Align Hexuronate transporter (characterized)
to candidate H281DRAFT_03828 H281DRAFT_03828 MFS transporter, ACS family, hexuronate transporter
Query= SwissProt::P0AA78 (432 letters) >FitnessBrowser__Burk376:H281DRAFT_03828 Length = 429 Score = 212 bits (539), Expect = 2e-59 Identities = 121/404 (29%), Positives = 205/404 (50%), Gaps = 7/404 (1%) Query: 8 RWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTVMQPVAGY 67 RW + AL+ TV+ Y+ R + AP L ++ S QY I+ A+SA Y V G Sbjct: 16 RWTVCALLFFATVINYMDRQILGLLAPLLQHDIGWSQVQYGRIVIAFSAFYAVGLLCFGR 75 Query: 68 VLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGLKASSEWF 127 ++D LGT+I YA+ ++W++ A GS G A+ R +G E PA +K ++EWF Sbjct: 76 IVDWLGTRISYALAMLIWSIAAMLHAAVGSVTGFAMVRALLGIGEGGNFPAAIKTTAEWF 135 Query: 128 PAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMAWLIFYK- 186 P +ER++A G FN G++IGA+ AP ++ + W+ AF+I GAL +W W FY+ Sbjct: 136 PRRERALATGIFNSGANIGAVFAPAIIPPLALAFGWRSAFVIIGALGIVWLAVWFAFYRS 195 Query: 187 -HPRDQKHLTDEERDYIINGQEAQHQVSTAKKMSVGQILRNRQFWGIALPRFLAEPAWGT 245 PR +E RD + + + A+ G ++R RQ W + +FL +P W Sbjct: 196 AEPRSHDDDLEEARDEV---EALDAANANARAPGWGVLIRKRQTWAFLIGKFLTDPVWWF 252 Query: 246 FNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVNLIVSRKMV 305 + W+P ++ + G +++ I + +G I GG+L R G ++ +RK Sbjct: 253 YLFWLPKWLNESRGMDMQHIGLPLVCIYAMTTVGSIGGGWLSSALLR-AGWSVNAARKTA 311 Query: 306 VTLGAVLMIGPGMIGLFTNPYVAIMLLCIGGFAHQALSGALITLSSDVFGRNEVATANGL 365 + + A ++ + N + A+ ++ + AHQ S L T +SD+F + + G+ Sbjct: 312 MFICACCVLPIAFVSQVDNLWGAVAIVGLAAAAHQGWSANLFTTASDLFPKRALGAVVGI 371 Query: 366 TGMSAWLASTLFALVVGALADTIG-FSPLFAVLAVFDLLGALVI 408 GM+ + LF+ V+G + G + LFA+ A+ L+ V+ Sbjct: 372 GGMAGSIGGVLFSEVIGQVLQRTGHYWVLFAIGALAYLIAFAVM 415 Lambda K H 0.326 0.138 0.437 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: 618 Number of extensions: 29 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 432 Length of database: 429 Length adjustment: 32 Effective length of query: 400 Effective length of database: 397 Effective search space: 158800 Effective search space used: 158800 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: 51 (24.3 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