Align Hexuronate transporter (characterized)
to candidate BWI76_RS24735 BWI76_RS24735 MFS transporter
Query= SwissProt::P0AA78 (432 letters) >FitnessBrowser__Koxy:BWI76_RS24735 Length = 433 Score = 780 bits (2014), Expect = 0.0 Identities = 382/417 (91%), Positives = 403/417 (96%) Query: 1 MRKIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTV 60 MRKIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEEL+ISTQQYSYIIAAYSAAYTV Sbjct: 1 MRKIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELHISTQQYSYIIAAYSAAYTV 60 Query: 61 MQPVAGYVLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGL 120 MQPVAGYVLDVLGTKIGYA FA+ WAVFCG+TALAGSWGGLA+ARGAVGAAEAAMIPAGL Sbjct: 61 MQPVAGYVLDVLGTKIGYAFFAIAWAVFCGSTALAGSWGGLALARGAVGAAEAAMIPAGL 120 Query: 121 KASSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMA 180 KASSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISG LSF WAMA Sbjct: 121 KASSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGVLSFAWAMA 180 Query: 181 WLIFYKHPRDQKHLTDEERDYIINGQEAQHQVSTAKKMSVGQILRNRQFWGIALPRFLAE 240 WL+FYKHPRDQK LT+EER+YII GQE+ HQ + KKMS QILRNRQFWGIALPRFLAE Sbjct: 181 WLVFYKHPRDQKKLTEEERNYIIGGQESHHQTNNGKKMSPWQILRNRQFWGIALPRFLAE 240 Query: 241 PAWGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVNLIV 300 PAWGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCI+GGYLPPLFQRWFGVNLIV Sbjct: 241 PAWGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCIVGGYLPPLFQRWFGVNLIV 300 Query: 301 SRKMVVTLGAVLMIGPGMIGLFTNPYVAIMLLCIGGFAHQALSGALITLSSDVFGRNEVA 360 SRKMVVT+GA+LMIGPGMIGLFT+P+VAI LLC+GGFAHQALSGALITLSSDVFGRNEVA Sbjct: 301 SRKMVVTMGALLMIGPGMIGLFTSPFVAIALLCVGGFAHQALSGALITLSSDVFGRNEVA 360 Query: 361 TANGLTGMSAWLASTLFALVVGALADTIGFSPLFAVLAVFDLLGALVIWTVLQNKPA 417 TANG+TGM+AWLAST+FALVVGALADTIGFSPLFAVLAVFD+LGA+VIWTVL+NK A Sbjct: 361 TANGMTGMAAWLASTMFALVVGALADTIGFSPLFAVLAVFDVLGAVVIWTVLKNKSA 417 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: 871 Number of extensions: 25 Number of successful extensions: 1 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