Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate 202654 SO3553 sulfate permease family protein (NCBI ptt file)
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__MR1:202654 Length = 588 Score = 624 bits (1608), Expect = 0.0 Identities = 323/567 (56%), Positives = 427/567 (75%), Gaps = 14/567 (2%) Query: 6 SSHVMPFR---ALIDACWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGL 62 S+H+ R AL +AC K++Y+ RF +DL+AG+TVGIIAIPLAMALAI SGV PQYGL Sbjct: 8 SAHLFSLRIAHALNEACVKDRYSFKRFGQDLLAGLTVGIIAIPLAMALAIASGVPPQYGL 67 Query: 63 YTAAVAGIVIALTGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLA 122 YTA V G +IA+TGGSR+SVSGPTAAFVV+LYP++QQFGLAGLL+AT++SG+ L+ M + Sbjct: 68 YTAIVGGFIIAMTGGSRYSVSGPTAAFVVLLYPIAQQFGLAGLLIATVMSGMMLVAMAML 127 Query: 123 RFGRLIEYIPVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTIN 182 R GRLI YIP SVTLGFT+GIG+ I T+Q+KDF GLQ+ H+PE Y K+ AL ALP+++ Sbjct: 128 RLGRLILYIPESVTLGFTAGIGVVIATLQLKDFFGLQIEHMPEQYFAKLMALGQALPSLH 187 Query: 183 VGDAAIGIVTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLA 242 + I TL ++ WPRL I +P HLPA+ G + I+N +G + TIG++FHY L Sbjct: 188 LPSLFIAAATLATMLLWPRLKIPVPAHLPAIALGSILALILNAMGAEIETIGTRFHYQLT 247 Query: 243 DGSQGNGIPQLLPQLVLPW--DLPNSE-FTLTWDSIRTLLPAAFSMAMLGAIESLLCAVV 299 DG G+GIP +LP PW PN + F + + LLPAAF++AMLGAIESLLCAVV Sbjct: 248 DGGIGSGIPAVLPHFEWPWLQTGPNGQAFEFNLAAFQALLPAAFAIAMLGAIESLLCAVV 307 Query: 300 LDGMTGTKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSIL 359 LDGMTG +H ANSEL+GQG+GNIIAPFFGGI ATAAIARSAANV+AGA SPI+++IH+++ Sbjct: 308 LDGMTGKRHSANSELLGQGIGNIIAPFFGGIPATAAIARSAANVKAGAQSPIASMIHALV 367 Query: 360 VILALLVLAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTV 419 V++ L+ LA +L++LP+SAMAALLL+VAWNMSEA K V LL+ AP DI+V L C SLTV Sbjct: 368 VLIGLVALAGILAYLPMSAMAALLLVVAWNMSEAPKAVHLLKTAPTSDILVFLSCFSLTV 427 Query: 420 LFDMVIAISVGIVLASLLFMRRIARMTRLAPV-----VVD--VPDDVLVLRVIGPLFFAA 472 +FDMVIAISVGI+LA+LLFM+ IA MT+L + VD +P D VL++ GPLFFAA Sbjct: 428 IFDMVIAISVGIILAALLFMKEIAEMTKLYDISSNKRYVDQSLPADWAVLKINGPLFFAA 487 Query: 473 AEGLFTDLESRLEGKRIVILKWDAVPVLDAGGLDAFQRFVKRLP-EGCELRVCNVEFQPL 531 A+ +F ++ S + K++++L D V +LDAGGL A + +++ +L + +++FQP+ Sbjct: 488 ADRIFAEIASLTQDKQVIVLYLDGVSILDAGGLAALSKLIEKCKLNQTKLLITDLQFQPI 547 Query: 532 RTMARAGIQPIPGRLAFFPNRRAAMAD 558 RT+A+A IQP+ G L F+P R A+ + Sbjct: 548 RTLAKAKIQPVEGVLKFYPTLREALTE 574 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: 817 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: 588 Length adjustment: 36 Effective length of query: 523 Effective length of database: 552 Effective search space: 288696 Effective search space used: 288696 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