Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_008510542.1 BIBO1_RS17490 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_000182725.1:WP_008510542.1 Length = 333 Score = 277 bits (709), Expect = 3e-79 Identities = 147/323 (45%), Positives = 209/323 (64%), Gaps = 33/323 (10%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 M +L+L++V+K YGA + LK+I L + +GEF+I VGPSGCGKSTL+ IAGLE ++ G Sbjct: 1 MGSLQLKSVHKRYGA--QEVLKDINLEVNDGEFIIFVGPSGCGKSTLLRSIAGLEDVSAG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 ++I +DV+ P R IAMVFQSYALYP ++V+ N+ GLK P+ +I+ VA+ + Sbjct: 59 QVLINGEDVTVTPPSRRGIAMVFQSYALYPHLTVKANMGLGLKQAGAPKDEIEGRVAKAS 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 +L +E L R+P +LSGGQ+QRVA+GRAL R P+++LFDEPLSNLDA LRV+ R E+ Sbjct: 119 AMLALEPYLARRPAELSGGQRQRVAIGRALVRNPELFLFDEPLSNLDAALRVQTRLEIAK 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 +H+ LK T +YVTHDQ+EAMTL D++ V+ G I+Q G+P E+YN P N FVA FIGSP Sbjct: 179 LHRELKATMIYVTHDQVEAMTLADRIVVLNAGRIEQIGSPMELYNRPDNLFVAGFIGSPQ 238 Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300 MNF+ A + + AR +G+RPE + ++ G Sbjct: 239 MNFIE----------AARIGATGAR-----------------TIGIRPEHLSVSRESG-- 269 Query: 301 ASSIRAEVQVTEPTGPDTLVFVQ 323 + + +V E G DT+++V+ Sbjct: 270 --TWKGKVIHAEHLGADTILYVE 290 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: 347 Number of extensions: 16 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: 333 Length adjustment: 29 Effective length of query: 357 Effective length of database: 304 Effective search space: 108528 Effective search space used: 108528 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