Align [Citrate]•M2+ (Ca2+ preferring):H+ symporter, CitH (transports Ca2+, Ba2+ & Sr2+) (characterized)
to candidate Pf1N1B4_4465 Uncharacterized transporter, similarity to citrate transporter
Query= TCDB::P42308 (426 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4465 Length = 434 Score = 486 bits (1252), Expect = e-142 Identities = 247/431 (57%), Positives = 319/431 (74%), Gaps = 6/431 (1%) Query: 1 MLAILGFVMMIVFMYLIMSNRLSALIALIVVPIVFALISGFGKDLGEMMIQGVTDLAPTG 60 MLA+LG M++VF +LIM+ RLS ++AL VVPIVFA+I GFG G+MM+ G+ +AP+ Sbjct: 1 MLALLGLAMVVVFTFLIMTKRLSPIVALTVVPIVFAVIGGFGGTTGKMMLDGLKIVAPSA 60 Query: 61 IMLLFAILYFGIMIDSGLFDPLIAKILSFVKGDPLKIAVGTAVLTMTISLDGDGTTTYMI 120 +LLFAIL+FG+MIDSGLFDPLI KIL V GDP+KIAVGTA+L++T++LDGDGTTTYMI Sbjct: 61 ALLLFAILFFGLMIDSGLFDPLIRKILKRVNGDPMKIAVGTALLSLTVALDGDGTTTYMI 120 Query: 121 TIAAMLPLYKRLGMNRLVLAGIAMLGSGVMN-IIPWGGPTARVLASLKLDTSEVFTPLIP 179 T AAMLPLYKR+GMN ++LA IAML +M+ + PWGGP R +A+L LD F PL+P Sbjct: 121 TCAAMLPLYKRIGMNPMILATIAMLSLSIMSGMTPWGGPATRAIAALGLDAGAYFIPLLP 180 Query: 180 AMIAGILWVIAVAYILGKKERKRLGVISI-----DHAPSSDPEAAPLKRPALQWFNLLLT 234 M+ G WV+ A++LG+ ERKR+G + D + E P KRP L + NLLL Sbjct: 181 TMVGGAAWVVFTAFLLGRTERKRIGNTQLQSGGGDCYIKAILEDTPHKRPKLAYVNLLLV 240 Query: 235 VALMAALITSLLPLPVLFMTAFAVALMVNYPNVKEQQKRISAHAGNALNVVSMVFAAGIF 294 A+M AL+ ++ +LF+ F +ALM+NYP + Q++RI AH+GNA+ VV +VFAAGIF Sbjct: 241 TAVMVALVMGIMHSAILFLIGFVLALMINYPQLDIQKERILAHSGNAMTVVLLVFAAGIF 300 Query: 295 TGILSGTKMVDAMAHSLVSLIPDAMGPHLPLITAIVSMPFTFFMSNDAFYFGVLPIIAEA 354 GI SGTKMVDA+A +LV IP + G PL+ AI SMP TF +SNDA+YFGV+PI+A A Sbjct: 301 AGIFSGTKMVDALAQTLVDWIPPSWGHLFPLVVAITSMPLTFVLSNDAYYFGVVPILANA 360 Query: 355 ASAYGIDAAEIGRASLLGQPVHLLSPLVPSTYLLVGMAGVSFGDHQKFTIKWAVGTTIVM 414 A+AYGID EI RAS+LGQPVHL+SPLV ST LLVGM GD Q+ T+KWAV T++V+ Sbjct: 361 AAAYGIDPVEIARASILGQPVHLMSPLVASTLLLVGMVDRDIGDFQRATVKWAVLTSLVV 420 Query: 415 TIAALLIGIIS 425 T ALL G ++ Sbjct: 421 TALALLTGALT 431 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: 692 Number of extensions: 39 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