Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate WP_010961124.1 MCA_RS09200 dicarboxylate/amino acid:cation symporter
Query= CharProtDB::CH_014038 (428 letters) >NCBI__GCF_000008325.1:WP_010961124.1 Length = 430 Score = 482 bits (1240), Expect = e-140 Identities = 233/397 (58%), Positives = 318/397 (80%) Query: 5 LFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGM 64 +FK LY QV+ A+ +G+ LG +PE+G ++KPLGDGFVKLIKM+IAP++F TV GI + Sbjct: 6 IFKELYVQVILAVIVGVALGVAWPELGVKLKPLGDGFVKLIKMMIAPIVFLTVTLGIGKV 65 Query: 65 ESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQA 124 ++ +G G AL+YFE ++T+AL+IGL++VN++QPGAG++ DP TLDA A+ Y A Sbjct: 66 GDLRKIGSVGLKALIYFEALTTVALLIGLVVVNLLQPGAGIHADPKTLDAAAIGQYTGGA 125 Query: 125 KDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQV 184 K V F++++IP+S + AFA G+ILQVLL +VLFG A+ R G +G+ + +V+E S+ Sbjct: 126 KALSGVDFVLNIIPSSAVDAFAKGDILQVLLVSVLFGVAMSRQGERGKPVLDVLERVSEA 185 Query: 185 IFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKA 244 F I +IMR AP+GAFGAMAFTIGKYG TL+ LG+L+ Y+TC FVVLVLG++A+ Sbjct: 186 SFATIGLIMRAAPVGAFGAMAFTIGKYGPDTLLSLGKLMGGVYMTCASFVVLVLGAVARV 245 Query: 245 TGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDG 304 +GFS+++ ++ I+EEL +VLGTSSSE+ALPR+++K+E GC +S+VGLV+PTGYSFNLDG Sbjct: 246 SGFSLWRLLKLIKEELWLVLGTSSSEAALPRLMEKLEGAGCPRSIVGLVVPTGYSFNLDG 305 Query: 305 TSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 364 T+IYLTMAAVF+AQAT++ + + HQ+TLL VLLL+SKGAA VTG+GFI LAATLS++ + Sbjct: 306 TAIYLTMAAVFVAQATDTPLTLGHQLTLLAVLLLTSKGAAAVTGAGFITLAATLSSLDVV 365 Query: 365 PVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKW 401 PV GLAL+LG+DRFMSEARALTNL+GN VAT+ V +W Sbjct: 366 PVTGLALLLGVDRFMSEARALTNLIGNAVATLAVTRW 402 Lambda K H 0.327 0.142 0.401 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: 566 Number of extensions: 18 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: 428 Length of database: 430 Length adjustment: 32 Effective length of query: 396 Effective length of database: 398 Effective search space: 157608 Effective search space used: 157608 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 (21.7 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