Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate Pf1N1B4_4413 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4413 Length = 451 Score = 489 bits (1258), Expect = e-143 Identities = 240/438 (54%), Positives = 327/438 (74%), Gaps = 2/438 (0%) Query: 7 LYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGM 66 ++ LY QV++A+ +G ++G F P+TG ALKPLGD FIKLIKM++AP+IF TVV+GIA M Sbjct: 4 IFGKLYVQVLIAVILGAIVGVFVPETGTALKPLGDAFIKLIKMLLAPVIFLTVVTGIARM 63 Query: 67 QNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAG 126 +NMK +G+ G AL+YFE+VST+AL++GLVVV+V +PG GM+IDV++LD S +A Y TA Sbjct: 64 ENMKELGRVGFRALIYFEVVSTLALVVGLVVVDVFKPGAGMNIDVASLDTSSLATYTTAV 123 Query: 127 KDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHV 186 K S + F++N+IP+TIV AFA G++LQ+L+FS++ G AL +G K +D +D Sbjct: 124 KHASFMDFVMNIIPDTIVDAFAKGNVLQILLFSILLGVALAHVGPRAKVFVDTLDSLMQG 183 Query: 187 MFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICRA 246 MF I+NM+M+LAPIGA GA+AFTIG YG GSL LG+LM C Y+TC +FV+ VLG ICR Sbjct: 184 MFRIVNMVMRLAPIGAFGAIAFTIGKYGFGSLFSLGKLMACVYLTCAVFVIFVLGPICRY 243 Query: 247 HGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDG 306 GFS+ K +++I+EEL VLGTSSSES LP+M+ KME+ G K V G++IP+G +FN DG Sbjct: 244 SGFSLWKFLKFIKEELFTVLGTSSSESVLPQMISKMEKAGVSKPVAGMIIPSGLTFNPDG 303 Query: 307 TSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 366 +IY T+AA+FIAQAT+T + +T Q+ +L VL+ +SKG+AGVTGSGFI+LAATLS++G + Sbjct: 304 QAIYYTIAAIFIAQATNTPLTLTDQLIVLAVLMFTSKGSAGVTGSGFIILAATLSSLGTI 363 Query: 367 PVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGGRAISDT 426 PVAG+ L+LG+DRFMSEARA+TN +GN V T+ +AKWV LD ++ L G A Sbjct: 364 PVAGMVLLLGVDRFMSEARAITNTIGNGVGTMAIAKWVGALDTVKMHKAL--NGEAAEQK 421 Query: 427 REEDDLGVAEGPTPTTVK 444 E + P+ K Sbjct: 422 PETVQADIVAVPSAMPAK 439 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: 612 Number of extensions: 21 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: 444 Length of database: 451 Length adjustment: 33 Effective length of query: 411 Effective length of database: 418 Effective search space: 171798 Effective search space used: 171798 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 (21.6 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