Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate BWI76_RS16940 BWI76_RS16940 MFS transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__Koxy:BWI76_RS16940 Length = 439 Score = 372 bits (955), Expect = e-107 Identities = 184/434 (42%), Positives = 270/434 (62%), Gaps = 12/434 (2%) Query: 5 KPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQ 64 +P+ R IL +L + T INY DR + IA L +LGIDA +G +FSAF W Y Q Sbjct: 18 RPSRRRIGILALLAVGTMINYLDRTVLGIAAPQLTAELGIDAAMMGIVFSAFAWTYALAQ 77 Query: 65 IPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSF 124 IPGG LDRFG+K Y L++ WSLFT+ G ++ + +L + RF +G++EAP F Sbjct: 78 IPGGIFLDRFGNKVTYFLALTLWSLFTLFHG------MAVGLKSLLLCRFGLGVSEAPCF 131 Query: 125 PGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGII 184 P N+R+V+AWFP ER A+A++ +Y FAPL+ WI+ SFGW+ +FI +G G++ Sbjct: 132 PVNSRVVSAWFPQQERAKATAVYTVGEYLGLACFAPLLFWIMGSFGWRALFISVGAAGVL 191 Query: 185 FSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTNR 244 F+L+W + P + +N+ E HI G M G + T W +RQLL R Sbjct: 192 FALVWWRCYREPHEDKHLNQLEREHIINGGGM-----STGAEQHT-AFSWPLVRQLLAKR 245 Query: 245 MMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVIS 304 +LG +GQ+ N + FFLTWFP YL +R M +K GF A +P + G + GG +S Sbjct: 246 QILGASIGQFAGNTVLVFFLTWFPTYLATERHMPWIKVGFFAIMPFLAAAGGVMFGGWVS 305 Query: 305 DYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGWAV 364 D LL+ S RK PII GLL++S+I+A N++ + V+ M+ AFFG+G+ LGW + Sbjct: 306 DKLLKATGSANLGRKLPIIAGLLMASTIIAANWLTSDLAVILVMSFAFFGQGMVGLGWTL 365 Query: 365 VSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFSY 424 +SD +PK + GL+GGLFN NLA I TP++IG+I++ +G+F +AL+++G AL+ V +Y Sbjct: 366 ISDIAPKGLGGLTGGLFNFCANLAGILTPLIIGFIVAASGNFFYALIYIGGAALLGVAAY 425 Query: 425 LVIVGPIKRVVLKE 438 L I+G +KR+ L + Sbjct: 426 LFILGDVKRIELSQ 439 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: 654 Number of extensions: 39 Number of successful extensions: 3 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: 439 Length adjustment: 33 Effective length of query: 421 Effective length of database: 406 Effective search space: 170926 Effective search space used: 170926 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