Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate AO353_25895 AO353_25895 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25895 Length = 367 Score = 302 bits (774), Expect = 9e-87 Identities = 164/361 (45%), Positives = 235/361 (65%), Gaps = 7/361 (1%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 MA L+++N+ K + +K I+L + + EF++ VGPSGCGKSTL+ IAGLE +T G Sbjct: 1 MAHLKIKNLQKGFEGF--SIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 I + +D++ +SP RD+AMVFQ+YALYP MSVR+N+ F L + + +A+++ +V A Sbjct: 59 TIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAA 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++L++ +L RKP QLSGGQ+QRVA+GRA+ R PKI+LFDEPLSNLDA LRV+MR E+ Sbjct: 119 RILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELAR 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 +H+ L+ T +YVTHDQ+EAMTL DKV V+ G I+Q G+P E+Y+ PAN FVA F+G+P Sbjct: 179 LHKELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPK 238 Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300 M F+ ++ R + + +L R L L+ + V LG+RPE + LA GD Sbjct: 239 MGFLKGKVTRVERQNCEVLLDAGTRITLPLSGANLSIGGA-VTLGIRPEHLNLAL-PGDC 296 Query: 301 ASSIRAEVQVTEPTGPDTLVFV-QLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDA 359 + A+ V+E G DT V + + R+ D+A + GE L+L D LFDA Sbjct: 297 TLQVTAD--VSERLGSDTFCHVLTASGEALTMRIRGDLASRYGEQLSLHLDAEHCHLFDA 354 Query: 360 N 360 N Sbjct: 355 N 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: 379 Number of extensions: 16 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: 367 Length adjustment: 30 Effective length of query: 356 Effective length of database: 337 Effective search space: 119972 Effective search space used: 119972 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