Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_091525325.1 BM253_RS13430 ABC transporter ATP-binding protein
Query= TCDB::P54933 (332 letters) >NCBI__GCF_900115115.1:WP_091525325.1 Length = 585 Score = 102 bits (254), Expect = 2e-26 Identities = 75/225 (33%), Positives = 119/225 (52%), Gaps = 13/225 (5%) Query: 2 GKITLRNVQKRFGEAVV--IPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQ 59 GKI +NV + + + + ++ I +GE V F+G +G GKST+L+LI+ L DVS G Sbjct: 340 GKIEFKNVHFIYEDTKIHALNNISFTINEGETVAFLGKTGSGKSTILQLISRLYDVSSGS 399 Query: 60 IMIDGRDATEM--PPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNA 117 I ID D ++ + +A+V Q L+ T+K NI F A E E ++++ Sbjct: 400 ISIDNIDIKDLNVENLRDQIAVVPQDAFLFSD-TIKNNIQFGKENASQEEIEHFAKIADV 458 Query: 118 AKIL-----NLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNM 172 K + L R LSGGQ+QRV+I RA++++ L D+ LS +D + Sbjct: 459 HKNIMRFEKGYDTILGERGITLSGGQKQRVSIARALIKDAPVLLLDDCLSAVDTETEERI 518 Query: 173 RLEITELHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGS 217 + ++ S + T I VTH +V + ADKI++LN G I + G+ Sbjct: 519 LNNLKDI--SAKKTTIIVTH-RVSSAKNADKIIILNDGEIIEQGT 560 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: 345 Number of extensions: 10 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: 585 Length adjustment: 32 Effective length of query: 300 Effective length of database: 553 Effective search space: 165900 Effective search space used: 165900 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: 51 (24.3 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