Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 7023042 Shewana3_0280 ABC transporter related (RefSeq)
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__ANA3:7023042 Length = 367 Score = 154 bits (388), Expect = 4e-42 Identities = 94/226 (41%), Positives = 127/226 (56%), Gaps = 12/226 (5%) Query: 20 KDINLTVE----DGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIGG------QTVTT 69 K I L+ E GE + VGPSG GK+TLLR+I+GL AG I G Q+ T Sbjct: 16 KHIKLSAEFSCKAGEVLAVVGPSGGGKTTLLRMIAGLNHPDAGSIVFGETLWFDHQSRTA 75 Query: 70 TPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSLEDYLDR 129 P +R I + Q + L+P+L+ EN+ L + PK E AR + ++L DR Sbjct: 76 LTPQQRHIGYMPQHFGLFPNLTALENVVAGL--DHIPKSERIARAKDWLERVNLHGLPDR 133 Query: 130 RPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQLSASMIY 189 P LSGGQRQRVA+ RA+ REP + L DEP S +D R LE+ARL QL +I Sbjct: 134 LPMHLSGGQRQRVALARALAREPSVLLLDEPFSAVDRETRERLYLELARLKEQLLCPVIM 193 Query: 190 VTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIG 235 VTHD EA+ LAD ++++ G++ Q G P E+ + P N VA +G Sbjct: 194 VTHDLNEALLLADSMILISQGQMLQQGAPFEVLSRPRNEAVARQMG 239 Lambda K H 0.320 0.137 0.391 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: 267 Number of extensions: 12 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: 331 Length of database: 367 Length adjustment: 29 Effective length of query: 302 Effective length of database: 338 Effective search space: 102076 Effective search space used: 102076 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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