Align Citrate:H+ symporter (characterized)
to candidate 18139 b4111 proline/glycine betaine transporter (NCBI)
Query= TCDB::P16482 (444 letters) >FitnessBrowser__Keio:18139 Length = 500 Score = 224 bits (572), Expect = 4e-63 Identities = 128/410 (31%), Positives = 208/410 (50%), Gaps = 13/410 (3%) Query: 29 AILRVTSGNFLEQFDFFLFGFYATYIAHTFFPASSEFASLMMTFAVFGAGFLMRPIGAIV 88 AI + GN +E FDF ++GF A + FFP + ++ A F FL+RP+G + Sbjct: 26 AITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGGLF 85 Query: 89 LGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLLVLIGRLLQGFSAGAEL 148 G DK GR+K L +T+ IM+ TF I LIPSY TIG+WAP+L+LI ++ QGFS G E Sbjct: 86 FGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGGEY 145 Query: 149 GGVSVYLAEIATPGRKGFYTSWQSGSQQVAIMVAAAMGFALNAVLEPSAISDWGWRIPFL 208 G S+++AE + ++GF SW ++ A + ++ ++ + DWGWRIPF Sbjct: 146 TGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIPFF 205 Query: 209 FGVLIVPFIFILRRKLEETQEFTARRHHLAM----------RQVFATLLAN-WQVVIAGM 257 + + LR LEET F L + F + W+ ++ + Sbjct: 206 IALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLTCI 265 Query: 258 MMVAMTTTAFYLITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVGGALSDRFGRR 317 +V T +Y++ Y P++ L S +L+ + + I F PV G LSDRFGRR Sbjct: 266 GLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQPVMGLLSDRFGRR 325 Query: 318 SVLIAMTLLALATAWPALTMLANAPSFLMMLSVLLWLSFIYGMYNGAMIPALTEIMPAEV 377 ++ ++ A PA +L N+ ++ + LL L+ I + G M L + P + Sbjct: 326 PFVLLGSVALFVLAIPAF-ILINSNVIGLIFAGLLMLAVILNCFTGVMASTLPAMFPTHI 384 Query: 378 RVAGFSLAYSLATAVFGGFTPVISTALIEYTGDKASPGYWMSFAAICGLL 427 R + + A++++ V G TP ++ L+E + + P Y++ A+ GL+ Sbjct: 385 RYSALAAAFNISVLV-AGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLI 433 Lambda K H 0.329 0.139 0.421 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: 552 Number of extensions: 29 Number of successful extensions: 3 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: 444 Length of database: 500 Length adjustment: 33 Effective length of query: 411 Effective length of database: 467 Effective search space: 191937 Effective search space used: 191937 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 (21.9 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