Align Glucose/fructose transport protein (characterized, see rationale)
to candidate Ga0059261_1891 Ga0059261_1891 MFS transporter, sugar porter (SP) family
Query= uniprot:A0A0H3C6H3 (478 letters) >FitnessBrowser__Korea:Ga0059261_1891 Length = 466 Score = 586 bits (1510), Expect = e-172 Identities = 290/462 (62%), Positives = 361/462 (78%), Gaps = 3/462 (0%) Query: 19 KVNMTFVAAIVAVATIGGFMFGYDSGVINGTQEGLESAFNLSKLGTGLNVGAILIGCAIG 78 + NM + AIVAVATIGG +FGYDSG +NGTQ+GL+SAF LS+ G G VG++LIGC IG Sbjct: 6 RANMGLIMAIVAVATIGGLLFGYDSGAVNGTQDGLKSAFALSEGGLGFTVGSLLIGCFIG 65 Query: 79 AFAAGRLADVWGRRTVMIISALLFVISAIGTGAAESSIVFIIFRLIGGLGVGAASVLCPV 138 AF AGRLAD+ GRR VMI++A+LF+I A+ G + +F+ R+ GG+ VGAASVL P Sbjct: 66 AFLAGRLADLIGRRNVMILTAVLFLIGALIQGFSHEQWIFVAARIAGGMAVGAASVLSPA 125 Query: 139 YISEVTPANIRGRLSSVQQIMIITGLTGAFVANYALAHTAGSSTAEFWLGLPAWRWMFWM 198 YISEV PANIRGR++++QQIMII+GLT AFV NY LA TAG+ST FW G AWRWM+WM Sbjct: 126 YISEVAPANIRGRMTTIQQIMIISGLTAAFVVNYWLAKTAGASTNLFWGGYEAWRWMYWM 185 Query: 199 QIIPAGVFFLCLLGIPESPRYLVAKGKDAQAEAILSRLFGAGQGAKKVEEIRASLSADHK 258 Q IPA VF + L IPESPRYLV+KG++A+A +L+ LFGAG K+ EI+AS S DH+ Sbjct: 186 QAIPATVFLIALFFIPESPRYLVSKGRNAEATRVLTSLFGAGTATNKLTEIQASFS-DHR 244 Query: 259 PTFSDLLDPTTKKLRVILWAGLVLAVFQQLVGINIVFYYGSVLWQSVGFTEDDSLKINIL 318 PT D+LDP +R I+WAGL+LAVFQQLVGIN++FYYG+ LWQ GFTE+D+L INI+ Sbjct: 245 PTLRDILDPVKGGVRPIVWAGLLLAVFQQLVGINVIFYYGATLWQLAGFTENDALLINIV 304 Query: 319 SGTLSILACLLAIGLIDKIGRKPLLLIGSAGMAVTLGVLTWCFSTAT-TVNGALTLGDQI 377 SG +SI AC + + L+D+IGRKPLLLIGSAGMAV L + + FS + G L L Q+ Sbjct: 305 SGFVSIAACFVTVALVDRIGRKPLLLIGSAGMAVALFAMVFAFSRGSLDAQGKLVLSQQL 364 Query: 378 GLTALIAANLYVIFFNLSWGPVMWVMLGEMFPNQMRGSALAVCGFAQWIANFAISVSFPA 437 G+ A+IAANLYV+FFN+SWGPVMWVMLGEMFPNQ+RGSALAVCGFAQW +N+ I+ SFP Sbjct: 365 GIIAVIAANLYVVFFNVSWGPVMWVMLGEMFPNQIRGSALAVCGFAQWFSNYLIAQSFPI 424 Query: 438 LAAA-SLPMTYGFYALSAVVSFFLVQKLVHETRGKELEAMQG 478 +AA L ++Y FYA+ AV+SFFLV K +HET+G ELE MQG Sbjct: 425 MAAGLGLAVSYSFYAVCAVISFFLVSKFIHETKGVELEDMQG 466 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: 776 Number of extensions: 40 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: 478 Length of database: 466 Length adjustment: 33 Effective length of query: 445 Effective length of database: 433 Effective search space: 192685 Effective search space used: 192685 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 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