Align Hexuronate transporter (characterized)
to candidate WP_053935923.1 WG78_RS01030 MFS transporter
Query= SwissProt::P0AA78 (432 letters) >NCBI__GCF_001294205.1:WP_053935923.1 Length = 432 Score = 517 bits (1331), Expect = e-151 Identities = 239/428 (55%), Positives = 325/428 (75%), Gaps = 6/428 (1%) Query: 1 MRKIKGLRWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTV 60 M K+KG+RW+M+ +VT G ++ YL RNT++ AAPT+M +L+++T++YSY++ A+ A Y + Sbjct: 1 MGKVKGMRWWMVGMVTAGLIVNYLARNTLSVAAPTMMHDLHMTTKEYSYVVVAWQACYAL 60 Query: 61 MQPVAGYVLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGL 120 MQPVAGY+LD +GTKIG+A+FA W+V C A A AG+W GLAV RG +G EAA IPAG+ Sbjct: 61 MQPVAGYILDAIGTKIGFAIFACAWSVACAAAAFAGNWQGLAVFRGMLGLTEAAGIPAGV 120 Query: 121 KASSEWFPAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMA 180 KA++EWFPA+ERS+A+G+FN+GSSIGA++APPLVVWAI+ SW+ AF+I G L IW Sbjct: 121 KATTEWFPARERSVAIGWFNIGSSIGALLAPPLVVWAIMAGSWEWAFVIVGVLGGIWTAL 180 Query: 181 WLIFYKHPRDQKHLTDEERDYIINGQEAQHQ---VSTAKKMSVGQILRNRQFWGIALPRF 237 W++FYKHP++QK L+D ERDYI+ GQEAQ++ + A + I+++R F IA+PRF Sbjct: 181 WMLFYKHPKNQKALSDAERDYILAGQEAQYREEGAAVAPRARWTAIVKSRNFRAIAIPRF 240 Query: 238 LAEPAWGTFNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVN 297 L+EPAW TFNAWIPL+M NLKEIAMFAW+P L AD+GC+LGGYL P F ++ V Sbjct: 241 LSEPAWQTFNAWIPLYMATERHMNLKEIAMFAWLPFLAADMGCVLGGYLSPFFHKYCNVG 300 Query: 298 LIVSRKMVVTLGAVLMIGPGMIGLFTNPYVAIMLLCIGGFAHQALSGALITLSSDVFGRN 357 L SRK+V+ GAV MIGP IGL ++PY AI LLC+GGFAHQ LSGAL ++SD+FG+N Sbjct: 301 LFQSRKLVMITGAVCMIGPACIGLVSSPYTAIALLCVGGFAHQTLSGALYAITSDMFGKN 360 Query: 358 EVATANGLTGMSAWLASTLFALVVGALADTIGFSPLFAVLAVFDLLGALVIWTVLQNK-- 415 EVATA GL GM +L +TLF L G L +G+SPLF +LA+FD++ A+ + + + + Sbjct: 361 EVATATGLGGMCGYLGATLFTLFFGVLVTQVGYSPLFVMLAIFDVIAAITLCLLARERTT 420 Query: 416 -PAIEVAQ 422 PA+ +A+ Sbjct: 421 PPALPLAE 428 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: 682 Number of extensions: 29 Number of successful extensions: 3 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: 432 Length adjustment: 32 Effective length of query: 400 Effective length of database: 400 Effective search space: 160000 Effective search space used: 160000 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 24 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