Align L-rhamnose/H+ symporter (characterized, see rationale)
to candidate 352480 BT2953 L-rhamnose-proton symporter (NCBI ptt file)
Query= uniprot:Q8A1A1 (339 letters) >FitnessBrowser__Btheta:352480 Length = 335 Score = 165 bits (418), Expect = 1e-45 Identities = 104/333 (31%), Positives = 157/333 (47%), Gaps = 7/333 (2%) Query: 3 ILIGLLIIAIGSFCQSSSYVPIKKVKEWSWESFWLVQGVFAWLVFPFLGSLLGIPAGGSL 62 ++ G L+I + C + +P K +W WE+ W + + A LV P++ + + IP S+ Sbjct: 5 VISGFLLILLAGGCSGTFALPFKHNSQWKWENNWFIWSIIALLVAPWIMAFISIPDLESV 64 Query: 63 FDLWGAGGAGMSIFYGVLWGIGGLTFGLSMRYLGVALGQSIALGTCAGFGTLFPAIFAG- 121 + + + F+G+LWGIG + FG + YLGV+L I G GTL P I Sbjct: 65 Y-AHESNTVLLVAFFGLLWGIGAILFGKGIDYLGVSLSLPIMQGLINVVGTLMPVILRNP 123 Query: 122 TNLFEGNGLILLLGVCITLAGIAIIGYAGGLRAQNMSEEEKRAAVKDFALTKGLLVALLA 181 + L GL LL G I LAGI AG R + +K KGL++ LLA Sbjct: 124 SELLTPTGLKLLTGTVIILAGIIFFAIAGHNRDSKSRQTHSETPIKK-NFRKGLIICLLA 182 Query: 182 GVMSACFALGLDAGTPIKEAALAGGVDGLYAGLPVIFLVTLGGFMTNAAYCLQQNIANKS 241 G+ G P++E A+A G LYA + + GF+ N C++ N+S Sbjct: 183 GIFGPMINFAFVYGAPLQEKAVATGASSLYAANVIWSIALSAGFIINLLECIRLFGKNQS 242 Query: 242 VGDYAKGKVWGNNLVFCALAGVLWYMQFFGLEMGKSFLTESPVLLAFSWCILMALNVTFS 301 Y G L+ +LAGVLWY+ MG SF+ + + W + + + Sbjct: 243 WKTYRHRTTGG--LIMASLAGVLWYLSIMFYGMGGSFM--GVLGASVGWATMQSTAIIAG 298 Query: 302 NVWGIILKEWKGVSAKTITVLICGLVVLIFSLV 334 NV G+ EWKG + I +++ GLV LI +V Sbjct: 299 NVAGLASGEWKGATRYAIRMMVIGLVCLIGGVV 331 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: 462 Number of extensions: 45 Number of successful extensions: 7 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: 335 Length adjustment: 28 Effective length of query: 311 Effective length of database: 307 Effective search space: 95477 Effective search space used: 95477 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