Align Hexuronate transporter (characterized)
to candidate BPHYT_RS24120 BPHYT_RS24120 hexuronate transporter ExuT
Query= SwissProt::P0AA78 (432 letters) >FitnessBrowser__BFirm:BPHYT_RS24120 Length = 430 Score = 501 bits (1291), Expect = e-146 Identities = 227/406 (55%), Positives = 308/406 (75%) Query: 3 KIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTVMQ 62 KIKG+RW+M++LV G ++ YL RNT++ AAP LM++L+I+T+QY++++ A+ Y MQ Sbjct: 2 KIKGIRWWMVSLVAAGLIINYLARNTLSVAAPALMKDLHITTEQYAHVVVAWQLCYAFMQ 61 Query: 63 PVAGYVLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGLKA 122 PVAG++LD +GTKIG+A FA+ W++ C A A + W LA RG +G AEAA IPAG+KA Sbjct: 62 PVAGFLLDTVGTKIGFAAFALAWSLACAAAAWSTGWRSLAFFRGLLGIAEAAGIPAGVKA 121 Query: 123 SSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMAWL 182 +SEWFPAKERS+A+G+FN+GSSIGA++APPLVVWA++ WQ+AF+I G +W++ W+ Sbjct: 122 TSEWFPAKERSVAIGWFNIGSSIGALLAPPLVVWALLHGEWQLAFVIVGVAGIVWSVLWM 181 Query: 183 IFYKHPRDQKHLTDEERDYIINGQEAQHQVSTAKKMSVGQILRNRQFWGIALPRFLAEPA 242 YKHPR+QK L D ERDYI++GQEA+H + A K + +L +R FW I +PR L+EPA Sbjct: 182 ALYKHPRNQKLLGDAERDYILSGQEAKHSDAGAAKRNWIAMLGSRDFWAIGIPRILSEPA 241 Query: 243 WGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVNLIVSR 302 W TFNAWIPL+M NLKE+A++AWMP L AD+GC+LGGYL PLF ++ V+L SR Sbjct: 242 WQTFNAWIPLYMMTERHMNLKEVALYAWMPFLAADIGCVLGGYLSPLFHKYAKVSLFTSR 301 Query: 303 KMVVTLGAVLMIGPGMIGLFTNPYVAIMLLCIGGFAHQALSGALITLSSDVFGRNEVATA 362 KMV +GA+ MIGP +GL +PYVA+ LLC+GGFAHQ LSGAL ++SD+FG+NEVATA Sbjct: 302 KMVFVVGALFMIGPACVGLVASPYVAVALLCVGGFAHQTLSGALYAITSDMFGKNEVATA 361 Query: 363 NGLTGMSAWLASTLFALVVGALADTIGFSPLFAVLAVFDLLGALVI 408 G+ GM+ +L + F + G L IG+SPLF VLAVFD++ A V+ Sbjct: 362 TGMGGMAGYLGAAAFTALFGVLVTQIGYSPLFVVLAVFDIIAAGVV 407 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: 713 Number of extensions: 21 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: 430 Length adjustment: 32 Effective length of query: 400 Effective length of database: 398 Effective search space: 159200 Effective search space used: 159200 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