Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_090446622.1 BLS63_RS16455 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_900100495.1:WP_090446622.1 Length = 372 Score = 239 bits (611), Expect = 7e-68 Identities = 131/303 (43%), Positives = 184/303 (60%), Gaps = 5/303 (1%) Query: 4 LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63 L+ NV KTY +KN L + +GEF+ L+GPSG GK+T + +AG E +T G I+ Sbjct: 11 LQFTNVKKTYDHRTL-VVKNFNLDVAKGEFITLLGPSGSGKTTCLMMLAGFEDVTSGEIL 69 Query: 64 IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123 I + V+ ++P R+I MVFQ YAL+P M++REN+ + LKIRK P+A+I A+V L+ Sbjct: 70 INGRSVTSIAPYARNIGMVFQQYALFPHMTIRENLAYPLKIRKKPKAEIRAKVDEYLALV 129 Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 +++ R PGQLSGGQ+QRVA+ RAL P I L DEPL LD KLR +M+ E+K +H Sbjct: 130 ELQAFGGRYPGQLSGGQRQRVALARALIFAPDIVLMDEPLGALDKKLREQMQFEIKRLHD 189 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243 +L T +YVTHDQ EA+T+ D++AV +GI+QQ P +Y PAN FVA FIG Sbjct: 190 QLGFTVIYVTHDQTEALTMSDRIAVFNNGIVQQCAPPHVLYERPANLFVADFIGE-SNKL 248 Query: 244 VPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDSASS 303 + D R+ LD G L N TE GL + +RPE++ G + + Sbjct: 249 KGVIASVGDDRVSVRLDDGAQVSTLKANCTEVGL---PTTVSIRPEKLTFTDRLGSAGNQ 305 Query: 304 IRA 306 ++A Sbjct: 306 VKA 308 Lambda K H 0.318 0.135 0.382 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: 352 Number of extensions: 18 Number of successful extensions: 2 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: 386 Length of database: 372 Length adjustment: 30 Effective length of query: 356 Effective length of database: 342 Effective search space: 121752 Effective search space used: 121752 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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