Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate GFF3298 HP15_3240 sulfate permease family protein
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__Marino:GFF3298 Length = 572 Score = 605 bits (1559), Expect = e-177 Identities = 316/542 (58%), Positives = 399/542 (73%), Gaps = 11/542 (2%) Query: 14 ALIDACWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIA 73 A +AC E Y RF RD++AG+TVGIIAIPLAMALAI SGVAPQYGLYTA +AG VIA Sbjct: 4 AFREACIDEPYRGRRFLRDVMAGLTVGIIAIPLAMALAIASGVAPQYGLYTAIIAGFVIA 63 Query: 74 LTGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPV 133 LTGGSRFS+SGPTAAFVVILYP++Q +GL GLL+ATL+SG+ LILM L R GR IEYIP Sbjct: 64 LTGGSRFSISGPTAAFVVILYPIAQSYGLGGLLLATLMSGVLLILMALMRLGRFIEYIPE 123 Query: 134 SVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTL 193 SVTLGFT GI + I T+QI+DFLGLQ++ +PEHY K+ L ALP + A + VTL Sbjct: 124 SVTLGFTGGIAVVIATLQIRDFLGLQVSDMPEHYWDKLALLAGALPEFDGMSALVAGVTL 183 Query: 194 GILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQL 253 ++ WPRL +P HLPA++ G + +N G + TIGS+F Y+L DG++G GIP Sbjct: 184 ACMLLWPRLKTPVPPHLPAVVIGSLLALWLNAQGAAIDTIGSRFSYLLPDGTEGAGIPPF 243 Query: 254 LPQLVLPWDLPNSE---FTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKA 310 LP+ PW + L+W +R LLPAAF++AMLGAIESLLCAVVLDGMTG +H A Sbjct: 244 LPEFAWPWQQAGASGEPVGLSWSLVRDLLPAAFAIAMLGAIESLLCAVVLDGMTGKRHSA 303 Query: 311 NSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPL 370 NSEL+GQGLGNII PFFGGITATAAIARSAAN RAGA SP+SA++HS++V+LAL+ LA L Sbjct: 304 NSELMGQGLGNIITPFFGGITATAAIARSAANYRAGAESPVSAMVHSLVVLLALVSLAGL 363 Query: 371 LSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVG 430 L++LP+ AMAALL+MVAWNMSEA K + LL+ AP+ DI+V L C SLTVL DMVIAI+ G Sbjct: 364 LAYLPMPAMAALLVMVAWNMSEAPKSLHLLKTAPRSDILVFLTCFSLTVLLDMVIAITTG 423 Query: 431 IVLASLLFMRRIARMTRLAPVVVD-------VPDDVLVLRVIGPLFFAAAEGLFTDLESR 483 ++LA++LFMR +A+MTR+ + +PD V ++ GPLFFAAA+ +F +L Sbjct: 424 VLLAAVLFMREMAQMTRVTDITQSKRIAESRLPDGWQVFKINGPLFFAAADRIFGELAVL 483 Query: 484 LEGKRIVILKWDAVPVLDAGGLDAFQRFVKRLP-EGCELRVCNVEFQPLRTMARAGIQPI 542 R IL D V +LDAGGL A + + +G ++ + +++FQPLRT+ARAG+ PI Sbjct: 484 ARNARGFILYMDGVTILDAGGLSALNKLIATCERDGTQIVIADLQFQPLRTLARAGVAPI 543 Query: 543 PG 544 G Sbjct: 544 AG 545 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: 36 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: 572 Length adjustment: 36 Effective length of query: 523 Effective length of database: 536 Effective search space: 280328 Effective search space used: 280328 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