Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate Pf6N2E2_5239 Putative sulfate permease
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5239 Length = 580 Score = 536 bits (1380), Expect = e-156 Identities = 290/550 (52%), Positives = 390/550 (70%), Gaps = 14/550 (2%) Query: 11 PFRALIDACWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGI 70 P A W+ YT R DL+AG+TVGIIAIPLAMALAI GV PQ+GLYT VA Sbjct: 7 PLFAAWRQAWRAGYTLERLRGDLVAGLTVGIIAIPLAMALAIAVGVPPQHGLYTVLVAAP 66 Query: 71 VIALTGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEY 130 +IALTGGSRF+VSGPTAAFVVIL P++QQ GL GLL+ T+L+G+ LI +GL R GRLI+Y Sbjct: 67 LIALTGGSRFNVSGPTAAFVVILLPITQQHGLGGLLLCTMLAGLILITLGLMRAGRLIQY 126 Query: 131 IPVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGI 190 IP V LGFT+GIG+ I T+Q+KD LGL +HY++++G L +ALP+ +GD IG+ Sbjct: 127 IPYPVILGFTAGIGVVIATLQLKDLLGLTTVGQAKHYIEQLGELIVALPSARLGDGIIGV 186 Query: 191 VTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGG-HVATIGSQFHYVLADGSQGNG 249 L +L WPR R+PGHL ALL G A++G+ GG VAT+G +F Y + DG G Sbjct: 187 TCLAVLFAWPRWVPRVPGHLVALLVG-ALLGLALERGGWPVATLGERFSY-MVDGISHPG 244 Query: 250 IPQLLPQLVLPWDLPNSE---FTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGT 306 IP LP PW+LP+ + TL++D IR LL AF++AMLGAIESLLCAVV DGMTG+ Sbjct: 245 IPPFLPSFEWPWNLPDGQGHPLTLSYDLIRQLLGPAFAIAMLGAIESLLCAVVADGMTGS 304 Query: 307 KHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLV 366 KH N+EL+GQGLGN++AP FGGITATAAIARSA NVR+GA+SP++A+IHS++V+LA+++ Sbjct: 305 KHDPNAELIGQGLGNLVAPLFGGITATAAIARSATNVRSGASSPLAAIIHSLVVLLAMVL 364 Query: 367 LAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIA 426 LAPL S+LP++A+AALL++VAWNMSEA V+ LR AP+ D++V+L C+SLTVLFDMV+A Sbjct: 365 LAPLFSYLPMAALAALLVIVAWNMSEAGHVLHTLRIAPRSDVLVLLTCLSLTVLFDMVMA 424 Query: 427 ISVGIVLASLLFMRRIARMTRLAPV-------VVDVPDDVLVLRVIGPLFFAAAEGLFTD 479 ++VG++LA+ LF++R++ +T A + ++D+P+ V + GPLFF AAE Sbjct: 425 VAVGLLLAAGLFIKRMSELTDSAELPRHFHQALLDMPEHVRCYAIRGPLFFGAAEKALDV 484 Query: 480 LESRLEGKRIVILKWDAVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVEFQPLRTMARAG 538 L G R+V+++ AVP+LD L AF+ +K +G L + + + RAG Sbjct: 485 LRKFDPGVRVVVVEMSAVPMLDMTALAAFENILKDYRKQGIGLILVATAPRVRLKLRRAG 544 Query: 539 IQPIPGRLAF 548 I +LA+ Sbjct: 545 IHREQRQLAY 554 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: 798 Number of extensions: 44 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: 580 Length adjustment: 36 Effective length of query: 523 Effective length of database: 544 Effective search space: 284512 Effective search space used: 284512 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