Align Glucose/fructose transport protein (characterized, see rationale)
to candidate WP_057508163.1 ABB28_RS08195 MFS transporter
Query= uniprot:A0A0H3C6H3 (478 letters) >NCBI__GCF_001431535.1:WP_057508163.1 Length = 474 Score = 548 bits (1412), Expect = e-160 Identities = 277/473 (58%), Positives = 356/473 (75%), Gaps = 4/473 (0%) Query: 10 SAGMSADGGKV--NMTFVAAIVAVATIGGFMFGYDSGVINGTQEGLESAFNLSKLGTGLN 67 S +SA G N F+ I VATIGGF+FG+DSGVINGT +GL +AFN S+ G Sbjct: 2 STALSASSGTQGENTAFIVLISCVATIGGFLFGFDSGVINGTVDGLRTAFNSSEAALGFE 61 Query: 68 VGAILIGCAIGAFAAGRLADVWGRRTVMIISALLFVISAIGTGAAESSIVFIIFRLIGGL 127 V ++L+GCAIGAF AGRL D+ GRR+V+IISA+LF++SA+G GAA +S +F+ R+IGG Sbjct: 62 VASMLLGCAIGAFLAGRLGDLLGRRSVLIISAVLFLLSALGAGAAHASWLFVAARVIGGF 121 Query: 128 GVGAASVLCPVYISEVTPANIRGRLSSVQQIMIITGLTGAFVANYALAHTAGSSTAEFWL 187 VGAASV+ P YI+EV A RG+L++VQQI II+GL AF++NY LA AG+ST WL Sbjct: 122 AVGAASVMAPAYIAEVASARYRGKLATVQQIAIISGLFAAFLSNYLLARAAGASTEVLWL 181 Query: 188 GLPAWRWMFWMQIIPAGVFFLCLLGIPESPRYLVAKGKDAQAEAILSRLFGAGQGAKKVE 247 G AWRWMFWMQ IP+ +F LL IPESPR+LV KG+ A+A A+L+RL+GA + K+ Sbjct: 182 GQEAWRWMFWMQAIPSLLFLALLLVIPESPRFLVVKGRRAEASAVLTRLYGAVEAQAKLG 241 Query: 248 EIRASLSA-DHKPTFSDLLDPTTKKLRVILWAGLVLAVFQQLVGINIVFYYGSVLWQSVG 306 EI SL+ H+P+F+DL D + KLR I+W G+ LAV QQLVGIN+VFYYG+VLWQ+VG Sbjct: 242 EIEHSLAQHQHRPSFADLKDKASGKLRGIVWVGIGLAVLQQLVGINVVFYYGAVLWQAVG 301 Query: 307 FTEDDSLKINILSGTLSILACLLAIGLIDKIGRKPLLLIGSAGMAVTLGVLTWCFSTATT 366 F+E+D+L IN+LSG LSI ACL+ + LID+IGRKPLL +GS GMA+ L ++ FS+ + Sbjct: 302 FSENDALLINVLSGALSIGACLVTVVLIDRIGRKPLLWVGSVGMAIALALMVVAFSSGSL 361 Query: 367 VNGALTLGDQIGLTALIAANLYVIFFNLSWGPVMWVMLGEMFPNQMRGSALAVCGFAQWI 426 V+G L L D +G AL+AAN+YV+FFN+SWGPVMWVMLGEMFPNQ+RGSALAV G AQW Sbjct: 362 VDGRLQLSDGMGRLALVAANVYVVFFNMSWGPVMWVMLGEMFPNQIRGSALAVAGAAQWT 421 Query: 427 ANFAISVSFP-ALAAASLPMTYGFYALSAVVSFFLVQKLVHETRGKELEAMQG 478 +NFAI+V+FP LA L Y YA++A +S F V + V ET+GKELE M+G Sbjct: 422 SNFAITVTFPILLAGIGLAGAYSIYAVAAFLSIFFVIRYVRETKGKELEQMEG 474 Lambda K H 0.325 0.138 0.417 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: 744 Number of extensions: 23 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: 478 Length of database: 474 Length adjustment: 33 Effective length of query: 445 Effective length of database: 441 Effective search space: 196245 Effective search space used: 196245 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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