Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate 16873 b2789 predicted D-glucarate transporter (NCBI)
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__Keio:16873 Length = 450 Score = 625 bits (1612), Expect = 0.0 Identities = 289/433 (66%), Positives = 358/433 (82%) Query: 5 KPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQ 64 K T+ RY I++MLF+VT+ NY DRAT++IAGS + KD+G+D V +GY+FSAF WAYV GQ Sbjct: 13 KRTNARYWIVVMLFIVTSFNYGDRATLSIAGSEMAKDIGLDPVGMGYVFSAFSWAYVIGQ 72 Query: 65 IPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSF 124 IPGGWLLDRFGSK+VY SIF WS+FT+LQG+V F +VALF LRF+VGLAEAPSF Sbjct: 73 IPGGWLLDRFGSKRVYFWSIFIWSMFTLLQGFVDIFSGFGIIVALFTLRFLVGLAEAPSF 132 Query: 125 PGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGII 184 PGN+RIVAAWFP ERGTA +IFNSAQYFATV+FAP+MGW+ + GW HVF MG +GI+ Sbjct: 133 PGNSRIVAAWFPAQERGTAVSIFNSAQYFATVIFAPIMGWLTHEVGWSHVFFFMGGLGIV 192 Query: 185 FSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTNR 244 S IWLKVIH P QHP +N+ E +IAA GA+++MDQ K K KW I+QLL +R Sbjct: 193 ISFIWLKVIHEPNQHPGVNKKELEYIAAGGALINMDQQNTKVKVPFSVKWGQIKQLLGSR 252 Query: 245 MMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVIS 304 MM+GVY+GQYCIN +TYFF+TWFPVYLVQ RGM+ILKAGF+AS+PA+CGFIGGVLGG+IS Sbjct: 253 MMIGVYIGQYCINALTYFFITWFPVYLVQARGMSILKAGFVASVPAVCGFIGGVLGGIIS 312 Query: 305 DYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGWAV 364 D+L+R+ SL ARK PI+ G+L+S +V CNYV++EWM++GFMALAFFGKG+GALGWAV Sbjct: 313 DWLMRRTGSLNIARKTPIVMGMLLSMVMVFCNYVNVEWMIIGFMALAFFGKGIGALGWAV 372 Query: 365 VSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFSY 424 ++DT+PK+I+GLSGGLFN FGN++ I TPI IGYI+ TTGSF AL++VG +AL+AV SY Sbjct: 373 MADTAPKEISGLSGGLFNMFGNISGIVTPIAIGYIVGTTGSFNGALIYVGVHALIAVLSY 432 Query: 425 LVIVGPIKRVVLK 437 LV+VG IKR+ LK Sbjct: 433 LVLVGDIKRIELK 445 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: 806 Number of extensions: 37 Number of successful extensions: 1 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: 450 Length adjustment: 33 Effective length of query: 421 Effective length of database: 417 Effective search space: 175557 Effective search space used: 175557 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