Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate Pf6N2E2_4131 Sulfate permease
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4131 Length = 522 Score = 212 bits (539), Expect = 3e-59 Identities = 158/510 (30%), Positives = 253/510 (49%), Gaps = 51/510 (10%) Query: 20 WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79 W + T A RDL+ G++ I+A+P ++A A+ +G+ P+YGLY A V ++ L G S Sbjct: 15 WLPRQTRASVGRDLVVGLSGAILALPQSIAYALIAGLPPEYGLYAAIVPVLIACLWGSSW 74 Query: 80 FSVSGPTAAFVVILY--------PVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYI 131 + GPTAA ++LY P SQ + + +L+ T+L+GIF L+GL RFG L+ ++ Sbjct: 75 HLICGPTAAISIVLYATVSPLAVPASQDY-ITLILLLTVLAGIFQWLLGLLRFGALVNFV 133 Query: 132 PVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHY------LQKVGALFMALPTINVGD 185 SV LGFT G + I Q+ + LGL + + + +GA+ + +G Sbjct: 134 SHSVVLGFTLGAAVVIALGQLPNLLGLDLPNEATALRGLLMLVSHIGAVDKPSLLLGLGT 193 Query: 186 AAIGIVTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGS 245 +G+V +L WP L L L+ V+ + + GHVA + + Sbjct: 194 LVLGVVLKRLLPRWPSL-------LITLVISSLVVWLWPAMFGHVALVSAF--------- 237 Query: 246 QGNGIPQLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTG 305 +P P LP DL + I LLP A ++ MLG + SL A L +G Sbjct: 238 -AGRLPPFTP---LPLDL---------ELILRLLPGAVAVGMLGLVTSLSIARSLSVRSG 284 Query: 306 TKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALL 365 AN E+ QGL NI+ FF G + + RS + AGA SP++ V ++ V L + Sbjct: 285 QLLDANQEVRAQGLSNIVGGFFSGSLSAGSFTRSGLSYEAGACSPLAGVFSALWVALFAV 344 Query: 366 VLAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVI 425 A L++ +P+ AMA +L++AW + + H+ + L + + +VM L T+L ++ Sbjct: 345 AGANLIAHIPIPAMAGSILLIAWGLVD-HRGIRALYRVSRAEFVVMGLTCLATLLLELQT 403 Query: 426 AISVGIVLASLLFMRRIARMTRLAPVVVDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLE 485 AI G VLASL F + R+ + +LRV G +FF A+ L L+ RL+ Sbjct: 404 AIYAG-VLASLFFYLKRTSQPRVQHF---REGEAEILRVGGSIFFGASHYLQARLQ-RLQ 458 Query: 486 GKRIVILKWDAVPVLDAGGLDAFQRFVKRL 515 +R+VI + +D G++ + +RL Sbjct: 459 AQRVVI-DAQQINFIDYSGVEMLHQEARRL 487 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: 664 Number of extensions: 42 Number of successful extensions: 4 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: 522 Length adjustment: 35 Effective length of query: 524 Effective length of database: 487 Effective search space: 255188 Effective search space used: 255188 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: 52 (24.6 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