Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_025331514.1 SALWKB2_RS09875 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_000600005.1:WP_025331514.1 Length = 311 Score = 139 bits (351), Expect = 8e-38 Identities = 74/234 (31%), Positives = 131/234 (55%), Gaps = 2/234 (0%) Query: 4 LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63 L + +NK + + ++ L + +G+ + ++G SG GKSTL+N AGL G I Sbjct: 2 LSWQQINKKFSDKV--VAADLSLEVADGQLVAVLGESGSGKSTLLNMAAGLVQPDSGNIF 59 Query: 64 IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123 I +++++ + P+ R I ++FQ YAL P ++V +N+ FGL++ ++ + + ++ + Sbjct: 60 INEENITFLLPEQRRIGLMFQDYALLPHLNVWQNVAFGLRMHRVSKPQAQHQAMQMLAEV 119 Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 + R+ LSGG+QQRVA+ RAL +P+ L DEP S LD LR ++ + + Sbjct: 120 GLSEAAARQVDVLSGGEQQRVALARALVLQPQALLLDEPFSALDTTLRASLQQLTVRLLR 179 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIG 237 + K V VTH +EA L D++ +++ G Q GT ++ PA+ + A +G Sbjct: 180 QQKCPAVLVTHSPLEAFALADRICLLRHGRWIQQGTAAQLLARPADAWAARLLG 233 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: 242 Number of extensions: 10 Number of successful extensions: 1 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: 311 Length adjustment: 29 Effective length of query: 357 Effective length of database: 282 Effective search space: 100674 Effective search space used: 100674 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