Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate HSERO_RS02920 HSERO_RS02920 major facilitator superfamily protein
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__HerbieS:HSERO_RS02920 Length = 428 Score = 215 bits (547), Expect = 3e-60 Identities = 126/423 (29%), Positives = 215/423 (50%), Gaps = 19/423 (4%) Query: 9 VRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQIPGG 68 ++ + L L L +NY DR+T++IA S+ ++L + A +G + SAF AY Q+P G Sbjct: 14 IQVVALSFLMLAGIVNYLDRSTLSIANHSVSQELNLSASQMGLLLSAFSLAYAFSQLPIG 73 Query: 69 WLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSFPGNA 128 +LD+FG++ + +F WS+ + G+V + + R +GL EAP FP A Sbjct: 74 AMLDKFGARVMLGAGMFIWSVAQLAGGFVNN------LQQFLVARVFLGLGEAPQFPAGA 127 Query: 129 RIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGIIFSLI 188 ++V+ WF ERG + IF ++ L P++ ++ SFGW+ +F++MGV+GI S+ Sbjct: 128 KVVSEWFAMRERGGPTGIFVASSTIGPALAPPILTILMLSFGWRMMFVIMGVLGIAVSVG 187 Query: 189 WLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTNRMMLG 248 W + + R + +E ++A D D D K +W + L T R G Sbjct: 188 WY-LFYRNRNEVQLTPSEVLYLAD-----DHDNDPNANAKLSWSEW---KSLFTYRTTWG 238 Query: 249 VYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVISDYLL 308 + G + + + +LTW P YL +R ++I + G++ +P I G +G + G I+D L+ Sbjct: 239 MLFGFMGVIYMVWLYLTWLPAYLEHERHLSIARTGWVVVIPYIFGTLGMLSSGYIADGLM 298 Query: 309 RKGHSLTFARKAPIIGGLLISSSI-VACNYVDIEWMVVGF--MALAFFGKGVGALGWAVV 365 ++G +RK PI GL+ + + + Y M + + +A+AF G WA+V Sbjct: 299 KRGMPAIRSRKWPICAGLIGAGAFTIPAAYTPSTTMAIVYISLAMAFVNMASGG-AWALV 357 Query: 366 SDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFSYL 425 S P+++ G + N G L P++ G ++ T SF AL+ A A A Y+ Sbjct: 358 SVAIPRRLVASLGSMQNFGGYLGGSLAPVITGVVVDQTHSFVNALLISAAVAFAAALVYM 417 Query: 426 VIV 428 +V Sbjct: 418 FVV 420 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: 619 Number of extensions: 40 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