Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate PfGW456L13_643 Sulfate permease
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_643 Length = 522 Score = 212 bits (539), Expect = 3e-59 Identities = 158/504 (31%), Positives = 254/504 (50%), Gaps = 39/504 (7%) Query: 20 WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79 W + T A RDLI G++ I+A+P ++A A+ +G+ P+YGLY A + ++ L G S Sbjct: 15 WLPRQTRASVGRDLIVGLSGAILALPQSIAYALIAGLPPEYGLYAAIIPVLIACLWGSSW 74 Query: 80 FSVSGPTAAFVVILY--------PVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYI 131 + GPTAA ++LY P SQ + + +L+ T L+GIF L+GL RFG L+ ++ Sbjct: 75 HLICGPTAAISIVLYASVSPLAVPASQDYVML-ILLLTFLAGIFQWLLGLLRFGALVNFV 133 Query: 132 PVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIV 191 SV LGFT G + I Q+ + LGL + L L L ++ A+G+ Sbjct: 134 SHSVVLGFTLGAAVVIAIGQLPNLLGLDLPSQATA-LDSFITLLRHLGEMDKPSLALGLA 192 Query: 192 TLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIP 251 T+ + V L R P L L+ G ++ + + GHV + + Sbjct: 193 TVVVGVILKLLLPRWPTLLITLILGGLLVWLWPSMFGHVQLVSAF-------------TG 239 Query: 252 QLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKAN 311 +L P LP DL D I LLP+A ++ MLG + SL A + + AN Sbjct: 240 KLPPFSPLPLDL---------DLILRLLPSAVAVGMLGLVTSLSIARSISARSQQLLDAN 290 Query: 312 SELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLL 371 E+ QGL NI+ FF G + + RS + AGA SP++ + ++ V L + A L+ Sbjct: 291 QEVRAQGLSNIVGAFFSGSLSAGSFTRSGLSYEAGACSPLAGIFSALWVALFAIFGASLI 350 Query: 372 SWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGI 431 + +P+ AMA +L++AW + + + LLR + + +++ L C++ T+L ++ AI G Sbjct: 351 AHIPIPAMAGSILLIAWGLVDHRGIRALLRVSRAEFVVMALTCVA-TLLLELQTAIYAG- 408 Query: 432 VLASLLFMRRIARMTRLAPVVVDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKRIVI 491 VLASL F + R+ V D +LRV G +FF A+ L L+ R+ G R+VI Sbjct: 409 VLASLFFYLKRTSQPRVQHVRDGEED---ILRVGGSIFFGASHYLQVRLQ-RMHGARVVI 464 Query: 492 LKWDAVPVLDAGGLDAFQRFVKRL 515 + + +D G++ + +RL Sbjct: 465 -EAQQINFIDYSGVEMLHQEARRL 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: 654 Number of extensions: 38 Number of successful extensions: 3 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