Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate GFF2270 PS417_11575 spermidine/putrescine ABC transporter ATPase
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__WCS417:GFF2270 Length = 342 Score = 247 bits (631), Expect = 3e-70 Identities = 135/310 (43%), Positives = 193/310 (62%), Gaps = 20/310 (6%) Query: 20 LQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQID 79 LQL + K +G+ + + DL V+ GEFV +GPSGCGK+T L+ IAG D + G + +D Sbjct: 4 LQLNALSKRYGAVDAVVATDLAVEKGEFVSLLGPSGCGKTTTLQMIAGFVDVSGGQILLD 63 Query: 80 GVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLSL 139 G ++ H PA RG+ +VFQSYAL+PH++V+DN+ GLK VP AEI KV ++ L Sbjct: 64 GRDITHAKPASRGLGVVFQSYALFPHMSVRDNVAFGLKMRKVPAAEIASKVKTVLELVRL 123 Query: 140 EPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRSL 199 P+ R P ELSGGQRQRVA+ RA+V EP + L DEPLSNLDA LR + EI R+ ++ Sbjct: 124 APHADRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQCAV 183 Query: 200 KATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFI--------- 250 T + VTHDQ EA++++D++VV+ AGR+ Q+ +P +LY P F++ F+ Sbjct: 184 GITTLMVTHDQAEALSISDRVVVMQAGRVTQIDAPYKLYEHPRTRFISDFVGKANLLPGD 243 Query: 251 ----GSPQMNFIEAAKLGDGEAKTIGIRPEHIGL-SRESGDWKGKVIHVEHLGADTIIYI 305 GSPQ+ + GDGE T+ +RPE I L SG +GKV+ G+ + I Sbjct: 244 YDLLGSPQVRH----ESGDGEL-TLSLRPEKIQLVDAGSGRLQGKVLDSYFFGSQWLYRI 298 Query: 306 ESETVGLLTV 315 + ++G +TV Sbjct: 299 HT-SLGEITV 307 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: 307 Number of extensions: 6 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: 342 Length adjustment: 29 Effective length of query: 323 Effective length of database: 313 Effective search space: 101099 Effective search space used: 101099 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