Align SmoG, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate SM_b21219 SM_b21219 sugar ABC transporter permease
Query= TCDB::O30833 (276 letters) >FitnessBrowser__Smeli:SM_b21219 Length = 281 Score = 140 bits (352), Expect = 4e-38 Identities = 93/281 (33%), Positives = 146/281 (51%), Gaps = 11/281 (3%) Query: 4 RTSTRRTLIVTLAAWTIAFLIFFPILWTVLMSFKSEGDAIKAPFAMLFSDWTLQSYADVQ 63 R S ++ + +A +A +I P+ W ++MS D P A SD L Y + Sbjct: 3 RQSPLFSVFIHASALLLAVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLL 62 Query: 64 ER------SNYARHFMNSVVISLGSTLVALAIAIPAAWAMAFVPGRRTKDVLMWMLSTKM 117 + + +NS+ ++ +TL A+ +A+PAAWA++ P L +++T M Sbjct: 63 SAVENSAGAAFIASLLNSIKVAGMATLAAVVVAVPAAWAVSRTPAVAWS--LYAVIATYM 120 Query: 118 MPAVGVLIPLYLIFRDTGLLDTRIGLVIVLTLINLPIVVWMLYTYFKEIPGEILEAARMD 177 +P V + +PLY+ GLL++ GL +V I P W+L + F IP EI AA +D Sbjct: 121 LPPVALAVPLYMGLAYFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMID 180 Query: 178 GATLGSEILYILT-PMAVPGIASTLLLNVILAWNEAFWTLQLTT-SRAAPLTQFIASYSS 235 GA L +IL ILT P+A P +A++ L +LAW+E F+ L T+ RA LT IA + Sbjct: 181 GARL-DQILRILTLPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAG 239 Query: 236 PEGLFYAKLSAASTMAIAPILILGWFSQKQLVRGLTFGAVK 276 Y ++ A +A P +++G Q+ L+ GLT G VK Sbjct: 240 GRVSDYGLIATAGVLAALPPVLIGLIMQRALISGLTSGGVK 280 Lambda K H 0.327 0.137 0.416 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: 239 Number of extensions: 15 Number of successful extensions: 2 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: 276 Length of database: 281 Length adjustment: 25 Effective length of query: 251 Effective length of database: 256 Effective search space: 64256 Effective search space used: 64256 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: 47 (22.7 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