Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate Pf1N1B4_4413 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4413 Length = 451 Score = 493 bits (1270), Expect = e-144 Identities = 234/418 (55%), Positives = 324/418 (77%) Query: 5 LFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGM 64 +F LY QVL A+ +G ++G F PE G +KPLGD F+KLIKM++APVIF TVVTGIA M Sbjct: 4 IFGKLYVQVLIAVILGAIVGVFVPETGTALKPLGDAFIKLIKMLLAPVIFLTVVTGIARM 63 Query: 65 ESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQA 124 E+MK +GR G AL+YFE+VST+AL++GL++V+V +PGAGMN+D A+LD ++A Y Sbjct: 64 ENMKELGRVGFRALIYFEVVSTLALVVGLVVVDVFKPGAGMNIDVASLDTSSLATYTTAV 123 Query: 125 KDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQV 184 K + F+M++IP +++ AFA GN+LQ+LLF++L G AL +G + ++ + ++S Q Sbjct: 124 KHASFMDFVMNIIPDTIVDAFAKGNVLQILLFSILLGVALAHVGPRAKVFVDTLDSLMQG 183 Query: 185 IFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKA 244 +F I+NM+MRLAPIGAFGA+AFTIGKYG G+L LG+L+ C Y+TC +FV+ VLG I + Sbjct: 184 MFRIVNMVMRLAPIGAFGAIAFTIGKYGFGSLFSLGKLMACVYLTCAVFVIFVLGPICRY 243 Query: 245 TGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDG 304 +GFS++KF+++I+EEL VLGTSSSES LP+M+ KMEK G K V G++IP+G +FN DG Sbjct: 244 SGFSLWKFLKFIKEELFTVLGTSSSESVLPQMISKMEKAGVSKPVAGMIIPSGLTFNPDG 303 Query: 305 TSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 364 +IY T+AA+FIAQATN+ + + Q+ +L VL+ +SKG+AGVTGSGFI+LAATLS++G + Sbjct: 304 QAIYYTIAAIFIAQATNTPLTLTDQLIVLAVLMFTSKGSAGVTGSGFIILAATLSSLGTI 363 Query: 365 PVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRAPDGK 422 PVAG+ L+LG+DRFMSEARA+TN +GNGV T+ +AKWV LD K+ LN A + K Sbjct: 364 PVAGMVLLLGVDRFMSEARAITNTIGNGVGTMAIAKWVGALDTVKMHKALNGEAAEQK 421 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: 594 Number of extensions: 20 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: 451 Length adjustment: 32 Effective length of query: 396 Effective length of database: 419 Effective search space: 165924 Effective search space used: 165924 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 17 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