Align Hexuronate transporter (characterized)
to candidate BWI76_RS09050 BWI76_RS09050 MFS transporter
Query= SwissProt::P0AA78 (432 letters) >FitnessBrowser__Koxy:BWI76_RS09050 Length = 433 Score = 375 bits (963), Expect = e-108 Identities = 181/416 (43%), Positives = 262/416 (62%), Gaps = 1/416 (0%) Query: 2 RKIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTVM 61 R +K LRW+M+ L LG + Y+TRN++ AP L L I+T+QYS+I+ A+ AYT+ Sbjct: 16 RIVKNLRWWMLVLFLLGVTVNYITRNSLGIIAPELKTSLGITTEQYSWIVGAFQLAYTIF 75 Query: 62 QPVAGYVLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGLK 121 QP+ G+++DV+G K+G+ + A LWA+ C A A AGSW LA+ R +G AEAA PA K Sbjct: 76 QPLCGWLIDVIGLKLGFMICATLWAIACIAHAGAGSWLHLAILRFFMGGAEAAATPANAK 135 Query: 122 ASSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMAW 181 EWFP ER IA G+ VG SIGAM+APP++ +A WQ AF+ +GAL+ +W + W Sbjct: 136 TLGEWFPKSERPIAAGWAGVGFSIGAMLAPPIIYFAHASFGWQGAFMFTGALALVWVVLW 195 Query: 182 LIFYKHPRDQKHLTDEERDYIINGQEAQHQVSTAKKMSVGQILRNRQFWGIALPRFLAEP 241 FY +P +L E I EA V ++ + +N++F+GIA+P F+AEP Sbjct: 196 WAFYHNPEKHPNLGKAELALIQQDNEAP-PVKLPFFTALKTVSKNKRFYGIAIPAFMAEP 254 Query: 242 AWGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVNLIVS 301 AW + W+PL++ K +G +LK+IAMFAW+P L ADLG + GYL L+ RWFG + + S Sbjct: 255 AWAVLSFWVPLYLAKEHGMDLKQIAMFAWLPFLAADLGSVASGYLTKLYTRWFGCSRVNS 314 Query: 302 RKMVVTLGAVLMIGPGMIGLFTNPYVAIMLLCIGGFAHQALSGALITLSSDVFGRNEVAT 361 GA LMI + + +PY+ I+L+ IGGF HQ +S L L + F + ++AT Sbjct: 315 VVASSVTGAFLMISLATVAITRDPYITIVLISIGGFGHQIISCMLSALVVESFDKGQMAT 374 Query: 362 ANGLTGMSAWLASTLFALVVGALADTIGFSPLFAVLAVFDLLGALVIWTVLQNKPA 417 NG+ G +AW+AS LF+L++G AD IGF+PLF + FDL+GA+ + + + A Sbjct: 375 VNGMRGSAAWIASFLFSLLIGVTADKIGFNPLFIAMGFFDLIGAVFLVAFIAERRA 430 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: 638 Number of extensions: 31 Number of successful extensions: 2 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: 432 Length of database: 433 Length adjustment: 32 Effective length of query: 400 Effective length of database: 401 Effective search space: 160400 Effective search space used: 160400 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