Align D-fructose transporter, sugar porter family (characterized)
to candidate 17022 b2943 D-galactose transporter (NCBI)
Query= reanno::Korea:Ga0059261_1777 (458 letters) >FitnessBrowser__Keio:17022 Length = 464 Score = 239 bits (610), Expect = 1e-67 Identities = 149/434 (34%), Positives = 238/434 (54%), Gaps = 23/434 (5%) Query: 29 AALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADRFGR 88 AAL GLLFG D VI+GA + +F +T + V+S + G +G++ +G + + GR Sbjct: 22 AALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVSSMMFGAAVGAVGSGWLSFKLGR 81 Query: 89 KGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGR 148 K ++ AI +V SL + AP++ ++ R + GLA+G AS P+Y++E++P + RG Sbjct: 82 KKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPLYLSEIAPEKIRGS 141 Query: 149 LVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTLLLPESPRW 208 +++M QL I +GIL A+LS+ + Y AWRWM G++ +P+ + L+ LP+SPRW Sbjct: 142 MISMYQLMITIGILGAYLSDTAFS----YTGAWRWMLGVIIIPAILLLIGVFFLPDSPRW 197 Query: 209 LAIHGQADRARDVMQRLGFADPRAELARIELAEARE----EAAGKPRLFQRSHF-TPVAC 263 A + A V+ RL D AE A+ EL E RE + +G + S+F V Sbjct: 198 FAAKRRFVDAERVLLRL--RDTSAE-AKRELDEIRESLQVKQSGWALFKENSNFRRAVFL 254 Query: 264 AIAIAMFNQLSGINALLYYAPRIFELAG-AGADSALLQSIAVGGTNLVFTVAALFLIDRF 322 + + + Q +G+N ++YYAP+IFELAG + ++ VG TN++ T A+ L+DR+ Sbjct: 255 GVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLTNVLATFIAIGLVDRW 314 Query: 323 GRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFG---LLGFIAAFAMSQGAVIWVFI 379 GR+P L +G ++ AA + ++G + + F LL FI FAMS G +IWV Sbjct: 315 GRKPTLTLGFLVMAAGMGVLGTMMHIGIHSPSAQYFAIAMLLMFIVGFAMSAGPLIWVLC 374 Query: 380 SEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVGG----WVFAFFGAMMLLQLLW 435 SE+ P R G + T+W+ + F ++G WV+A + +L LW Sbjct: 375 SEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFWVYAALNVLFILLTLW 434 Query: 436 TWKFMPETNGIALE 449 +PET ++LE Sbjct: 435 ---LVPETKHVSLE 445 Lambda K H 0.327 0.139 0.420 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: 575 Number of extensions: 28 Number of successful extensions: 6 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: 458 Length of database: 464 Length adjustment: 33 Effective length of query: 425 Effective length of database: 431 Effective search space: 183175 Effective search space used: 183175 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 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