Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate BWI76_RS17830 BWI76_RS17830 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__Koxy:BWI76_RS17830 Length = 364 Score = 321 bits (823), Expect = 2e-92 Identities = 179/374 (47%), Positives = 246/374 (65%), Gaps = 25/374 (6%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 M ++ L +V K+YG +K++ L+I +GEF +LVGPSGCGKSTL+ IAGLE I+GG Sbjct: 1 MGSVVLNSVRKSYGDA--HVIKDVSLTIPDGEFCVLVGPSGCGKSTLLRMIAGLEEISGG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 + I +++V+ + PK RDIAMVFQSYALYP M+VREN+ F LK+ K+P+A+I+ +V A Sbjct: 59 EVHINERNVTEVEPKLRDIAMVFQSYALYPQMTVRENMGFALKMAKLPKAEINQKVNEAA 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 LL +E LL R P LSGGQ+QRVAMGRA+ R+P+++LFDEPLSNLDAKLR ++R E++ Sbjct: 119 ALLGLEPLLERLPKDLSGGQRQRVAMGRAIVRKPQVFLFDEPLSNLDAKLRTQVRGEIRE 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 +H+RLKTT+VYVTHDQIEAMT+G + V++DG I+Q GTP E+Y+ PAN FVA FIGSP Sbjct: 179 LHRRLKTTSVYVTHDQIEAMTMGQMIVVLRDGRIEQAGTPLELYDRPANLFVAGFIGSPE 238 Query: 241 MNFVP---------LRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQI 291 +N +P L+ KDG L+AL L T+ + V+ +RPEQ+ Sbjct: 239 INQLPGEVVLNGNATSLRLKDGSLLAL--------PAGLRVTDG----QQVVYAIRPEQV 286 Query: 292 MLAAGEGDSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDP 351 + D A + A+V E TG D +F +A + G+ + LQ Sbjct: 287 NVVHEARDDA--LAAKVTAVENTGSDMQLFCDTGGGAFTSVFKQRLAVKEGDKIWLQPKL 344 Query: 352 SKVLLFDANTGERL 365 S V LFDA +G+R+ Sbjct: 345 SGVHLFDAQSGQRI 358 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: 413 Number of extensions: 15 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: 364 Length adjustment: 30 Effective length of query: 356 Effective length of database: 334 Effective search space: 118904 Effective search space used: 118904 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