Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_008510542.1 BIBO1_RS17490 ABC transporter ATP-binding protein
Query= TCDB::P54933 (332 letters) >NCBI__GCF_000182725.1:WP_008510542.1 Length = 333 Score = 407 bits (1046), Expect = e-118 Identities = 203/332 (61%), Positives = 250/332 (75%) Query: 1 MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI 60 MG + L++V KR+G V+ ++L++ DGEF++FVGPSGCGKSTLLR IAGLEDVS GQ+ Sbjct: 1 MGSLQLKSVHKRYGAQEVLKDINLEVNDGEFIIFVGPSGCGKSTLLRSIAGLEDVSAGQV 60 Query: 61 MIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI 120 +I+G D T PP++RG+AMVFQSYALYPH+TVK N+ L+ A EIE RV+ A+ + Sbjct: 61 LINGEDVTVTPPSRRGIAMVFQSYALYPHLTVKANMGLGLKQAGAPKDEIEGRVAKASAM 120 Query: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH 180 L L YL RRP +LSGGQRQRVAIGRA+VR P FLFDEPLSNLDAALRV RLEI +LH Sbjct: 121 LALEPYLARRPAELSGGQRQRVAIGRALVRNPELFLFDEPLSNLDAALRVQTRLEIAKLH 180 Query: 181 QSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMN 240 + L+ TMIYVTHDQVEAMT+AD+IVVLNAGRIEQ+GSP+ LY P NLFVAGFIGSP+MN Sbjct: 181 RELKATMIYVTHDQVEAMTLADRIVVLNAGRIEQIGSPMELYNRPDNLFVAGFIGSPQMN 240 Query: 241 LIEGPEAAKHGATTIGIRPEHIDLSREAGAWEGEVGVSEHLGSDTFLHVHVAGMPTLTVR 300 IE GA TIGIRPEH+ +SRE+G W+G+V +EHLG+DT L+V +T R Sbjct: 241 FIEAARIGATGARTIGIRPEHLSVSRESGTWKGKVIHAEHLGADTILYVETETAGLVTAR 300 Query: 301 TGGEFGVHHGDRVWLTPQADKIHRFGADGKAL 332 GE + D ++LTP+ K H F GKA+ Sbjct: 301 LFGEQHYNEDDVIFLTPEEGKTHYFDEAGKAI 332 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: 381 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: 333 Length adjustment: 28 Effective length of query: 304 Effective length of database: 305 Effective search space: 92720 Effective search space used: 92720 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 24 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