Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate WP_029131733.1 A3GO_RS0100480 C4-dicarboxylic acid transporter DauA
Query= SwissProt::P0AFR2 (559 letters) >NCBI__GCF_000428045.1:WP_029131733.1 Length = 563 Score = 504 bits (1298), Expect = e-147 Identities = 261/549 (47%), Positives = 383/549 (69%), Gaps = 14/549 (2%) Query: 12 FRALIDACWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIV 71 F AL A E+ + + +++AG+TVG+IA+PL+MALAI SGV PQ+GLYTA VAGIV Sbjct: 2 FSALRTALVNER-SLSSIQSNILAGLTVGVIALPLSMALAIASGVPPQHGLYTAIVAGIV 60 Query: 72 IALTGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYI 131 IALTGGS+ ++SGPTAAFVV+L P+ QQ+G+ GLLV+ L+GI L+L+GLAR GRLIE + Sbjct: 61 IALTGGSKVNISGPTAAFVVVLLPIVQQYGIGGLLVSGFLAGIILVLLGLARLGRLIEIV 120 Query: 132 PVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIV 191 P VT+GFT+GIG+ I T QIKDFLGL + + HY+ K+ + ++P+IN + IG + Sbjct: 121 PYPVTVGFTAGIGVVIATFQIKDFLGLNIQSLDGHYIDKLWLILQSVPSINWQETMIGSL 180 Query: 192 TLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGG--HVATIGSQFHYVLADGSQGNG 249 +LG+L+ WPRL R+PGHL ALL G +++ + VATIGS+FHY L +G G+G Sbjct: 181 SLGVLILWPRLQSRIPGHLVALLIGSVAAWLISQITSDFSVATIGSRFHYEL-NGITGSG 239 Query: 250 IPQLLPQLVLPWDLPNSE---FTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGT 306 IP LP PW+LP++E ++ + TLL +A ++A+LG++ESLLCAVV DGM+G Sbjct: 240 IPPFLPGFEWPWNLPDAEGNSIGFSFSLLNTLLASAITIAILGSLESLLCAVVADGMSGK 299 Query: 307 KHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLV 366 KH N EL+GQG+GN++A FGGI ATAAIAR+AANVRAG TSP+++V+H + +++A+L Sbjct: 300 KHNPNDELIGQGIGNMVASLFGGIPATAAIARTAANVRAGGTSPLASVVHGLFILVAILS 359 Query: 367 LAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIA 426 L+P+L+++P+++MAALLLMVAWNMSEA + L+ AP+DDI+ ++ C LTVLFDM IA Sbjct: 360 LSPVLAYIPMASMAALLLMVAWNMSEAKHFIRTLKIAPRDDILTLVTCFLLTVLFDMTIA 419 Query: 427 ISVGIVLASLLFMRRIARMTRLAPV------VVDVPDDVLVLRVIGPLFFAAAEGLFTDL 480 + VG+ LA++LF+ R R+T V +++P + + + GPLFF +A+ ++ Sbjct: 420 VGVGMGLAAMLFIHRSIRLTENTKVESGRMNELELPSQISIYDINGPLFFGSAQKALKNI 479 Query: 481 ESRLEGKRIVILKWDAVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVEFQPLRTMARAGI 539 + R+++L V ++D + A + V L + L + N++ + + + RAG+ Sbjct: 480 TAITPEVRVIVLDMTEVTMVDMSAIVAMESIVANLAAKNVGLVISNLQPRIILKLRRAGV 539 Query: 540 QPIPGRLAF 548 + PGR+ F Sbjct: 540 RTRPGRIRF 548 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: 727 Number of extensions: 28 Number of successful extensions: 6 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: 563 Length adjustment: 36 Effective length of query: 523 Effective length of database: 527 Effective search space: 275621 Effective search space used: 275621 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 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