Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate H281DRAFT_00667 H281DRAFT_00667 Sugar phosphate permease
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__Burk376:H281DRAFT_00667 Length = 428 Score = 261 bits (666), Expect = 4e-74 Identities = 147/429 (34%), Positives = 234/429 (54%), Gaps = 27/429 (6%) Query: 8 HVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQIPG 67 ++R++++L+ FL INY DRA +A+A ++QK L I +G I S F W Y Q+P Sbjct: 3 NMRWIVILLCFLAIAINYIDRANMAVAAPAIQKALDIGPAQMGLILSGFFWTYALMQMPF 62 Query: 68 GWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSFPGN 127 GW +DR G++ L++ WSLFT L +T+V A+F R ++G+ EA ++P Sbjct: 63 GWFVDRIGARIALPLAVGWWSLFTALTA------AATSVGAMFGCRLLLGIGEAGAYPSC 116 Query: 128 ARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGIIFSL 187 A++V+ WF A+R A++IF+S + L P++ I+ GW+ F++ GV+G ++ L Sbjct: 117 AKLVSQWFKRAQRALATSIFDSGSRVGSALSIPVVALIISGLGWEASFVITGVVGFVWVL 176 Query: 188 IWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTNRMML 247 W V +P + + E++ D+ Q G+K W L +R + Sbjct: 177 GWFLVYRNPSRGDLTGESDG----------DVPQTAVPGRKVP---W---LSLFRHRTLW 220 Query: 248 GVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVISDYL 307 G+ LG +C+N + YFF+TWFP YLVQ RG ++ G + +PA+ G LGG +SD L Sbjct: 221 GMMLGFFCLNFVIYFFITWFPSYLVQTRGFSLKSLGTLGMIPALMAIPSGWLGGFVSDAL 280 Query: 308 LRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALG-WAVVS 366 R+G SLT ARK ++ G+L+SS I C + ++++ F +A+ A W++ + Sbjct: 281 YRRGWSLTKARKTCMVAGMLLSSVITLCAFTTNIYLMLAFFGIAYGSLAFAAASIWSLPA 340 Query: 367 DT--SPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTT-GSFKWALVFVGANALVAVFS 423 D +P +A + GG+ N N A I G ++S T GSF L G ++ FS Sbjct: 341 DVAPTPDHVASI-GGIQNFASNCAGIVITTFTGLMVSLTHGSFTIPLCVAGGFCVLGAFS 399 Query: 424 YLVIVGPIK 432 YLVIV I+ Sbjct: 400 YLVIVQKIE 408 Lambda K H 0.327 0.142 0.444 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: 609 Number of extensions: 44 Number of successful extensions: 5 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: 454 Length of database: 428 Length adjustment: 32 Effective length of query: 422 Effective length of database: 396 Effective search space: 167112 Effective search space used: 167112 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