Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate WP_019866698.1 METMI_RS0112815 dicarboxylate/amino acid:cation symporter
Query= CharProtDB::CH_014038 (428 letters) >NCBI__GCF_000384075.1:WP_019866698.1 Length = 442 Score = 531 bits (1367), Expect = e-155 Identities = 268/417 (64%), Positives = 335/417 (80%) Query: 1 MKTSLFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTG 60 M ++ + LY QVL AI +GILLGHF PE MKPLGDGF+KLIKM+IAP++FCTVVTG Sbjct: 26 MLKNIHRHLYAQVLAAIFMGILLGHFCPETAVAMKPLGDGFIKLIKMLIAPIVFCTVVTG 85 Query: 61 IAGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVY 120 IAGM+SM+ VGR G LLYFE+VST+AL+IGL++V+++QPGAGMN+D LDA+++ Y Sbjct: 86 IAGMQSMERVGRVGIKLLLYFEVVSTLALVIGLLVVHIIQPGAGMNIDARNLDAQSLQGY 145 Query: 121 ADQAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIES 180 + AK V+F++++IP SV+ AFA G+ILQVLLFAVLFG +L +G KG L+ I + Sbjct: 146 TEAAKTHNTVSFLLNIIPVSVVDAFAKGDILQVLLFAVLFGCSLAVIGDKGALVMRFIHN 205 Query: 181 FSQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGS 240 S+V+FGI+ IM+LAP+GAFGAMAFTIG+YGV L L +L+ FY+ C +F+ VLG Sbjct: 206 VSEVLFGIVETIMKLAPLGAFGAMAFTIGQYGVHALAPLAKLMGSFYLACGVFIFGVLGL 265 Query: 241 IAKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSF 300 IA+ +GFS+ KFI YI++ELLIVLGTSSSES LPR++ K+E+LGC K VVGLVIPTGYSF Sbjct: 266 IARWSGFSLVKFIIYIKDELLIVLGTSSSESVLPRIMGKLERLGCAKPVVGLVIPTGYSF 325 Query: 301 NLDGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSA 360 NLDGTSIYLTMAAVF+AQATN+ + ++TLL VLLL+SKGAAG+TGSGFI LAATLS Sbjct: 326 NLDGTSIYLTMAAVFVAQATNTPLTWGQELTLLGVLLLTSKGAAGITGSGFITLAATLST 385 Query: 361 VGHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNR 417 V +PVAGLALILGIDRFMSEARALTNL+GNGVAT+V A+W LD +L LN + Sbjct: 386 VPTIPVAGLALILGIDRFMSEARALTNLIGNGVATVVAARWENALDETQLSSELNGK 442 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: 628 Number of extensions: 34 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: 428 Length of database: 442 Length adjustment: 32 Effective length of query: 396 Effective length of database: 410 Effective search space: 162360 Effective search space used: 162360 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