Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_009140161.1 HMPREF9452_RS00665 amino acid ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc02869 (352 letters) >NCBI__GCF_000225705.1:WP_009140161.1 Length = 260 Score = 150 bits (380), Expect = 3e-41 Identities = 92/254 (36%), Positives = 145/254 (57%), Gaps = 11/254 (4%) Query: 8 SSFNPRGRHVGSL-----QLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLL 62 +S NP G ++ Q+ + KA+G + VL+GIDLDV GE V+ +GPSG GKST+L Sbjct: 5 TSNNPNGGAADAIEEPVVQIHGLHKAYGDNVVLRGIDLDVHRGEVVVVLGPSGSGKSTML 64 Query: 63 RTIAGLEDATSGSVQIDGVEVG----HVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQ 118 R + LE T+GS+ ++GV++ + + + MVFQ + L+PHL+ K N+ + ++ Sbjct: 65 RCVNLLETPTNGSIVVEGVDITKKGVEINKVRSTLGMVFQQFNLFPHLSAKRNVMIAQQK 124 Query: 119 AGVPKAEIEEKVAK-AAGMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPL 177 E E++A+ + L + P++LSGGQ+QRVAI RA+ P + LFDE Sbjct: 125 VLKRSKEEAERIAEMELAKVGLADRVDFMPSQLSGGQQQRVAIARALAMNPHVMLFDEAT 184 Query: 178 SNLDAALRVNTRLEIARLHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMEL 237 S LD L V L + R TMI VTH+ A +AD+++ ++ G I + G+P E+ Sbjct: 185 SALDPEL-VRDVLGVMRDLARGGMTMIVVTHEMGFARDVADRVIFMDGGVIVEQGTPEEV 243 Query: 238 YNRPANLFVAGFIG 251 ++ P + F+G Sbjct: 244 FDHPKSERTKDFLG 257 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: 234 Number of extensions: 10 Number of successful extensions: 4 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: 260 Length adjustment: 27 Effective length of query: 325 Effective length of database: 233 Effective search space: 75725 Effective search space used: 75725 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 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