Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate AO353_10315 AO353_10315 sulfate transporter
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10315 Length = 552 Score = 375 bits (963), Expect = e-108 Identities = 214/525 (40%), Positives = 322/525 (61%), Gaps = 37/525 (7%) Query: 31 RDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFSVSGPTAAFV 90 R++++G+ VG++A+PLAMA AI SGV P+ G+YTA V+G++++L GGSR ++GPT AFV Sbjct: 20 RNIVSGVIVGVVALPLAMAFAIASGVKPEQGIYTAIVSGLLVSLFGGSRLQIAGPTGAFV 79 Query: 91 VILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFTSGIGITIGTM 150 VIL V+ ++G+ GL +AT+++G L+L+G+ + G +I++IP V +GFT+GIG+ I Sbjct: 80 VILSGVTAKYGVDGLQIATMMAGAILLLLGITKLGAIIKFIPDPVIVGFTAGIGVIIWVG 139 Query: 151 QIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFWPRL-GIR-LPG 208 Q KDF GL EH+ +++ L ALP+ +V + + +L +++ P++ GIR +PG Sbjct: 140 QWKDFFGLPKIS-GEHFHERLWHLVQALPSFHVPTTLLALSSLVLVITAPKIPGIRRVPG 198 Query: 209 HLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQLLPQLVLPWDLPNSEF 268 L A++ A+ G VATIGS F GIPQ LP++ LP Sbjct: 199 PLIAMVVVTALQAFFQFAG--VATIGSAF----------GGIPQGLPEVGLP-------- 238 Query: 269 TLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQGLGNIIAPFFG 328 +T + L+ AF++AMLGAIESLL AVV DGM GTKH +N EL+GQG+ N++ P FG Sbjct: 239 AITLPQVIELIGPAFAIAMLGAIESLLSAVVADGMAGTKHDSNQELIGQGIANLVTPLFG 298 Query: 329 GITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSAMAALLLMVAW 388 G AT AIAR+A N+R G SPI+ +H++ +IL +L LAPL S +PL A+AA+L +VA+ Sbjct: 299 GFAATGAIARTATNIRNGGNSPIAGFVHALTLILLILFLAPLASDIPLCALAAILFVVAY 358 Query: 389 NMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLFMRRIARMTRL 448 NMSE +++ APK D+ ++L+ SLTV D+ IA+++G++LA L FMRR+A + Sbjct: 359 NMSELKHFQRMVKRAPKADVAILLITFSLTVFSDLAIAVNIGVILAMLQFMRRMASSVEV 418 Query: 449 APVV-------------VDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKRIVILKWD 495 +V V +P VLV + GPLFF AAE L +I++ Sbjct: 419 QQMVEKELEVELRINGHVRLPPGVLVYTIEGPLFFGAAETFERVLAQTHTDPGTLIIRLK 478 Query: 496 AVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVEFQPLRTMARAGI 539 VP +D GL ++ L +++C + L + +AGI Sbjct: 479 RVPFMDITGLQTLLEVIEHLRKRSIVVKLCEANEKVLGKLDKAGI 523 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: 662 Number of extensions: 35 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: 552 Length adjustment: 36 Effective length of query: 523 Effective length of database: 516 Effective search space: 269868 Effective search space used: 269868 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