Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate AO356_28585 AO356_28585 ABC transporter
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28585 Length = 379 Score = 298 bits (763), Expect = 2e-85 Identities = 163/364 (44%), Positives = 229/364 (62%), Gaps = 21/364 (5%) Query: 4 LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63 L+L NVNK G L+++ L I GEF++ VGPSGCGKSTL+ IAGL++I GG ++ Sbjct: 4 LKLDNVNKQLGGAR--ILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLL 61 Query: 64 IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123 I + V+ + P++R + MVFQSYALYP MSV +NI FGLK+ K + + V + A++L Sbjct: 62 IDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKTSLRERVLKTAQIL 121 Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 Q++ LL RKP +LSGGQ+QRVAMGRA+AR P I LFDEPLSNLDA LRV+MR E+ +H Sbjct: 122 QLDKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHG 181 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243 RL +T +YVTHDQ+EAMTL DK+ V+ G I+Q G+P+E+Y PA++FVA F+GSP MNF Sbjct: 182 RLGSTMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYERPASRFVAGFLGSPRMNF 241 Query: 244 V------PLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGE 297 + P + + ++ + LA NT + LG+RPE I L A + Sbjct: 242 LAAFLHTPGETSQVESLVLGMTSLPFDSSGLAANT--------QLSLGIRPEHIALKAAQ 293 Query: 298 GDSASSIRAEVQVTEPTGPDTLVFVQL-NDTKVCCRLAPDVAPQVGETLTLQFDPSKVLL 356 G + ++ E G +T V + D + CR + +VG+ + LQ D + + Sbjct: 294 GTAGIAVSG----VEYLGSETYVHLDTGQDDPMVCRCEVNAGWRVGDRVELQLDIDNLHV 349 Query: 357 FDAN 360 FD + Sbjct: 350 FDTH 353 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: 394 Number of extensions: 18 Number of successful extensions: 3 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: 379 Length adjustment: 30 Effective length of query: 356 Effective length of database: 349 Effective search space: 124244 Effective search space used: 124244 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