Align D-fructose transporter, sugar porter family (characterized)
to candidate AO356_27270 AO356_27270 MFS transporter
Query= reanno::Korea:Ga0059261_1777 (458 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27270 Length = 472 Score = 245 bits (625), Expect = 3e-69 Identities = 148/432 (34%), Positives = 229/432 (53%), Gaps = 9/432 (2%) Query: 29 AALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADRFGR 88 A GGLLFGFDT VI+GA ++ GLT G ++ LIG ++G+L +G +D GR Sbjct: 35 ATFGGLLFGFDTGVINGALLYMKDDLGLTPFTEGLVASALLIGAMMGALFSGRLSDLKGR 94 Query: 89 KGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGR 148 + ++L +A+ + + +L LAP LN + RF GLA+G ASVV P Y+AE++P+ RGR Sbjct: 95 RRIILFLAVVFFLGALACALAPTLNVMVAARFTLGLAVGGASVVVPAYLAEMAPSSIRGR 154 Query: 149 LVAMNQLNIVLGILIAFLSNYIIAGLV-QYDVAWRWMFGIVAVPSTIFLLVTLLLPESPR 207 ++ N+L IV G +AF +N + L D WRWM + +P+ L L +PESPR Sbjct: 155 IITRNELMIVTGQFLAFTTNATLGNLFSDLDGVWRWMLALATLPAVALWLGMLYMPESPR 214 Query: 208 WLAIHGQADRARDVMQRLG---FADPRAELARIELAEAREEAAGKPR-LFQRSHFTPVAC 263 WLA G+ +V++ + +A E +++ R G R L Q+ Sbjct: 215 WLATKGRFREGLEVLKLVREEYYAKAEMEAITQQISNERFIKKGGWRDLSQKGARRIFLI 274 Query: 264 AIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAALFLIDRFG 323 I IA+ +QL+G+N+++Y+ +I AG SAL+ ++ G ++ T + L+DR G Sbjct: 275 GIGIAVTSQLTGVNSIMYFGTQILTEAGLEQRSALIANVVNGVISIGATFVGIALLDRVG 334 Query: 324 RRPLLFVGSVICAATLLLVGWQLESAKPDGT---LILFGLLGFIAAFAMSQGAVIWVFIS 380 RRP++ +G +LLL+G P T LIL + F+A+ G WV ++ Sbjct: 335 RRPMMLLGFTGTTLSLLLIGLVSVFVDPSVTRAMLILGAMAMFLASMQGLIGPAFWVLLA 394 Query: 381 EVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQLLWTWKF 439 E+FP +RG + W+ I FP A++G G F F LL L + + Sbjct: 395 EIFPMRIRGGCMGMAIAAFWLTNVMIGMFFPSLVATIGIGQTFFVFVGAGLLSLTFVAVW 454 Query: 440 MPETNGIALEDM 451 +PET G LE++ Sbjct: 455 VPETRGSTLEEI 466 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: 588 Number of extensions: 36 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: 472 Length adjustment: 33 Effective length of query: 425 Effective length of database: 439 Effective search space: 186575 Effective search space used: 186575 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