Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_106712312.1 CU102_RS17070 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc02869 (352 letters) >NCBI__GCF_003010955.1:WP_106712312.1 Length = 332 Score = 403 bits (1035), Expect = e-117 Identities = 203/332 (61%), Positives = 251/332 (75%) Query: 17 VGSLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSV 76 +GS+ L+ + K+FG+ V+ IDL++ DGEFV+FVGPSGCGKSTLLR IAGLED + G + Sbjct: 1 MGSITLQKVSKSFGTTSVIPEIDLEINDGEFVVFVGPSGCGKSTLLRMIAGLEDLSGGRI 60 Query: 77 QIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136 IDG ++ + APAKRG++MVFQSYALYPH++V N+ LK G K I++KV AA + Sbjct: 61 VIDGKDMSNEAPAKRGLSMVFQSYALYPHMSVYGNIAFPLKMDGQDKTAIDKKVKDAAHI 120 Query: 137 LSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLH 196 L+L YL RRP +LSGGQRQRVAIGRAIVR+PK FLFDEPLSNLDAALR N RLEI+ LH Sbjct: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVRQPKAFLFDEPLSNLDAALRGNMRLEISDLH 180 Query: 197 RSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMN 256 LK TMIYVTHDQVEAMT+ADKIVVLNAGRIEQVGSP++LY P N+FVAGFIGSP+MN Sbjct: 181 HQLKTTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLDLYRSPRNVFVAGFIGSPRMN 240 Query: 257 FIEAAKLGDGEAKTIGIRPEHIGLSRESGDWKGKVIHVEHLGADTIIYIESETVGLLTVR 316 IE + A T+G+RPEH+ +S+ G WKG V EHLG+DT I+++ + VG +TVR Sbjct: 241 LIEGQEAAKQSAVTLGVRPEHMRISKTEGTWKGIVGVTEHLGSDTFIHVQVDGVGKITVR 300 Query: 317 LFGEHRYATDDIVHATPVIGSMHRFDADGRVI 348 G+ V+ TP +HRFDADG+ I Sbjct: 301 TDGDFSTEFGQQVYLTPEPARLHRFDADGQAI 332 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: 398 Number of extensions: 11 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: 332 Length adjustment: 29 Effective length of query: 323 Effective length of database: 303 Effective search space: 97869 Effective search space used: 97869 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 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