Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate BWI76_RS17465 BWI76_RS17465 C4-dicarboxylic acid transporter DauA
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__Koxy:BWI76_RS17465 Length = 559 Score = 1013 bits (2620), Expect = 0.0 Identities = 508/559 (90%), Positives = 547/559 (97%) Query: 1 MNKIFSSHVMPFRALIDACWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQY 60 MN++FSSHVMPFRALIDACWKEKYTA+RFTRD+IAGITVGIIAIPLAMALAIGSGVAPQY Sbjct: 1 MNRLFSSHVMPFRALIDACWKEKYTASRFTRDVIAGITVGIIAIPLAMALAIGSGVAPQY 60 Query: 61 GLYTAAVAGIVIALTGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMG 120 GLYT+AVAGIVIALTGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATL+SGIFLIL G Sbjct: 61 GLYTSAVAGIVIALTGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATLMSGIFLILFG 120 Query: 121 LARFGRLIEYIPVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPT 180 LARFGRLIEYIP+SVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGAL MALPT Sbjct: 121 LARFGRLIEYIPLSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALAMALPT 180 Query: 181 INVGDAAIGIVTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYV 240 IN GDAAIG+VTLG L+ WPRLGIRLPGHLPALLAGCAVMG+VNLLGGHVATIGSQFHY+ Sbjct: 181 INPGDAAIGVVTLGTLIIWPRLGIRLPGHLPALLAGCAVMGVVNLLGGHVATIGSQFHYI 240 Query: 241 LADGSQGNGIPQLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVL 300 LADGSQGNGIPQLLPQLVLPWD+P S+FTL+W S++ LLPAAFSMAMLGAIESLLCAVVL Sbjct: 241 LADGSQGNGIPQLLPQLVLPWDMPGSDFTLSWSSLQALLPAAFSMAMLGAIESLLCAVVL 300 Query: 301 DGMTGTKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILV 360 DGMTGTKHKANSEL+GQGLGNI+APFFGGITATAAIARSAANVRAGATSP+SAVIH++LV Sbjct: 301 DGMTGTKHKANSELIGQGLGNIVAPFFGGITATAAIARSAANVRAGATSPVSAVIHALLV 360 Query: 361 ILALLVLAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVL 420 I+ALLVLAPLLSWLPLSAMAALLLMVAWNMSEAHKVV+LLR+APKDDIIVML+CMSLTVL Sbjct: 361 IMALLVLAPLLSWLPLSAMAALLLMVAWNMSEAHKVVNLLRYAPKDDIIVMLMCMSLTVL 420 Query: 421 FDMVIAISVGIVLASLLFMRRIARMTRLAPVVVDVPDDVLVLRVIGPLFFAAAEGLFTDL 480 FDMVIAISVGIVLASLLFMRRIARMTRLAPV V+VPDDVLVLRVIGPLFFAAAEGLFTDL Sbjct: 421 FDMVIAISVGIVLASLLFMRRIARMTRLAPVNVEVPDDVLVLRVIGPLFFAAAEGLFTDL 480 Query: 481 ESRLEGKRIVILKWDAVPVLDAGGLDAFQRFVKRLPEGCELRVCNVEFQPLRTMARAGIQ 540 E+R+ GKRIV+LKWDAVPVLDAGGLDAFQRFVK+LPEGCELRV N+EFQPLRT+ARAG++ Sbjct: 481 ETRVAGKRIVVLKWDAVPVLDAGGLDAFQRFVKKLPEGCELRVSNLEFQPLRTLARAGVK 540 Query: 541 PIPGRLAFFPNRRAAMADL 559 PIPGRL+F+P+R AA+AD+ Sbjct: 541 PIPGRLSFYPDRNAALADI 559 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: 1008 Number of extensions: 28 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: 559 Length of database: 559 Length adjustment: 36 Effective length of query: 523 Effective length of database: 523 Effective search space: 273529 Effective search space used: 273529 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 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