Align sodium:C4-dicarboxylate symporter (dctA) (characterized)
to candidate Pf1N1B4_4413 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate
Query= reanno::pseudo5_N2C3_1:AO356_18980 (450 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4413 Length = 451 Score = 493 bits (1269), Expect = e-144 Identities = 242/440 (55%), Positives = 331/440 (75%), Gaps = 6/440 (1%) Query: 7 LYKSLYFQVIVAIAIGILLGHFYPQTGVALKPFGDGFIKLIKMVIAPIIFCTVVSGIGGM 66 ++ LY QV++A+ +G ++G F P+TG ALKP GD FIKLIKM++AP+IF TVV+GI M Sbjct: 4 IFGKLYVQVLIAVILGAIVGVFVPETGTALKPLGDAFIKLIKMLLAPVIFLTVVTGIARM 63 Query: 67 QNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGAGMHIDVSTLDTSKIAGFISAG 126 +NMK +G+ G AL+YFE+VST+AL++GLVVV+V +PGAGM+IDV++LDTS +A + +A Sbjct: 64 ENMKELGRVGFRALIYFEVVSTLALVVGLVVVDVFKPGAGMNIDVASLDTSSLATYTTAV 123 Query: 127 KDQSIIAFILNVIPNTIVGAFANGDILQVLMFSVLFGFALHRLGAYGKPVLDFIDRFAHV 186 K S + F++N+IP+TIV AFA G++LQ+L+FS+L G AL +G K +D +D Sbjct: 124 KHASFMDFVMNIIPDTIVDAFAKGNVLQILLFSILLGVALAHVGPRAKVFVDTLDSLMQG 183 Query: 187 MFIIINMIMKLAPLGAFGAMAFTIGAYGVGSLVQLGQLMICFYITCVVFVLVVLGAICRA 246 MF I+NM+M+LAP+GAFGA+AFTIG YG GSL LG+LM C Y+TC VFV+ VLG ICR Sbjct: 184 MFRIVNMVMRLAPIGAFGAIAFTIGKYGFGSLFSLGKLMACVYLTCAVFVIFVLGPICRY 243 Query: 247 HGFSVIKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDG 306 GFS+ K +++I+EEL VLGTSSSES LP+M+ KME+ G K V G++IP+G +FN DG Sbjct: 244 SGFSLWKFLKFIKEELFTVLGTSSSESVLPQMISKMEKAGVSKPVAGMIIPSGLTFNPDG 303 Query: 307 TSIYLTMAAVFIAQATDTPMDLTHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 366 +IY T+AA+FIAQAT+TP+ LT Q+ +L VL+ +SKG+AGVTGSGFI+LAATLS++G + Sbjct: 304 QAIYYTIAAIFIAQATNTPLTLTDQLIVLAVLMFTSKGSAGVTGSGFIILAATLSSLGTI 363 Query: 367 PVAGLALILGIDRFMSEARALTNLVGNAVATIVVAKWVKELDEDQLQTELASGGRGISDV 426 PVAG+ L+LG+DRFMSEARA+TN +GN V T+ +AKWV LD ++ L + Sbjct: 364 PVAGMVLLLGVDRFMSEARAITNTIGNGVGTMAIAKWVGALDTVKMHKALN------GEA 417 Query: 427 REDDEQIAAAQIAAAETSAP 446 E + A I A ++ P Sbjct: 418 AEQKPETVQADIVAVPSAMP 437 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: 625 Number of extensions: 18 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: 450 Length of database: 451 Length adjustment: 33 Effective length of query: 417 Effective length of database: 418 Effective search space: 174306 Effective search space used: 174306 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