Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate YP_004144924.1 Mesci_5852 sodium:dicarboxylate symporter
Query= TCDB::Q848I3 (444 letters) >NCBI__GCF_000185905.1:YP_004144924.1 Length = 452 Score = 511 bits (1316), Expect = e-149 Identities = 248/411 (60%), Positives = 325/411 (79%) Query: 4 RQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGI 63 R+ Y LY QV+ AIA+G+ +G+ YP TG ALKPLGD FIKL+KM+IAP+IF TV +GI Sbjct: 33 RKAFYAQLYVQVLTAIALGVAVGYLYPGTGEALKPLGDAFIKLVKMIIAPVIFLTVTTGI 92 Query: 64 AGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYV 123 AGM ++K VG+ G A++YF S++AL++GLVV NVVQPG+G+ ID ++LD V YV Sbjct: 93 AGMNDLKKVGRVAGKAMIYFLTFSSLALMVGLVVANVVQPGSGLDIDPASLDGQAVQGYV 152 Query: 124 TAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRF 183 DQS+ GF++N+IP+TIVGAFA G+ILQVL FS++FG AL G GKPVL + Sbjct: 153 AKVHDQSVTGFLMNIIPSTIVGAFAEGNILQVLFFSILFGSALAMAGDTGKPVLSLLQAL 212 Query: 184 AHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAI 243 +F ++ ++M+ AP+GA GAMAFTIG YG+GS+V L L+ FY T +FV +LGA+ Sbjct: 213 LAPVFKLVGILMQAAPVGAFGAMAFTIGKYGIGSVVNLAMLVATFYFTAFVFVFGILGAV 272 Query: 244 CRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFN 303 CR +GFS+ L+RYI+EELL+VL TSSSE+ALP ++ KME+ GAK+SVVGLVIPTGYSFN Sbjct: 273 CRYNGFSIFSLVRYIKEELLLVLATSSSEAALPSLMEKMEKAGAKRSVVGLVIPTGYSFN 332 Query: 304 LDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAV 363 LDGT+IY+T+AA+FIAQAT+TH+ + QI LL+V +LSSKGAAG+TG+GF+ LAATLS + Sbjct: 333 LDGTNIYMTLAALFIAQATNTHLSVADQILLLVVAMLSSKGAAGITGAGFVTLAATLSVI 392 Query: 364 GHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQA 414 +PVAG+ALILG+DRFMSE RALTN+VGNAVA +VVA+W ELDE +++A Sbjct: 393 PTVPVAGMALILGVDRFMSECRALTNVVGNAVAALVVARWEGELDEARMKA 443 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: 634 Number of extensions: 20 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: 452 Length adjustment: 33 Effective length of query: 411 Effective length of database: 419 Effective search space: 172209 Effective search space used: 172209 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 24 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