Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate WP_013451892.1 CALNI_RS08970 SulP family inorganic anion transporter
Query= SwissProt::P0AFR2 (559 letters) >NCBI__GCF_000183405.1:WP_013451892.1 Length = 535 Score = 248 bits (633), Expect = 4e-70 Identities = 162/494 (32%), Positives = 262/494 (53%), Gaps = 47/494 (9%) Query: 32 DLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFSVSGPTAAFVV 91 DL GIT GI+A+PLA+A + SG+ + GLY A G AL GG++ VSGPT V Sbjct: 15 DLFGGITAGIVALPLALAFGVASGMGAKAGLYGAIFLGFFAALLGGTKTQVSGPTGPMTV 74 Query: 92 ILYPV--SQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFTSGIGITIGT 149 ++ + + + ++ +++ LL+GIF IL G+ + G I YIP V GF SGIGI I Sbjct: 75 VMASIVSAVKGDISTVVMIVLLAGIFQILFGIVKLGSFIRYIPYPVVSGFMSGIGIIIII 134 Query: 150 MQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFWPR-LGIRLPG 208 +QI LG + P + +G+ L IN+ + I TL IL P+ +G +P Sbjct: 135 LQINPALGSPVKGSPILTIANLGS---TLSNINIQALLVFITTLLILYLTPKKIGKIIPT 191 Query: 209 HLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQLLPQLVLPWDLPNSEF 268 L AL+ V I ++L + IG+ IPQ LP ++P Sbjct: 192 PLLALII---VTPIASILNFDIQKIGT--------------IPQGLPAPIIP-------- 226 Query: 269 TLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQGLGNIIAPFFG 328 ++ I + S+A+LGAI+SLL ++V D +T TKH N EL+GQG+GN +A FG Sbjct: 227 SINLHMISIAFTFSLSLAILGAIDSLLTSLVADSITRTKHNPNRELIGQGVGNALAGLFG 286 Query: 329 GITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSAMAALLLMVAW 388 GI A R+ NV+ G S +S +IH++ + + L+ S++P++ ++ +L+ V Sbjct: 287 GIPGAGATMRTVINVKTGGNSRLSGMIHAVFLFVVLIGAGKYASYVPMALLSGILIKVGV 346 Query: 389 NMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLFMRRIARMTRL 448 ++ + +K + L++ APK D+IVM LTVL D+++A+ VG+VLAS+L R+A+ + Sbjct: 347 DIID-YKFLKLIKFAPKHDVIVMATVFFLTVLVDLIVAVGVGLVLASILLTYRMAKQMNI 405 Query: 449 APVVVDVPDDVL-------------VLRVIGPLFFAAAEGLFTDLESRLEGKRIVILKWD 495 ++ D + V+R+ GP FF + + D + L ++V+ Sbjct: 406 -DILTPQQDQKISGEIDTIGEKCLRVIRIDGPFFFGSMTKV-VDRGNELLDTKVVLFDCS 463 Query: 496 AVPVLDAGGLDAFQ 509 +P +D+ + A + Sbjct: 464 KIPFIDSSAVFALE 477 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: 607 Number of extensions: 34 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: 535 Length adjustment: 36 Effective length of query: 523 Effective length of database: 499 Effective search space: 260977 Effective search space used: 260977 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 24 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