Align L-rhamnose/H+ symporter (characterized, see rationale)
to candidate CA265_RS02625 CA265_RS02625 rhamnose/proton symporter RhaT
Query= uniprot:Q8A1A1 (339 letters) >FitnessBrowser__Pedo557:CA265_RS02625 Length = 364 Score = 243 bits (619), Expect = 7e-69 Identities = 133/358 (37%), Positives = 202/358 (56%), Gaps = 28/358 (7%) Query: 1 MDILIGLLIIAIGSFCQSSSYVPIKKVKEWSWESFWLVQGVFAWLVFPFLGSLLGIPAGG 60 M ++G++ G F S Y+P KKVK W+WES+W+V G+F+WL+ P L + L IP Sbjct: 1 MQAILGVIFHFFGGFASGSFYIPYKKVKGWAWESYWIVGGIFSWLIVPPLAAFLTIPNFT 60 Query: 61 SLFDLWGAGGAGMSIFYGVLWGIGGLTFGLSMRYLGVALGQSIALGTCAGFGTLFPAIF- 119 ++ ++ F+GVLWGIGGLT+GL +RYLGV+LG SI LG C G++ P+I+ Sbjct: 61 AIITSTNGSILWLTYFFGVLWGIGGLTYGLGVRYLGVSLGSSIILGLCMVLGSILPSIYF 120 Query: 120 -----AGTNLF-----EGNGLILLLGVCITLAGIAIIGYAGGLRAQNM----SEEEKRAA 165 AG + F G ++LLG+ + + GI I G AG ++ + M ++ Sbjct: 121 DFFPQAGKDTFTMFLHTDWGRMVLLGLLVCVVGIIICGKAGMMKEKEMKTGITDPHGMEV 180 Query: 166 VKDFALTKGLLVALLAGVMSACFALGLDAGTPIKEAA--------LAGGVDGLYAGLPVI 217 ++ GL V +++GV+SACF G++AG P+ +AA A + L+ Sbjct: 181 KTEYKFGLGLFVGIVSGVLSACFNFGIEAGKPMADAANAIWKAANPAEPGNFLFQNNVTY 240 Query: 218 FLVTLGGFMTNAAYCLQQNIANKSVGDYAK-GKVWGNNLVFCALAGVLWYMQFFGLEMGK 276 +V GG TN +C+ N NK+ GDY K N +F ALAG W++QFF MG+ Sbjct: 241 VIVLWGGLTTNFIWCMVLNARNKTFGDYTNAAKPLLKNYIFSALAGTTWFLQFFFYGMGE 300 Query: 277 SFLTESPVLLAFSWCILMALNVTFSNVWGIILKEWKGVSAKTITVLICGLVVLIFSLV 334 S + A SW + MA + +NVWG++LKEWKGVS KT+ ++ G++ +I S++ Sbjct: 301 SKMGNG----ASSWILHMAFIILIANVWGLVLKEWKGVSRKTLITVLAGILTIIISVL 354 Lambda K H 0.327 0.144 0.461 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: 522 Number of extensions: 33 Number of successful extensions: 6 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: 339 Length of database: 364 Length adjustment: 29 Effective length of query: 310 Effective length of database: 335 Effective search space: 103850 Effective search space used: 103850 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: 49 (23.5 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