Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate GFF4002 Psest_4075 Na+/H+-dicarboxylate symporters
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__psRCH2:GFF4002 Length = 419 Score = 223 bits (569), Expect = 7e-63 Identities = 125/400 (31%), Positives = 218/400 (54%), Gaps = 11/400 (2%) Query: 11 LYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQNMK 70 L+ Q+++ +A+G+ G + L P+G F+ IKM+I P++F ++V+GI MQ+ Sbjct: 19 LWQQILIGLALGVAAGMAFGADAQLLAPIGTLFLNAIKMLIVPLVFVSLVAGITSMQDSA 78 Query: 71 SVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAGKDQS 130 +G+ + + + + A+ IGL+ + PG GM++ S + +K A S Sbjct: 79 KLGRISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNMVASGNEQAKQAP--------S 130 Query: 131 IVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHVMFNI 190 +V ++ ++P V AFA G+ILQ+++F++ G +++ +G G P + D A + + Sbjct: 131 LVSILVGLVPANPVTAFAEGNILQIIVFAIALGVSINLIGERGAPAVRLFDALAETFYKL 190 Query: 191 INMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICRAHG-F 249 +++M++APIG A +G++G L+ L ++ Y+ + VL+V G + Sbjct: 191 TDLVMRVAPIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGLLGLLARL 250 Query: 250 SVLKLIRYIREELLIVLGTSSSESALPRML-IKMERLGAKKSVVGLVIPTGYSFNLDGTS 308 + L+ + I L + TSSS LP + + LG + V G V+P G + N+DGT+ Sbjct: 251 NPLRFFQGIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGTA 310 Query: 309 IYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPV 368 IY + A+FIAQA + ++L L+S G AG+ G+G I+L L+A G LP+ Sbjct: 311 IYQGVLALFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAG-LPL 369 Query: 369 AGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELD 408 G+ALI GIDR + AR N+ G+ + T +V + +ELD Sbjct: 370 EGVALIAGIDRILDMARTTVNVAGDLMTTTLVGRSEQELD 409 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: 501 Number of extensions: 26 Number of successful extensions: 7 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: 419 Length adjustment: 32 Effective length of query: 412 Effective length of database: 387 Effective search space: 159444 Effective search space used: 159444 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 Apr 09 2024. 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