Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_012048722.1 SWIT_RS12715 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc02869 (352 letters) >NCBI__GCF_000016765.1:WP_012048722.1 Length = 261 Score = 132 bits (333), Expect = 8e-36 Identities = 87/215 (40%), Positives = 117/215 (54%), Gaps = 20/215 (9%) Query: 17 VGSLQ----LKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDAT 72 VG LQ L+ +AFG V+ G+DLD+ GEFV +G SG GK+TLLRT+A L+ A Sbjct: 9 VGQLQPVVRLRGFSRAFGETVVIDGLDLDIAPGEFVALLGHSGSGKTTLLRTLANLDQAD 68 Query: 73 SGSVQIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAK 132 V I P+ R A+VFQ L P V N+ LGL P E+ Sbjct: 69 GQDVTI---------PSAR--AVVFQDSRLLPWKRVWKNVVLGL-----PGRRARERAEA 112 Query: 133 AAGMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEI 192 A + L + P LSGG+ QR A+ RA+VREP+L L DEP + LDA R+ + Sbjct: 113 ALAEVGLSHRVDAWPLTLSGGEAQRTALARALVREPQLLLLDEPFAALDALTRLRMHELV 172 Query: 193 ARLHRSLKATMIYVTHDQVEAMTLADKIVVLNAGR 227 L R+ + ++ VTHD EA+ LAD+++VL GR Sbjct: 173 LNLWRAHRPAVLLVTHDVDEAIALADRVLVLAKGR 207 Lambda K H 0.320 0.137 0.393 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: 229 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: 352 Length of database: 261 Length adjustment: 27 Effective length of query: 325 Effective length of database: 234 Effective search space: 76050 Effective search space used: 76050 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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