Align C4-dicarboxylate transport protein 2 (characterized)
to candidate WP_010961124.1 MCA_RS09200 dicarboxylate/amino acid:cation symporter
Query= SwissProt::Q9I4F5 (436 letters) >NCBI__GCF_000008325.1:WP_010961124.1 Length = 430 Score = 495 bits (1274), Expect = e-144 Identities = 244/402 (60%), Positives = 313/402 (77%) Query: 1 MTKQPFYKSLYVQVLVAIAIGIALGHWYPETAVAMKPFGDGFVKLIKMAIAPIIFCTVVT 60 M + +K LYVQV++A+ +G+ALG +PE V +KP GDGFVKLIKM IAPI+F TV Sbjct: 1 MAGRHIFKELYVQVILAVIVGVALGVAWPELGVKLKPLGDGFVKLIKMMIAPIVFLTVTL 60 Query: 61 GIAGMQSMKSVGKTGGMALLYFEVVSTVALIIGLVVVNVVQPGAGMHVDPNTLDTSKIAA 120 GI + ++ +G G AL+YFE ++TVAL+IGLVVVN++QPGAG+H DP TLD + I Sbjct: 61 GIGKVGDLRKIGSVGLKALIYFEALTTVALLIGLVVVNLLQPGAGIHADPKTLDAAAIGQ 120 Query: 121 YAAAGEKQSTVDFLMNVIPGTVVGAFANGDILQVLFFSVLFGYALHRLGSYGKPVFEFIE 180 Y + S VDF++N+IP + V AFA GDILQVL SVLFG A+ R G GKPV + +E Sbjct: 121 YTGGAKALSGVDFVLNIIPSSAVDAFAKGDILQVLLVSVLFGVAMSRQGERGKPVLDVLE 180 Query: 181 RVSHVMFNIINVIMKVAPIGAFGAMAFTIGAYGVGSLVQLGQLMLCFYITCILFVLIVLG 240 RVS F I +IM+ AP+GAFGAMAFTIG YG +L+ LG+LM Y+TC FV++VLG Sbjct: 181 RVSEASFATIGLIMRAAPVGAFGAMAFTIGKYGPDTLLSLGKLMGGVYMTCASFVVLVLG 240 Query: 241 GIARAHGFSILRFIRYIREELLIVLGTSSSESALPRMIDKMEKLGCNKSVVGLVIPTGYS 300 +AR GFS+ R ++ I+EEL +VLGTSSSE+ALPR+++K+E GC +S+VGLV+PTGYS Sbjct: 241 AVARVSGFSLWRLLKLIKEELWLVLGTSSSEAALPRLMEKLEGAGCPRSIVGLVVPTGYS 300 Query: 301 FNLDGTSIYLTMAAVFIAQATDTPMDITHQITLLLVLLIASKGAAGVTGSGFIVLAATLS 360 FNLDGT+IYLTMAAVF+AQATDTP+ + HQ+TLL VLL+ SKGAA VTG+GFI LAATLS Sbjct: 301 FNLDGTAIYLTMAAVFVAQATDTPLTLGHQLTLLAVLLLTSKGAAAVTGAGFITLAATLS 360 Query: 361 AVGHLPVAGLALILGIDRFMSEARALTNLVGNGVATVVVSKW 402 ++ +PV GLAL+LG+DRFMSEARALTNL+GN VAT+ V++W Sbjct: 361 SLDVVPVTGLALLLGVDRFMSEARALTNLIGNAVATLAVTRW 402 Lambda K H 0.325 0.140 0.406 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: 590 Number of extensions: 13 Number of successful extensions: 1 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: 436 Length of database: 430 Length adjustment: 32 Effective length of query: 404 Effective length of database: 398 Effective search space: 160792 Effective search space used: 160792 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 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