Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate WP_043765232.1 U743_RS02380 C4-dicarboxylic acid transporter DauA
Query= SwissProt::P0AFR2 (559 letters) >NCBI__GCF_000733765.1:WP_043765232.1 Length = 574 Score = 478 bits (1231), Expect = e-139 Identities = 262/563 (46%), Positives = 362/563 (64%), Gaps = 15/563 (2%) Query: 11 PFRALIDACWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGI 70 P + A K Y A RD++AGITVG +AIPL+MALAI +GV PQ+GLYTA VAG Sbjct: 5 PLFTALRASLKAGYGIATLRRDVLAGITVGTVAIPLSMALAIATGVPPQHGLYTAIVAGA 64 Query: 71 VIALTGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEY 130 V ALTGG+RF+V+GPTAAFVVIL+P+ ++G+ GLLVATL++G+ L+ +G + GRL+++ Sbjct: 65 VAALTGGARFNVTGPTAAFVVILFPIVAEYGIGGLLVATLMAGLILVALGASGMGRLVQF 124 Query: 131 IPVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGI 190 IP V LGFT+GI + I +Q+ FLG+ H+L + ++ +LP + A G+ Sbjct: 125 IPYPVVLGFTAGIALVIAVLQVPQFLGIADGEGAGHFLSGLASIGRSLPELEPLTLATGV 184 Query: 191 VTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLL---GGHVATIGSQFHYVLADGSQG 247 +TL L+ WPRL + +P L L G N + VATI SQF + A+G G Sbjct: 185 ITLATLLLWPRLQLPVPAPLAGLAVGAVAAWFFNAMQAGDAPVATIASQFEWT-AEGRSG 243 Query: 248 NGIPQLLPQLVLPWDLPNSE---FTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMT 304 +GIP L P VLPW LP ++ + + IR L AF++AML AIESLLC+VV DGMT Sbjct: 244 SGIPPLAPGFVLPWRLPGADGAPLVVDFALIRDLAGPAFAIAMLAAIESLLCSVVADGMT 303 Query: 305 GTKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILAL 364 T+H +N EL+GQGL N+ APFFGGITATAAIAR+A +R+GA SPI+A++HS++V+LA+ Sbjct: 304 RTRHDSNGELIGQGLSNLAAPFFGGITATAAIARTATGIRSGAQSPIAAIVHSLVVLLAM 363 Query: 365 LVLAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMV 424 L+LAPLL +P+SA+AALL +VAWNMSEA + LR AP D++V++ C LTVLFDMV Sbjct: 364 LLLAPLLGLVPMSALAALLFVVAWNMSEARHFLHTLRSAPPGDVLVLVTCFGLTVLFDMV 423 Query: 425 IAISVGIVLASLLFMRRIARMTRL-------APVVVDVPDDVLVLRVIGPLFFAAAEGLF 477 +A++VGI LA+ LF+RR+A +T A VPD V + V GPLFFAAAE Sbjct: 424 LAVAVGIGLAAALFIRRMALLTSADRVRQEGAATTTRVPDSVALYDVNGPLFFAAAEKAL 483 Query: 478 TDLESRLEGKRIVILKWDAVPVLDAGGLDAFQRFVKRLPE-GCELRVCNVEFQPLRTMAR 536 + L R I+ VP +DA + + + + + G L + + + + R Sbjct: 484 STLRMVDPEVRTAIVDMHDVPSMDATAIVTLRSIIDEMQQHGVALIFVGLPTRIIAKLRR 543 Query: 537 AGIQPIPGRLAFFPNRRAAMADL 559 AGI+ PGRL + + A+A + Sbjct: 544 AGIRKQPGRLGYCSSLDTALATI 566 Lambda K H 0.328 0.142 0.425 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: 783 Number of extensions: 46 Number of successful extensions: 5 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: 559 Length of database: 574 Length adjustment: 36 Effective length of query: 523 Effective length of database: 538 Effective search space: 281374 Effective search space used: 281374 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: 53 (25.0 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