Align Facilitated trehalose transporter Tret1; PvTret1 (characterized)
to candidate Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family
Query= SwissProt::A5LGM7 (504 letters) >FitnessBrowser__Korea:Ga0059261_1777 Length = 458 Score = 186 bits (471), Expect = 2e-51 Identities = 131/446 (29%), Positives = 215/446 (48%), Gaps = 26/446 (5%) Query: 44 ILAAIAVSMGSMVVGFASAYTSPALVSMQNTTITSFKVTEQEASWVGGIMPLAGLAGGIA 103 IL+A ++G ++ GF +A S A ++Q F +T+ + + + G + Sbjct: 23 ILSAAGAALGGLLFGFDTAVISGATQALQ----LQFGLTDAMLGFTVASALIGTVLGSLI 78 Query: 104 GGPFIEYLGRKNTILATAVPFIVAWLLIAFANSIWMVLAGRALSGFCVGIASLSLPVYLG 163 G + GRK +L A+ ++V+ L A + L R + G +G AS+ P+Y+ Sbjct: 79 AGAPADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIA 138 Query: 164 ETVQPEVRGTLGLLPTAFGNIGILICFVAGKY--------VNWSGLAFIGSILPIPFMVL 215 E RG L + +GILI F++ V W + I ++ F+++ Sbjct: 139 EVSPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLV 198 Query: 216 TLLIPETPRWFVTRGREERARKALQWLRGKKADVEPELKGIVKSHCEAERHASQNAIFDL 275 TLL+PE+PRW G+ +RAR +Q L AD EL I + E L Sbjct: 199 TLLLPESPRWLAIHGQADRARDVMQRLGF--ADPRAELARIELAEAREEAAGKPR----L 252 Query: 276 MKRSNLKPLLIALGLMFFQQLSGINAVIFYTVSIFKDAGSTIDENLC-TIIVGVVNFGAT 334 +RS+ P+ A+ + F QLSGINA+++Y IF+ AG+ D L +I VG N T Sbjct: 253 FQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFT 312 Query: 335 FFATVLIDRLGRKILLYISEVAMVITLLTLGTFFYYKNSGNDVSNIGWLPLASFVIYVIG 394 A LIDR GR+ LL++ V TLL +G + +++ D G L L + ++ Sbjct: 313 VAALFLIDRFGRRPLLFVGSVICAATLLLVG--WQLESAKPD----GTLILFGLLGFIAA 366 Query: 395 FSSGVGPIPWLMLGEILPGKIRGSAASVATGFNWTCTFIVTKTFADIVAAIGNHGAFWFF 454 F+ G + W+ + E+ P +RG ++ + +W +T F A++G F FF Sbjct: 367 FAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVGG-WVFAFF 425 Query: 455 GVICLIGLFFVIFFVPETQGKSLEEI 480 G + L+ L + F+PET G +LE++ Sbjct: 426 GAMMLLQLLWTWKFMPETNGIALEDM 451 Lambda K H 0.326 0.141 0.428 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: 570 Number of extensions: 32 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: 504 Length of database: 458 Length adjustment: 34 Effective length of query: 470 Effective length of database: 424 Effective search space: 199280 Effective search space used: 199280 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