Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate GFF25 PS417_00130 SulP family inorganic anion transporter
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__WCS417:GFF25 Length = 530 Score = 209 bits (532), Expect = 2e-58 Identities = 156/511 (30%), Positives = 258/511 (50%), Gaps = 53/511 (10%) Query: 20 WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79 W + T A RD + G++ ++A+P ++A A+ +G+ P+YGLY A + ++ L G S Sbjct: 15 WLPRQTRASVGRDAMVGLSGAVLALPQSIAYALIAGLPPEYGLYAAIIPVLIACLWGSSW 74 Query: 80 FSVSGPTAAFVVILY--------PVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYI 131 + GPTAA ++LY P SQ + + +L+ T L+G+F L+G+ RFG L+ ++ Sbjct: 75 HLICGPTAAISIVLYASVSPLAVPGSQDY-ITLILLLTFLAGVFQWLLGMLRFGALVNFV 133 Query: 132 PVSVTLGFTSGIGITIGTMQIKDFLGLQM---AHVPEHYLQKV---GALFMALPTINVGD 185 SV LGFT G + I Q+ + LGL + A + L + G A + +G Sbjct: 134 SHSVVLGFTLGAAVVIALGQLPNLLGLDLPSQATAINNLLTLIHHSGEWDPASVILGLGT 193 Query: 186 AAIGIVTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGS 245 +G + ++ WP L L AL G V + + GHVA + S Sbjct: 194 LLVGALLKYLVPRWPTL-------LIALTLGSLVTWLWPAMFGHVALVSSF--------- 237 Query: 246 QGNGIPQLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTG 305 I +L P LP DL D I LLP+A ++ MLG + SL A L + Sbjct: 238 ----IGKLPPLSPLPMDL---------DVILRLLPSAVAVGMLGLVTSLSIARSLSVRSQ 284 Query: 306 TKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALL 365 AN E+ QG NI+ FF G + + RS + AGA SP++ V ++ V L L Sbjct: 285 QLLDANQEIRAQGFSNIVGGFFSGYLSAGSFTRSGLSYEAGACSPLAGVFSALWVALFAL 344 Query: 366 VLAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVI 425 A L++ +P+ +MAA +L+++W + + + L R + + +++ L C++ T+L ++ Sbjct: 345 FGAALIAHIPIPSMAASILLISWGLVDRRGIRALFRVSRAEFVVMSLTCVA-TLLLELQT 403 Query: 426 AISVGIVLASLLFMRRIARMTRLAPVVVDVPD-DVLVLRVIGPLFFAAAEGLFTDLESRL 484 AI G++ + +++R ++ P V D D VLRV G +FF A+ L L+S L Sbjct: 404 AIYAGVLASLFFYLKRTSQ-----PRVQQWRDGDEDVLRVGGSIFFGASHYLQVRLQS-L 457 Query: 485 EGKRIVILKWDAVPVLDAGGLDAFQRFVKRL 515 +GKR+VI + + +D G++ + +RL Sbjct: 458 QGKRVVI-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: 635 Number of extensions: 41 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: 530 Length adjustment: 35 Effective length of query: 524 Effective length of database: 495 Effective search space: 259380 Effective search space used: 259380 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