Align D-fructose transporter, sugar porter family (characterized)
to candidate Echvi_2810 Echvi_2810 MFS transporter, sugar porter (SP) family
Query= reanno::Korea:Ga0059261_1777 (458 letters) >FitnessBrowser__Cola:Echvi_2810 Length = 450 Score = 317 bits (813), Expect = 4e-91 Identities = 181/427 (42%), Positives = 269/427 (62%), Gaps = 10/427 (2%) Query: 30 ALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVAS-ALIGTVLGSLIAGAPADRFGR 88 +L G LFGFDTAVISGA L+ + +D GF + S AL GTV+G+L+ G P GR Sbjct: 13 SLTGFLFGFDTAVISGANLPLKALWQTSDWFHGFFIMSVALWGTVIGALLGGIPCHHLGR 72 Query: 89 KGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGR 148 K + + + ++VS+LGT LA D F +RF+GG+AIGA+S+ P Y++E+S A RGR Sbjct: 73 KNTLFWIGVMFLVSALGTALATDPFVFSFYRFVGGVAIGASSIAAPTYVSEISQAYQRGR 132 Query: 149 LVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTLLLPESPRW 208 V + Q+NIV GIL+A++SNY++ G+ ++ WRWM +P+ I+L L +PESPRW Sbjct: 133 RVGLYQINIVSGILVAYVSNYLLQGVGDHN-DWRWMLAAEIIPAIIYLAFILDIPESPRW 191 Query: 209 LAIHGQAD-RARDVMQRLGFADPRAELARIELAEAREEAAGKPRLFQRSHFTPVACAIAI 267 L + + + A+ V++++ L I+ R + K +LF + P+ A I Sbjct: 192 LILKQKDESAAQKVLKKITTGKIDQLLLSIKHDSLRSK---KMKLFSAKNRLPLFLAGII 248 Query: 268 AMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAALFLIDRFGRRPL 327 A+FNQLSGIN +LYYAP I E AG ++LL ++ +G TNL+FT+ + LID+ GR+ L Sbjct: 249 AIFNQLSGINFILYYAPEIMEKAGFVTTTSLLGAVCIGFTNLIFTLIGMSLIDKTGRKQL 308 Query: 328 LFVGSVICAATLLLVGWQL-ESAKPDGTLILFGLLGFIAAFAMSQGAVIWVFISEVFPSA 386 + +GS+ +L LV + +S+ P IL +L FIAA + QGAVIWVFISE+FP+ Sbjct: 309 MLIGSMGYIISLGLVSYGFYDSSSP--LFILTSILIFIAAHGIGQGAVIWVFISEIFPNK 366 Query: 387 VRGKGQALGSTTHWVMAAAITWAFPVFAASVGGW-VFAFFGAMMLLQLLWTWKFMPETNG 445 VR GQ+ G+ HW AA IT V ++ + +F F A+M+LQ ++ W++MPET G Sbjct: 367 VRAMGQSFGAGVHWGGAAMITLFGAVLIDTLMPFQIFMVFMALMILQFVFVWRYMPETKG 426 Query: 446 IALEDMN 452 + LE+++ Sbjct: 427 LELENLH 433 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: 576 Number of extensions: 27 Number of successful extensions: 7 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: 450 Length adjustment: 33 Effective length of query: 425 Effective length of database: 417 Effective search space: 177225 Effective search space used: 177225 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