Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate Ac3H11_2058 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::P54933 (332 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2058 Length = 360 Score = 235 bits (600), Expect = 1e-66 Identities = 128/300 (42%), Positives = 179/300 (59%), Gaps = 20/300 (6%) Query: 4 ITLRNVQKRFGE----AVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQ 59 I RN+ KR+G A+ + + ++ G +GPSGCGK+T LR+IAGLE + G+ Sbjct: 8 IVFRNITKRYGTDSSAALAVKGISFEVPRGTLTTILGPSGCGKTTTLRMIAGLESPTSGE 67 Query: 60 IMIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAK 119 I I G+D T + PA+R ++M+FQSYAL+PHM V +N+ + LRM+ ++ + A + Sbjct: 68 IFIGGKDVTTLGPAQRNVSMMFQSYALFPHMNVVENVMYGLRMSGQPKEQARAKAVEALR 127 Query: 120 ILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITEL 179 + L + DR P +LSGGQ+QRVA+ RA+V EP LFDEPLSNLDA LR MR EI L Sbjct: 128 GVGLVGFDDRLPSELSGGQQQRVALARALVLEPEVLLFDEPLSNLDARLRREMREEIRAL 187 Query: 180 HQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKM 239 Q L T+ YVTHDQ EAM ++D+I+V+N G I Q GSP LY P + FVAGF+G + Sbjct: 188 QQRLSLTVAYVTHDQAEAMAVSDQIIVMNQGLIAQKGSPRALYETPHSEFVAGFMGEAML 247 Query: 240 ---------NLIEGP------EAAKHGATTIGIRPEHIDLSREA-GAWEGEVGVSEHLGS 283 + GP A K G + +RPE ++R+ G + S +LG+ Sbjct: 248 FPAVADADGTVALGPLVLRPRVAVKSGPVKVAVRPEAWRITRQGEGLLPARLAKSAYLGA 307 Lambda K H 0.320 0.137 0.400 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: 313 Number of extensions: 10 Number of successful extensions: 1 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: 332 Length of database: 360 Length adjustment: 29 Effective length of query: 303 Effective length of database: 331 Effective search space: 100293 Effective search space used: 100293 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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