Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate WP_051244599.1 H537_RS0138195 C4-dicarboxylate transporter DctA
Query= TCDB::Q848I3 (444 letters) >NCBI__GCF_000430725.1:WP_051244599.1 Length = 454 Score = 479 bits (1232), Expect = e-139 Identities = 232/439 (52%), Positives = 326/439 (74%), Gaps = 5/439 (1%) Query: 2 TTRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVS 61 T R PL + LY QV++ I +G+ LGHFYP G +KPLGDGFIKLIKM++AP+IF T+V Sbjct: 9 TARVPLLRRLYVQVLIGILLGVALGHFYPAIGTDMKPLGDGFIKLIKMLLAPVIFATIVV 68 Query: 62 GIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAA 121 GIA M ++K VGK G ALLYFE++ST+AL++GL+VVNV++PG GM++D + LD ++A Sbjct: 69 GIARMGDLKEVGKVGAKALLYFEVLSTLALVVGLLVVNVIKPGVGMNVDPAALDGKSISA 128 Query: 122 YVTAGKDQ--SIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDF 179 Y + + Q V F++NVIP ++VG+FA G++LQ+L+F+V+FG A+ R G +P +D Sbjct: 129 YTSMAESQHTGAVDFLMNVIPKSVVGSFAEGNVLQILLFAVLFGAAMSRFGDRVRPFIDM 188 Query: 180 IDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVV 239 +D F MF I+ M+M LAPIGA GA+AFTIG YG+GS+ G+L++ Y TC LFVLVV Sbjct: 189 LDMFLQGMFGIVRMVMVLAPIGAFGAIAFTIGKYGIGSMAAYGKLIVAVYATCALFVLVV 248 Query: 240 LGAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTG 299 LGA+ R S+ +RYIREELLI GT+S+ES LP+M+ K+E G +KS+VG+V+P G Sbjct: 249 LGAVARICRISIRSYLRYIREELLITFGTASTESVLPQMMKKLEAAGCRKSIVGMVLPAG 308 Query: 300 YSFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAAT 359 Y+FN DGT+IYLT+AAVF+AQAT+ + ++ Q+ +L VL+L+SKG+AGV G+GF+ LAAT Sbjct: 309 YTFNPDGTAIYLTIAAVFVAQATNVPLSLSDQLVILSVLMLTSKGSAGVAGAGFVTLAAT 368 Query: 360 LSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASG 419 L ++ +PVAGL L+LG+DRF++EARA+TNL+GN +AT+ VAKW DE + E+ G Sbjct: 369 LGSLHTIPVAGLVLLLGVDRFLNEARAITNLIGNGLATIAVAKWEGAFDEARWH-EVTGG 427 Query: 420 GRAISDTREEDDLGVAEGP 438 G ++ + D L + P Sbjct: 428 G--VAQAQAGDGLPMESSP 444 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: 641 Number of extensions: 21 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: 454 Length adjustment: 33 Effective length of query: 411 Effective length of database: 421 Effective search space: 173031 Effective search space used: 173031 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