score = 171 bits (434), Expect = 5e-47 Identities = 99/312 (31%), Positives = 166/312 (53%), Gaps = 11/312 (3%) Query: 20 GNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGSGFLMRPIGAVVLGAYIDR 79 G E +DF+L+G ATYI T+F E + T F +GFL+RP GA+V G D Sbjct: 29 GTVFEWYDFYLYGSLATYIGATYFTQYPEATRNIFTLLAFAAGFLVRPFGALVFGRLGDL 88 Query: 80 IGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGRLLQGFSAGVELGGVSVYL 139 +GR+ ++T+ IMG T L+ ++PG +IG+ AP++++ RLLQG + G E GG + Y+ Sbjct: 89 VGRKYTFLVTILIMGMSTFLVGILPGAASIGIAAPIILIGLRLLQGLALGGEYGGAATYV 148 Query: 140 SEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDEISEWGWRIPFFIGCMIIP 199 +E A G +G++TSW + + + ++ ++ + + + + WGWRIPF + +++ Sbjct: 149 AEHAPNGRRGYFTSWIQTTATLGLFLSLIVIILVQSLMAPAQFAAWGWRIPFLVSVVLLG 208 Query: 200 LIFVLRRSLQETEAFLQRKHRPDTREIFTTIA----KNWRIITAGTLLVAM-TTTTFYFI 254 + +R + E+ AF + K + T A KN +I L M +Y Sbjct: 209 ISVWIRLKMNESPAFQRMKAEGKGSKAPLTEAFGQWKNAKIALIALLGATMGQAVVWYGG 268 Query: 255 TVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLP---IGGAISDRIGRRPVLMGITLLA 311 Y + + VL + D ++V I+ F+ P I G +SD+IGR+P++M L+A Sbjct: 269 QFYALFFLQNVLKV---DLFSANVMVAIALFLGTPFFVIFGGLSDKIGRKPIIMAGLLIA 325 Query: 312 LVTTLPVMNWLT 323 VT P+ +T Sbjct: 326 AVTYNPLFKAMT 337 Score = 40.0 bits (92), Expect = 2e-07 Identities = 20/61 (32%), Positives = 29/61 (47%) Query: 334 VLLWFSFFFGMYNGAMVAALTEVMPVYVRTVGFSLAFSLATAIFGGLTPAISTALVQLTG 393 +L + M G + A L E+ P +R G SL + + FGGL PA + A+ G Sbjct: 533 ILFVLVLYVTMVYGPIAALLVELFPTRIRYTGMSLPYHIGNGWFGGLLPATAFAMSAAAG 592 Query: 394 D 394 D Sbjct: 593 D 593 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: 639 Number of extensions: 38 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 431 Length of database: 628 Length adjustment: 35 Effective length of query: 396 Effective length of database: 593 Effective search space: 234828 Effective search space used: 234828 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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