Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_039106013.1 FPB0191_RS10720 sulfate/molybdate ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_000807275.1:WP_039106013.1 Length = 359 Score = 223 bits (569), Expect = 5e-63 Identities = 113/238 (47%), Positives = 161/238 (67%), Gaps = 6/238 (2%) Query: 4 LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63 + L+N+NK++ + LKNI SIK+GE + L+GPSGCGK+TL+ IAGLET + G I Sbjct: 3 ITLQNINKSFKNF--NALKNINFSIKQGELVALLGPSGCGKTTLLRIIAGLETASSGKIY 60 Query: 64 IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIR----KMPQADIDAEVARV 119 D DV+ +S K RDI VFQ+YAL+ M+V EN+ FGLK++ ++ + I+ V ++ Sbjct: 61 FTDTDVTPLSAKQRDIGFVFQNYALFRHMNVAENVAFGLKMKPRSIRLSKTAINERVNQL 120 Query: 120 AKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMK 179 L+Q+E+ R P QLSGGQ+QRVA+ RALA +P + L DEP S LDAK+R ++R ++ Sbjct: 121 LGLVQLENFAKRYPDQLSGGQRQRVALARALASKPNVLLLDEPFSALDAKVRKDLRRWLR 180 Query: 180 LMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIG 237 H L T+++VTHDQ EA+ + DK+ +M G I+Q GTP E+Y P FVA F+G Sbjct: 181 DFHHELNVTSIFVTHDQDEALEVADKIILMNQGQIEQIGTPTEVYKQPKTAFVAHFLG 238 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: 340 Number of extensions: 12 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: 359 Length adjustment: 30 Effective length of query: 356 Effective length of database: 329 Effective search space: 117124 Effective search space used: 117124 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: 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