Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate RR42_RS37305 RR42_RS37305 sulfate ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__Cup4G11:RR42_RS37305 Length = 366 Score = 210 bits (534), Expect = 5e-59 Identities = 135/354 (38%), Positives = 199/354 (56%), Gaps = 45/354 (12%) Query: 20 LQLKTIRKAFGS---HEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSV 76 L ++ + K FG + L G+ L V GE + +GPSGCGK+TLLR IAGLE +G + Sbjct: 13 LAVEQVGKRFGGAGGFQALDGVSLSVAQGELLCLLGPSGCGKTTLLRIIAGLEREDTGRI 72 Query: 77 QIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136 G E+ + P R ++FQSYAL+P+L+V N+ GL+ G+ +A E +VA+ + Sbjct: 73 HAGGRELTGLPPQARDYGILFQSYALFPNLSVARNVAYGLQGRGMGRAHREARVAEMLSL 132 Query: 137 LSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLH 196 + L + P +LSGGQ+QRVA+ RA+ P L L DEP+S LDA +R + RLE+ +L Sbjct: 133 VGLAGSERKFPGQLSGGQQQRVALARALAPAPSLLLLDEPMSALDARVREHLRLELRQLQ 192 Query: 197 RSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMN 256 R L T + VTHDQ EAM +AD+I V+ GRI QVG+P E+Y RPA+ FVA FIG Q N Sbjct: 193 RRLNVTTVMVTHDQDEAMAMADRIAVMEGGRIAQVGTPGEIYERPASAFVAEFIG--QAN 250 Query: 257 FIE----------------------AAKLGDGEAKTIGIRPEHIGLSRESGD---WKGKV 291 +++ A+++ DG A+ + RPE I L G+ ++ Sbjct: 251 WLDGRLSGRDTFSVGELDLAVSPARASEVADGAAR-LCCRPEAIRLHPVEGEPNRLLARI 309 Query: 292 IHVEHLGADTIIYIESETVGLLTVRLFGEHRYATDDIV----HATPVIGSMHRF 341 + +LG+ + +E++ RL G +A D++ H P GS H+F Sbjct: 310 VDQTYLGSRYRLMLEAD-------RLPGHTLFA--DVLREERHLLPAPGS-HKF 353 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: 322 Number of extensions: 10 Number of successful extensions: 1 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: 366 Length adjustment: 29 Effective length of query: 323 Effective length of database: 337 Effective search space: 108851 Effective search space used: 108851 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