Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate BWI76_RS06690 BWI76_RS06690 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__Koxy:BWI76_RS06690 Length = 369 Score = 313 bits (802), Expect = 5e-90 Identities = 170/363 (46%), Positives = 238/363 (65%), Gaps = 11/363 (3%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 M+ + LRNV K +G+ + TL + L I++GEF + VGPSGCGKSTL+ IAGLE ++ G Sbjct: 1 MSNIRLRNVTKRFGSTV--TLHQVNLDIEDGEFAVFVGPSGCGKSTLLRMIAGLEEVSEG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 ++IGD+ ++ + P R +AMVFQSYALYP M+V EN+ +GLK+ K+P+ +I +V VA Sbjct: 59 EVLIGDEVMNDVVPAHRGVAMVFQSYALYPHMTVAENMGYGLKVNKVPKDEIRRQVEMVA 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 K LQ+ HLL+RKP QLSGGQ+QRVA+GRA+ R P++++FDEPLSNLDA+LRVEMR + Sbjct: 119 KTLQLSHLLDRKPKQLSGGQRQRVAIGRAIVRNPRVFMFDEPLSNLDAELRVEMRLHIAK 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 +H LKTT VYVTHDQ+EAMTL DK+ VM G ++Q G+P +Y NP N+FVA FIGSP Sbjct: 179 LHHELKTTMVYVTHDQVEAMTLADKIVVMNYGKVEQMGSPMSLYYNPVNKFVAGFIGSPK 238 Query: 241 MNFVPLRLQR-KDGRLVALLDSGQARCELALNTTEAGLE-DRDVILGLRPEQIMLAAGEG 298 MNF+P + + G+L + L LN T + L+ V LG+RPE + G Sbjct: 239 MNFLPATVTAWQPGQLSVKMAQDH---NLTLNITTSPLQPGAAVTLGIRPEHLSTDVNIG 295 Query: 299 DSASSIRAEVQVTEPTGPDTLVFVQ-LNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLF 357 + + + +V E G +T +F Q V L DV + + +++ FD ++F Sbjct: 296 ---TVVEFQCEVVERLGNNTYLFGQCYGHDNVKILLPGDVHFRPWQKISVAFDDRYCMVF 352 Query: 358 DAN 360 D N Sbjct: 353 DEN 355 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: 383 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: 369 Length adjustment: 30 Effective length of query: 356 Effective length of database: 339 Effective search space: 120684 Effective search space used: 120684 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 17 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