Align [Citrate]•M2+ (Ca2+ preferring):H+ symporter, CitH (transports Ca2+, Ba2+ & Sr2+) (characterized)
to candidate AO356_28880 AO356_28880 damage-inducible protein CinA
Query= TCDB::P42308 (426 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28880 Length = 434 Score = 491 bits (1263), Expect = e-143 Identities = 248/431 (57%), Positives = 323/431 (74%), Gaps = 6/431 (1%) Query: 1 MLAILGFVMMIVFMYLIMSNRLSALIALIVVPIVFALISGFGKDLGEMMIQGVTDLAPTG 60 MLA+LG M++VF +LIM+ RLS ++AL VVPIVFA++ GFG G+MM+ G+ +AP+ Sbjct: 1 MLALLGLAMVVVFTFLIMTKRLSPIVALTVVPIVFAVLGGFGGTTGKMMLDGLKMVAPSA 60 Query: 61 IMLLFAILYFGIMIDSGLFDPLIAKILSFVKGDPLKIAVGTAVLTMTISLDGDGTTTYMI 120 +LLFAIL+FG+MID+GLFDPLI KIL V GDP+KIAVGTA+L++ ++LDGDGTTTYMI Sbjct: 61 ALLLFAILFFGLMIDAGLFDPLIRKILKRVNGDPMKIAVGTALLSLLVALDGDGTTTYMI 120 Query: 121 TIAAMLPLYKRLGMNRLVLAGIAMLGSGVMN-IIPWGGPTARVLASLKLDTSEVFTPLIP 179 T AAMLPLYKR+GMN ++LA I+ML +M+ + PWGGP R +A+L LD E F PL+P Sbjct: 121 TCAAMLPLYKRIGMNPMILATISMLSLSIMSGMTPWGGPATRAIAALGLDAGEYFVPLLP 180 Query: 180 AMIAGILWVIAVAYILGKKERKRLGVISI-----DHAPSSDPEAAPLKRPALQWFNLLLT 234 MI G +WV+ A++LG+ ERKR+G + + D ++ E P KRP L + NLLL Sbjct: 181 TMIGGAMWVVFTAFLLGRAERKRIGNVQLQSGGGDCYINAIIEDTPHKRPKLAYVNLLLV 240 Query: 235 VALMAALITSLLPLPVLFMTAFAVALMVNYPNVKEQQKRISAHAGNALNVVSMVFAAGIF 294 VA+M AL+ L+ +LF+ F +ALM+NYP + Q++RI AH+GNA+ VV +VFAAGIF Sbjct: 241 VAVMVALVMGLMHSAILFLIGFVLALMINYPQLDIQKERILAHSGNAMTVVLLVFAAGIF 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 QK T+KWAV T++V+ Sbjct: 361 AAAYGIDPVEIARASILGQPVHLMSPLVASTLLLVGMVDRDLGDFQKATVKWAVLTSLVI 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: 684 Number of extensions: 37 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