Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate HSERO_RS02645 HSERO_RS02645 MFS transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__HerbieS:HSERO_RS02645 Length = 484 Score = 180 bits (456), Expect = 1e-49 Identities = 129/451 (28%), Positives = 220/451 (48%), Gaps = 37/451 (8%) Query: 5 KPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQ 64 KPT R++++ ++FL+ I ADRA IA ++K+ GI G I S F +AY Q Sbjct: 38 KPTRYRWVVMGLIFLIWAIACADRANFGIALPYMKKEYGITNTEAGLIVSLFSFAYGLVQ 97 Query: 65 IPGGWLLDRFGSKKVYALSIFTWSLFTVLQG-YVGEFGVSTAVVALFMLRFMVGLAEAPS 123 IP G + R K L +S+F +L + G G +++V+ L + R +GL+E P Sbjct: 98 IPVGLMYKRLSEKTTGIL----FSVFMLLTSLFTGLMGTTSSVLLLQLYRVGLGLSEGPL 153 Query: 124 FPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGI 183 G ++ WFP E+GTA+ ++ +A ++ + ++ +GW+ +F V V GI Sbjct: 154 GIGCTNVINRWFPPEEKGTATGLWIAASKLGPLIVPTVCIIVIQLWGWREIFYVFAVPGI 213 Query: 184 IFSLIWLKVI-HSPRQHPMINEAEFNHIAAN----------------GAMVD-MDQDKGK 225 +++W ++ +SP ++ NEAE +I + GA V M G Sbjct: 214 FLAILWFFLVTNSPSENRFCNEAERRYITQDVAAGPATATASSRAHVGAQVTPMPWLDGI 273 Query: 226 GKKTDGPKWDYIRQLLTNRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFI 285 + P+ + +RQ+ T+ ++GV +G C+ GI+ F++W P YLV +G +K GF+ Sbjct: 274 NRTRRVPRLETLRQVFTSWNVIGVAIGYGCMIGISNIFMSWIPTYLVTVKGFASVKMGFL 333 Query: 286 ASLPAICGFIGGVLGGVISDYLL--RKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWM 343 AS P I G +LGGVISD LL R+ + + LL+ + + Y+ M Sbjct: 334 ASAPFIGAVAGNMLGGVISDRLLGGRRKPMMLLGALGTALMTLLLVEAPDSVLYLGAMLM 393 Query: 344 VVGFMALAFFGKGVGALGW-AVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIIST 402 + G M G+G G+ A + K + G+ N+ G + P+ +G ++ Sbjct: 394 LSGLML------GIGFAGYSAYPMGLATKATYPAAFGIVNSLGQIGGACAPLAVGMLLD- 446 Query: 403 TGSFKWALVF--VGANALVAVFSYLVIVGPI 431 + W+ VF + +L+ + L +V PI Sbjct: 447 --RYDWSSVFLYMVGTSLLCLALLLSVVEPI 475 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: 598 Number of extensions: 32 Number of successful extensions: 4 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: 484 Length adjustment: 33 Effective length of query: 421 Effective length of database: 451 Effective search space: 189871 Effective search space used: 189871 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