Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate BPHYT_RS13510 BPHYT_RS13510 C4-dicarboxylate transporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__BFirm:BPHYT_RS13510 Length = 416 Score = 478 bits (1231), Expect = e-139 Identities = 238/414 (57%), Positives = 315/414 (76%), Gaps = 1/414 (0%) Query: 4 RQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGI 63 R+PLYK LY QVIVAI IG+ LGHF P VA+KPLGD FIKL++M+I+P+IFCTVV+GI Sbjct: 3 RKPLYKVLYVQVIVAIIIGVALGHFLPADAVAMKPLGDAFIKLVRMIISPVIFCTVVTGI 62 Query: 64 AGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYV 123 A M +M+ VG+ GG ALLYFE+VST+AL IGL+ +V++PG G ++D STLDA +A+Y Sbjct: 63 ASMHDMRKVGRVGGKALLYFEVVSTLALAIGLLAAHVLKPGIGFNVDPSTLDAGAIASYA 122 Query: 124 T-AGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDR 182 A + + GF +++IP+T GAF GDIL VL+ +++FG AL LG KP++ ID Sbjct: 123 AQAAHGEGLAGFFMHIIPDTFAGAFTQGDILPVLLIAMLFGTALAVLGEPAKPLIGLIDL 182 Query: 183 FAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGA 242 + F I+ MI LAPIGA GA+AFTIG YG+ SL+ + +L+ FY+T LFV LG Sbjct: 183 LSKTFFRIVRMITSLAPIGAFGAIAFTIGKYGIVSLLPMMKLIGTFYLTAFLFVSCGLGL 242 Query: 243 ICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSF 302 I RA GFS+ + + YI++ELLIVLGTS+SE+ALP+++ K+ERLG + +VGLV+PTGYSF Sbjct: 243 IARACGFSLWRFVVYIKDELLIVLGTSTSEAALPQLMEKLERLGCSRGIVGLVVPTGYSF 302 Query: 303 NLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSA 362 NLDGT+IY+T+A +F+AQAT+TH+ I +ITLL V +L+SKG+ GVTG+GFI LAA+LS Sbjct: 303 NLDGTNIYMTLAVLFLAQATNTHLTIAQEITLLAVTMLTSKGSTGVTGAGFITLAASLSV 362 Query: 363 VGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAEL 416 V +PV + LILGIDRFMSE RALTN +GN VA++V+A W KELD +L A L Sbjct: 363 VPTVPVTAMVLILGIDRFMSECRALTNTMGNGVASIVIAAWEKELDRGKLNAAL 416 Lambda K H 0.326 0.142 0.402 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: 536 Number of extensions: 25 Number of successful extensions: 2 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: 416 Length adjustment: 32 Effective length of query: 412 Effective length of database: 384 Effective search space: 158208 Effective search space used: 158208 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 (21.6 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