Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate WP_089214098.1 CHB69_RS00850 MFS transporter
Query= SwissProt::P11551 (438 letters) >NCBI__GCF_900188185.1:WP_089214098.1 Length = 457 Score = 169 bits (429), Expect = 1e-46 Identities = 131/448 (29%), Positives = 208/448 (46%), Gaps = 45/448 (10%) Query: 19 GQSRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIP 78 G + + FA + LFF W +L D L+ + FTL++ +A L SAF+ Y ++ Sbjct: 12 GGRSTALAAFAAVTVLFFAWGFITSLIDPLVAAVKGIFTLSDAEAQLSASAFFIAYGVMS 71 Query: 79 IPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAA 138 PA L+ ++ I+ L G + AA + Y L L+GLF++A+G+ L+ AA Sbjct: 72 FPAAALIARVHSVPSILIALATMVGGCLVMLAAANLAVYPLVLLGLFMLASGITVLQVAA 131 Query: 139 NPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQLS 198 NP LG HFRL L+QTFNSFG I + G L L V + V+ + Sbjct: 132 NPLAAALGDPKRSHFRLTLSQTFNSFGTFIGPLIGAHLFLQGVEVKEGAVVTE------- 184 Query: 199 AYKHSLVLSVQTPYMIIVAIVLLVALLIMLTK---FPALQSDNHSDAKQGSF----SASL 251 A + + + + Y I ++ + L +++ A+ A+ F A Sbjct: 185 AVRKQALAGIDSAYFWICGLIAALFLFFWISRRIVDAAVPPPPLGTARANIFELMGEAFA 244 Query: 252 SRLARIRHWRWAVLAQFCYVGAQTACWSYLIRYAVEE-------------IPGMTAGF-- 296 SR AR+ LA F YVGA+ A + + + + + G T G Sbjct: 245 SRWARL-----GALAIFLYVGAEVAIGTQMALFLNSDAVWGQSDAPFGVPLLGFTMGSDG 299 Query: 297 ---AANYLTGTMVCFF-----IGRFTGTWLISRFAPHKVLAAYALIAMALCLISAFAGG- 347 + G V F+ +GR G+ L++R + K+LA + IA LCL GG Sbjct: 300 VAGVSLQEAGKAVAFYWGGAMVGRAIGSLLLARVSATKLLATFTAIACGLCLYVVTVGGA 359 Query: 348 HVGLIALTLCSAFMSIQYPTIFSLGIKNLGQDTKYGSSFIVMTIIGGGIVTPVMGFVSDA 407 G +AL + F SI +P IF+L ++ G + S + I+GG + ++G +SDA Sbjct: 360 TAGFVALAI-GLFNSIMFPVIFTLTLERAGARAEATSGLLCTAIVGGAAIPVLVGSLSDA 418 Query: 408 AGNIPTAELIPALCFAVIFIFARFRSQT 435 G TA ++PALC+A++ FA ++T Sbjct: 419 WG-YGTALILPALCYALLCAFALAAART 445 Lambda K H 0.329 0.140 0.425 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: 459 Number of extensions: 25 Number of successful extensions: 4 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: 438 Length of database: 457 Length adjustment: 33 Effective length of query: 405 Effective length of database: 424 Effective search space: 171720 Effective search space used: 171720 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 (21.8 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