Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate GFF1351 Psest_1386 Na+/H+-dicarboxylate symporters
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__psRCH2:GFF1351 Length = 409 Score = 192 bits (489), Expect = 1e-53 Identities = 126/406 (31%), Positives = 206/406 (50%), Gaps = 15/406 (3%) Query: 10 SLYFQVIVAIAIGILLGHFYP--------QTGV--ALKPLGDGFIKLIKMVIAPIIFCTV 59 SL Q+++A +G+ +G + GV A G FI L+KMV+ P+IF ++ Sbjct: 3 SLNLQILIAACLGVAIGWLTGTLPTDAPVREGVLYASTLAGSIFIGLLKMVLIPLIFTSI 62 Query: 60 VSGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKV 119 V G+A +Q V + G AL+YF + ++ A+L+ LV N+ +PG G+ +D+ + Sbjct: 63 VVGVANLQAHHQVHRVWGGALVYFTLTTSAAMLVALVAANLFKPGAGLSLDLFAEAMNDF 122 Query: 120 AAYVTAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDF 179 A + + F N+ N A ANG IL V++F++ G AL G + +L Sbjct: 123 EARQLT-LPEFFLHFFANLFQNPF-AALANGSILAVVVFAMFIGIALVAGGDRYRNILVV 180 Query: 180 IDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVV 239 + F +M II+ IM+LAP+G L + + V L +G + + T + VV Sbjct: 181 LQEFLELMMRIISWIMRLAPLGILALLIKLVAEQDVALLSAVGGFIALVFATTLFHGTVV 240 Query: 240 L-GAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRML-IKMERLGAKKSVVGLVIP 297 L G + A G S L R RE L+ TSSS + LP L + L + + G V+P Sbjct: 241 LPGILFLATGKSPLWFFRGTREALITAFATSSSAATLPISLRCAEDNLKVRPGIAGFVLP 300 Query: 298 TGYSFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLA 357 G + N+DGT++Y AA+F+A + + Q + +++S GA G+ +G + + Sbjct: 301 LGATMNMDGTALYEAAAALFVANLMGIELSLAQQAVVFFTAMIASTGAPGIPSAGMVTMV 360 Query: 358 ATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKW 403 L AVG LP +A++L IDR + R N+ G+ + +VVV ++ Sbjct: 361 MVLQAVG-LPAEAVAILLPIDRLLDTVRTAVNVEGDIIGSVVVQRF 405 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: 438 Number of extensions: 18 Number of successful extensions: 5 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: 409 Length adjustment: 32 Effective length of query: 412 Effective length of database: 377 Effective search space: 155324 Effective search space used: 155324 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