Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_900105005.1:WP_090274680.1 Length = 378 Score = 215 bits (548), Expect = 1e-60 Identities = 125/336 (37%), Positives = 197/336 (58%), Gaps = 23/336 (6%) Query: 4 LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63 +++ V+K + L + ++ L+I GE L+G SG GKSTL+ +AG ET + G ++ Sbjct: 21 VKIERVSKQFDDAL--AVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGFETPSEGRVL 78 Query: 64 IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123 + Q+++ + P R I M+FQSYAL+P M+V +NI FGLK K+ +I VA + KL+ Sbjct: 79 LDGQNITALPPHKRPINMMFQSYALFPHMTVEQNIAFGLKQDKLSNTEISERVAEMLKLV 138 Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 + RKP QLSGGQ+QRVA+ R+LA+RPK+ L DEP+ LD KLR +M+ E+ + + Sbjct: 139 HMAKYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIE 198 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243 R+ T + VTHDQ EAMT+ ++A+M G I Q GTP +IY +P N+ VA F+GS Sbjct: 199 RVGVTCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDIYESPVNRHVAEFVGS----- 253 Query: 244 VPLRLQRKDGRLVA------LLDSGQARCELALN---TTEAGLEDRDVILGLRPEQIMLA 294 + +G +VA +++ Q ++ L TT A ED+ I LRPE++ + Sbjct: 254 ----VNIFEGEIVADMDDHVIIECPQLDRQIYLGHGVTTRA--EDKSAIYALRPEKVFVT 307 Query: 295 AGEGDSASS-IRAEVQVTEPTGPDTLVFVQLNDTKV 329 + + + EV G ++ +++L+ K+ Sbjct: 308 TEQPEQPYNWAHGEVHDIAYLGGHSVYYIKLDSGKM 343 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: 316 Number of extensions: 6 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: 378 Length adjustment: 30 Effective length of query: 356 Effective length of database: 348 Effective search space: 123888 Effective search space used: 123888 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 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