Align Hexuronate transporter (characterized)
to candidate HSERO_RS23010 HSERO_RS23010 hexuronate transporter
Query= SwissProt::P0AA78 (432 letters) >FitnessBrowser__HerbieS:HSERO_RS23010 Length = 408 Score = 488 bits (1257), Expect = e-142 Identities = 229/406 (56%), Positives = 303/406 (74%), Gaps = 2/406 (0%) Query: 11 MIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTVMQPVAGYVLD 70 M+ LVTL ++ YL RNT++ AAPT+M+EL++STQQYSYI+ A+ Y VMQPVAGY+LD Sbjct: 1 MVTLVTLALIVNYLARNTLSVAAPTMMKELDMSTQQYSYIVVAWQICYAVMQPVAGYILD 60 Query: 71 VLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGLKASSEWFPAK 130 +GTKIG+ +FA+ W++ C A A A W LA R +G EAA IP G+KAS+EWFPAK Sbjct: 61 AVGTKIGFGIFALAWSLVCAAAAFATGWQSLAFFRALLGITEAAGIPGGVKASTEWFPAK 120 Query: 131 ERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMAWLIFYKHPRD 190 ERS+A+G+FN+GSSIGA+ APPLVVW I+ W+M+F++ GAL IW + W++FYK PRD Sbjct: 121 ERSVAIGWFNIGSSIGALCAPPLVVWTILHGGWKMSFVVVGALGVIWFVLWMLFYKSPRD 180 Query: 191 QKHLTDEERDYIINGQEAQHQVSTAKKMSVGQILRNRQFWGIALPRFLAEPAWGTFNAWI 250 QK L+ EER YI+ GQE + ++ S +I+R+R FW IA+PRFL+EPAW TFNAWI Sbjct: 181 QKLLSPEERAYILEGQEKSPE--KVQRESWTKIVRSRNFWSIAIPRFLSEPAWQTFNAWI 238 Query: 251 PLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVNLIVSRKMVVTLGA 310 PL+M N+KEIAMFAW+P L AD+GC+LGGYL PLF + V+L SRK+V+ +G+ Sbjct: 239 PLYMATERHMNIKEIAMFAWLPFLAADIGCVLGGYLSPLFHKHLKVSLFTSRKLVMLVGS 298 Query: 311 VLMIGPGMIGLFTNPYVAIMLLCIGGFAHQALSGALITLSSDVFGRNEVATANGLTGMSA 370 + MIGP +G +PYVAI LL IGGFAHQ LSGAL +++SDVF +N+VATA GLTGMS Sbjct: 299 LSMIGPACVGFVDSPYVAIALLSIGGFAHQTLSGALYSITSDVFTKNQVATATGLTGMSG 358 Query: 371 WLASTLFALVVGALADTIGFSPLFAVLAVFDLLGALVIWTVLQNKP 416 +L +TLF L+ G L IG+ PLF +LA FDL+ V++ + + +P Sbjct: 359 YLGATLFTLLFGILVTQIGYGPLFVLLAAFDLVAVAVVFAIARPRP 404 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: 656 Number of extensions: 22 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: 408 Length adjustment: 32 Effective length of query: 400 Effective length of database: 376 Effective search space: 150400 Effective search space used: 150400 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: 50 (23.9 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