Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein
Query= TCDB::P54933 (332 letters) >NCBI__GCF_002019605.1:WP_078429421.1 Length = 351 Score = 210 bits (535), Expect = 4e-59 Identities = 125/317 (39%), Positives = 178/317 (56%), Gaps = 31/317 (9%) Query: 1 MGKITLRNVQKRFGEAVV--IPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDG 58 M I NV K + A + L+L+I +GE + +GPSGCGK+T LR++AG E + G Sbjct: 1 MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60 Query: 59 QIMIDGR----DATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRV 114 +I I D +PP KRG+ MVFQ YAL+PH+T++KN+ F L + + ++ ++R Sbjct: 61 KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLN--RWKNRDKKKRA 118 Query: 115 SNAAKILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRL 174 +++ L + R P +LSGGQ+QRVA+ RA+ P L DEP SNLDA LR MR Sbjct: 119 QEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178 Query: 175 EITELHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFI 234 ++T + + T I VTHDQ +A ++D++VV+N G I+Q+ +P +YR PAN FVA F+ Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFV 238 Query: 235 GSPKMNLIEGP--EAAKHGATTIG------------------IRPEHIDLSREAGAWEGE 274 G K NLI G KH T IG IRPE L+ E G + G Sbjct: 239 G--KTNLISGTLCPDLKHVETHIGRVCLPQETDKVIENVMVSIRPEGCRLA-EKGRYAGL 295 Query: 275 VGVSEHLGSDTFLHVHV 291 V + G +HV + Sbjct: 296 VERVTYSGEYQEVHVRL 312 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: 295 Number of extensions: 9 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: 351 Length adjustment: 29 Effective length of query: 303 Effective length of database: 322 Effective search space: 97566 Effective search space used: 97566 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 Apr 09 2024. 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