Align [Citrate]•M2+ (Ca2+ preferring):H+ symporter, CitH (transports Ca2+, Ba2+ & Sr2+) (characterized)
to candidate PP_2057 PP_2057 Uncharacterized transporter YraO
Query= TCDB::P42308 (426 letters) >FitnessBrowser__Putida:PP_2057 Length = 434 Score = 493 bits (1268), Expect = e-144 Identities = 245/432 (56%), Positives = 323/432 (74%), Gaps = 6/432 (1%) Query: 1 MLAILGFVMMIVFMYLIMSNRLSALIALIVVPIVFALISGFGKDLGEMMIQGVTDLAPTG 60 MLA+LG +M++ F YLIMS RLS ++AL +VPIVFAL+ GF DLG+MM+ G+ +AP+ Sbjct: 1 MLALLGLIMVVTFTYLIMSKRLSPIVALTIVPIVFALVGGFAPDLGKMMLDGLKMVAPSA 60 Query: 61 IMLLFAILYFGIMIDSGLFDPLIAKILSFVKGDPLKIAVGTAVLTMTISLDGDGTTTYMI 120 +LLFAIL+FG+MID+GLFDPLI KIL V GDP+KIA+GTA+L++ ++LDGDGTTTYMI Sbjct: 61 ALLLFAILFFGLMIDAGLFDPLIRKILKRVNGDPIKIAIGTALLSLLVALDGDGTTTYMI 120 Query: 121 TIAAMLPLYKRLGMNRLVLAGIAMLGSGVMN-IIPWGGPTARVLASLKLDTSEVFTPLIP 179 T AAMLPLYKR+GMN ++LA ++ML +M+ + PWGGP R +A+L LD +E F P++P Sbjct: 121 TCAAMLPLYKRIGMNPMILATVSMLSLSIMSGMSPWGGPATRAIAALGLDATEYFIPMLP 180 Query: 180 AMIAGILWVIAVAYILGKKERKRLGVISIDHAPSSDPEAA-----PLKRPALQWFNLLLT 234 +I G WV+ AY+LG+ ER+R+G I+++ + P KRP L + NL+L Sbjct: 181 TVIGGAAWVVFTAYLLGRAERRRIGNIALESGGGNCYIKEILGDNPHKRPRLAYVNLVLV 240 Query: 235 VALMAALITSLLPLPVLFMTAFAVALMVNYPNVKEQQKRISAHAGNALNVVSMVFAAGIF 294 +A+M AL+ L+ +LFM F ALM+NYP + Q++RI AH+GNA+ VV +VFAAGIF Sbjct: 241 IAVMTALVLGLMHAAILFMIGFVAALMINYPQLDLQKERILAHSGNAMTVVLLVFAAGIF 300 Query: 295 TGILSGTKMVDAMAHSLVSLIPDAMGPHLPLITAIVSMPFTFFMSNDAFYFGVLPIIAEA 354 GI SGTKMVDA+A +LV IP+A PL+ A+ SMP TF +SNDA+YFGV+PI+A A Sbjct: 301 AGIFSGTKMVDALAQTLVDWIPEAWSHWFPLVVALTSMPLTFVLSNDAYYFGVVPILANA 360 Query: 355 ASAYGIDAAEIGRASLLGQPVHLLSPLVPSTYLLVGMAGVSFGDHQKFTIKWAVGTTIVM 414 A+AYGID EI RAS+LGQPVHL+SPLV ST LLVGM GD QK T+KWAV T++V+ Sbjct: 361 AAAYGIDPVEIARASVLGQPVHLMSPLVASTLLLVGMVDRDIGDFQKATVKWAVLTSLVI 420 Query: 415 TIAALLIGIISF 426 T ALL G +SF Sbjct: 421 TALALLTGALSF 432 Lambda K H 0.328 0.142 0.411 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: 709 Number of extensions: 40 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: 426 Length of database: 434 Length adjustment: 32 Effective length of query: 394 Effective length of database: 402 Effective search space: 158388 Effective search space used: 158388 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 (21.7 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