Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate 209213 DVU0279 sulfate permease family protein
Query= SwissProt::P0AFR2 (559 letters) >MicrobesOnline__882:209213 Length = 568 Score = 390 bits (1002), Expect = e-113 Identities = 226/552 (40%), Positives = 326/552 (59%), Gaps = 37/552 (6%) Query: 21 KEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRF 80 +E Y F +DL AG+TVGI+A+PLAMA AI SG P+ GL+TA VAG +I+L GGSR+ Sbjct: 22 REGYDGGTFFKDLAAGLTVGIVALPLAMAFAIASGTTPERGLFTAIVAGFLISLLGGSRY 81 Query: 81 SVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFT 140 + GPT AFV+I++ V + G GL+V TLL+G L++ GL RFG LI+YIP VT GFT Sbjct: 82 QIGGPTGAFVIIIFNVIMKHGYDGLVVTTLLAGAMLLVFGLCRFGALIKYIPYPVTTGFT 141 Query: 141 SGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFWP 200 +GI + I + Q+KDFLGL M VP + +K A T + I + LG ++ Sbjct: 142 AGIAVLIFSQQVKDFLGLSMQSVPPDFFEKWQAYIHNAATFDPATCGIAFLALGAIILTR 201 Query: 201 RLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQLLPQLVLP 260 + R+PG + ++ V LG V TIGS+F GIP LP LP Sbjct: 202 KTIPRIPGPVVGVVLASLT---VWALGLDVETIGSRF----------GGIPTELPTFTLP 248 Query: 261 WDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQGLG 320 T+T + +R LLP A ++A+L IESLL VV DGMTG KH +N EL QG Sbjct: 249 --------TVTLERVRQLLPDAMTIALLAGIESLLSCVVADGMTGDKHNSNVELAAQGAA 300 Query: 321 NIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSAMA 380 NI + FGGI AT AIAR+ N+R+G +P++ +IH+ +++ +L LAPL S++PL+++A Sbjct: 301 NIASVMFGGIPATGAIARTVTNIRSGGRTPVAGMIHAAVLVGFILYLAPLASFIPLASLA 360 Query: 381 ALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLFMR 440 A+L++VAW+MSE HK + LL HAPK D++VM L +LTV+ D+ +A+ VG++LASLLFMR Sbjct: 361 AVLMVVAWDMSEMHKFLRLL-HAPKSDVLVMCLTFALTVVIDLTVAVYVGVMLASLLFMR 419 Query: 441 RIARMTRLAPVV--------------VDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEG 486 R++ +T++ + +DVP+ V V + GP FF A+ L + Sbjct: 420 RMSEVTQICTCLDGEATKVQGRETAELDVPEGVKVYEIDGPFFFGVADRFQNVLAALDRQ 479 Query: 487 KRIVILKWDAVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVEFQPLRTMARAGIQPIPGR 545 + IL+ V LD+ ++A + F ++ +G +L + V T+ R G + G Sbjct: 480 PEVFILRMRKVSTLDSTAVNALEVFWRKCRSDGTQLLLSGVRETMRTTLRRMGTLSLIGE 539 Query: 546 LAFFPNRRAAMA 557 N AA+A Sbjct: 540 GNICENIDAALA 551 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: 673 Number of extensions: 38 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: 568 Length adjustment: 36 Effective length of query: 523 Effective length of database: 532 Effective search space: 278236 Effective search space used: 278236 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