Align D-fructose transporter, sugar porter family (characterized)
to candidate WP_103233202.1 C1634_RS24605 sugar porter family MFS transporter
Query= reanno::Korea:Ga0059261_1777 (458 letters) >NCBI__GCF_002899945.2:WP_103233202.1 Length = 436 Score = 357 bits (915), Expect = e-103 Identities = 195/433 (45%), Positives = 274/433 (63%), Gaps = 7/433 (1%) Query: 22 IILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVAS-ALIGTVLGSLIAG 80 I++ + AAL G LFGFD VISGA + LQ + +DA G V AL GTV+G++ G Sbjct: 4 ILMWSITAALAGFLFGFDVVVISGADKKLQTLWNSSDAFHGAVVMGMALWGTVIGAIFGG 63 Query: 81 APADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEV 140 P + GRK +L + + Y S++GT L+ D F FRFMGGL +GA+++ P YI+E+ Sbjct: 64 IPTNTLGRKKTLLIIGVLYAFSAIGTALSNDPYLFAFFRFMGGLGVGASTIAAPAYISEI 123 Query: 141 SPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTL 200 +PA+ RG++V++ Q NIVLGILIAFLSNY+++G+ D WRWM G+ A+P+ I+ L L Sbjct: 124 APAKDRGKMVSLYQFNIVLGILIAFLSNYLLSGIGDND--WRWMLGVQAIPAAIYTLCVL 181 Query: 201 LLPESPRWLAIHGQADRARDVMQRLGFADPRAELARIELAEAREEAAGKPRLFQRSHFTP 260 +PESPRWL H + + A+ VM+ L D ++ ++ + E+ K +F + + P Sbjct: 182 TIPESPRWLVSHSRIEEAKKVMKILS-PDQDSDTLITQMEDDHAESP-KENIFMKKYRFP 239 Query: 261 VACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAALFLID 320 + A +A FNQ+SGINA LYYAPRIF AG G +ALL SI +G N+VFT+ + LID Sbjct: 240 LMLAFLVAFFNQMSGINAFLYYAPRIFGEAGLGEKTALLSSIGIGVVNMVFTLVGVNLID 299 Query: 321 RFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAAFAMSQGAVIWVFIS 380 + GRR L+++GSV +L LV G I L FIA+ A+ QG VIWVFIS Sbjct: 300 KVGRRTLMYLGSVGYIISLGLVSMAF-YFHWSGLAIPIFLFLFIASHAIGQGTVIWVFIS 358 Query: 381 EVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQLLWTWKF 439 E+FP+ +R GQA GS+THW++AA I P +++G G VF F M+ QLL+ Sbjct: 359 EIFPNHLRASGQAFGSSTHWLLAAIIPSLIPTLFSTIGAGTVFLVFTVAMVFQLLFVMFM 418 Query: 440 MPETNGIALEDMN 452 MPET GI+LE ++ Sbjct: 419 MPETKGISLEKLS 431 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: 571 Number of extensions: 36 Number of successful extensions: 9 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: 436 Length adjustment: 33 Effective length of query: 425 Effective length of database: 403 Effective search space: 171275 Effective search space used: 171275 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 24 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