Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_000744815.1:WP_037572389.1 Length = 386 Score = 224 bits (571), Expect = 3e-63 Identities = 132/356 (37%), Positives = 201/356 (56%), Gaps = 15/356 (4%) Query: 4 LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63 L L + K +G+ + ++L+I +G F L+G SGCGK+T + I+GLE T G I Sbjct: 19 LRLTGLTKKFGSFT--AVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIH 76 Query: 64 IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123 +GDQDV+ P R + VFQ+YAL+P + + EN+ FGL+ R + + V + L+ Sbjct: 77 LGDQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGI--RSVKKPVEDMLDLV 134 Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 ++ HL RKP QLSGGQQQR+A+ RAL +P++ L DEPL LD KLR +M+ E+K + Sbjct: 135 ELGHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQL 194 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243 + T V+VTHDQ EAMT+ D +AVM G I+Q G+P E+Y NP FVA+F+G N Sbjct: 195 EVGLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQ--SNL 252 Query: 244 VPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGD---S 300 + ++ G +V + G++ LAL VILG+RPE++ +A E + Sbjct: 253 IAGTVESVSGDVVQVAAHGRS---LALPAARCRTTSGPVILGVRPEKVRIAKTEAEVPSG 309 Query: 301 ASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQV---GETLTLQFDPSK 353 A+ + +V G T V+L + + ++ G + + +DPS+ Sbjct: 310 ANHLTGKVTDASFIGVSTQYLVELPSGEELAVFEQNTGQEIQRPGAEVVVHWDPSQ 365 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: 356 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 386 Length of database: 386 Length adjustment: 30 Effective length of query: 356 Effective length of database: 356 Effective search space: 126736 Effective search space used: 126736 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 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