Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate 199928 SO0742 iron(III) ABC transporter, ATP-binding protein (NCBI ptt file)
Query= TCDB::P54933 (332 letters) >FitnessBrowser__MR1:199928 Length = 349 Score = 178 bits (451), Expect = 2e-49 Identities = 109/302 (36%), Positives = 166/302 (54%), Gaps = 13/302 (4%) Query: 4 ITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMID 63 + L V + ++ LDL + GE + +GPSGCGK+TLLR +AGL+ +S G+I I+ Sbjct: 5 LNLHQVHSDYQGQQILKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEIQIN 64 Query: 64 GRDATE----MPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAK 119 G+ + +P +RG+ M+FQ YAL+PH+TV +NI F + AK+ + + R+ + Sbjct: 65 GKTVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFGV--AKLTTAQRKARLDDMLA 122 Query: 120 ILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITEL 179 ++ L R P +LSGGQ+QRV+I RA+ EP L DEP SN+DA +R +M EI + Sbjct: 123 LVKLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAEIRSI 182 Query: 180 HQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKM 239 + + ++VTH + EA AD + + + G I Q G LY P + +VA F+GS Sbjct: 183 LKQRNVSAVFVTHSKDEAFVFADTLAIFSQGVIVQHGRAEDLYAAPNSRYVADFLGSG-- 240 Query: 240 NLIEGPEAAKHGATT-IGIRPEHIDLSREAGAWEGEVGVSEHLGSDTFLHVHVAGMPTLT 298 N + H TT IG LS ++ A+ G+V + L AG+ T+T Sbjct: 241 NYLPAEVVDGHSVTTPIGQLRSLTPLS-QSHAFNGQVFLRP---QQLALSADDAGVGTIT 296 Query: 299 VR 300 R Sbjct: 297 ER 298 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: 272 Number of extensions: 11 Number of successful extensions: 3 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: 349 Length adjustment: 28 Effective length of query: 304 Effective length of database: 321 Effective search space: 97584 Effective search space used: 97584 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