Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate SM_b20611 SM_b20611 C4-dicarboxylate transporter DctA
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Smeli:SM_b20611 Length = 441 Score = 524 bits (1350), Expect = e-153 Identities = 266/419 (63%), Positives = 327/419 (78%), Gaps = 2/419 (0%) Query: 4 RQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGI 63 + PLY+ LY QV+ AIA GILLGHFYP G LKPLGD FI+L+KM+IAP+IF TV +GI Sbjct: 12 KTPLYRHLYVQVLAAIAAGILLGHFYPDIGTELKPLGDAFIRLVKMIIAPVIFLTVATGI 71 Query: 64 AGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYV 123 AGM ++ VG+ G A++YF ST+AL++GLVV NVVQPG GMHID ++LDA VA Y Sbjct: 72 AGMTDLAKVGRVAGKAMIYFLAFSTLALVVGLVVANVVQPGAGMHIDPASLDAKAVATYA 131 Query: 124 TAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRF 183 +QSI GF++N+IP T+VGAFA GDILQVL SV+FG +L +G +PV+DF+ Sbjct: 132 EKAHEQSITGFLMNIIPTTLVGAFAEGDILQVLFISVLFGISLAIVGKKAEPVVDFLQAL 191 Query: 184 AHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAI 243 +F ++ ++MK APIGA GAMAFTIG YG+ S+ L L+ FY+T LFV +VLGA+ Sbjct: 192 TLPIFRLVAILMKAAPIGAFGAMAFTIGKYGIASIANLAMLIGTFYLTSFLFVFIVLGAV 251 Query: 244 CRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFN 303 R +GFS+L LIRYI+EELL+VLGTSSSE+ALP ++ KME+ G K+SVVGLVIPTGYSFN Sbjct: 252 ARYNGFSILSLIRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYSFN 311 Query: 304 LDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAV 363 LDGT+IY+T+AA+FIAQATDT + QI LLLV +LSSKGAAG+TG+GFI LAATLS V Sbjct: 312 LDGTNIYMTLAALFIAQATDTPLSYGDQILLLLVAMLSSKGAAGITGAGFITLAATLSVV 371 Query: 364 GHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGGRA 422 +PVAG+ALILGIDRFMSE RALTN VGNAVAT+VVAKW ELD+ QL A L GG A Sbjct: 372 PSVPVAGMALILGIDRFMSECRALTNFVGNAVATIVVAKWEGELDQAQLSAAL--GGEA 428 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: 570 Number of extensions: 12 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: 441 Length adjustment: 32 Effective length of query: 412 Effective length of database: 409 Effective search space: 168508 Effective search space used: 168508 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