Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__Miya:8499890 Length = 350 Score = 262 bits (670), Expect = 9e-75 Identities = 137/303 (45%), Positives = 192/303 (63%), Gaps = 18/303 (5%) Query: 17 VGSLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSV 76 + ++QL + + +G + + +V+ G ++ +GPSGCGKST LR IAGLE TSG + Sbjct: 1 MSAIQLLNVSRHWGDVRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60 Query: 77 QIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136 I +V H+ PA+R +AMVFQSYAL+PHLTV++N+ GL VP+AE E+++ +A + Sbjct: 61 MIGERDVTHLPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRLTRAVDI 120 Query: 137 LSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLH 196 L L L R+P ELSGGQ+QRVA+GRA+V E + L DEPLSNLDA LR R EI L Sbjct: 121 LGLSALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMRREIRALQ 180 Query: 197 RSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMN 256 ++L TM+YVTHDQ EAM++AD+I+++ GRI Q +P ELY+RPA F FIG+P MN Sbjct: 181 QTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNFIGTPPMN 240 Query: 257 FIE----------------AAKLGDGEAKTIGIRPEHIGLSRESGDWKGKVIHVEHLGAD 300 + + D +GIRPEHI + E W+ V VE+LG+ Sbjct: 241 LVRLDDARGSVCVAGSRSGTVSVVDSADYVLGIRPEHIRIVPEG--WRAVVESVEYLGSG 298 Query: 301 TII 303 +++ Sbjct: 299 SVL 301 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: 315 Number of extensions: 10 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: 350 Length adjustment: 29 Effective length of query: 323 Effective length of database: 321 Effective search space: 103683 Effective search space used: 103683 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