Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate 206179 DVU0753 amino acid ABC transporter, ATP-binding protein
Query= reanno::Smeli:SMc02121 (258 letters) >MicrobesOnline__882:206179 Length = 243 Score = 321 bits (822), Expect = 1e-92 Identities = 158/240 (65%), Positives = 192/240 (80%), Gaps = 1/240 (0%) Query: 19 IEITNMNKWY-GDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIVV 77 I +++KWY HVL DINL + +GE +V+ GPSGSGKST+IRCINRLE QKG IVV Sbjct: 2 IHFEHVHKWYPSGLHVLNDINLDIAQGEVVVICGPSGSGKSTLIRCINRLEAIQKGNIVV 61 Query: 78 DGIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKEAEQVAMHF 137 DGI++ + +R EVG VFQ FNL+PH+T+LEN TLAP VR +P+ EAE+ AM Sbjct: 62 DGIDINAPRTNLTLLRAEVGFVFQQFNLYPHMTVLENITLAPTLVRNIPRAEAERTAMEL 121 Query: 138 LERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVKEVLDTMV 197 LE+V IP++A YPGQLSGGQQQRVAIAR L M+P+I+LFDEPTSALDPEM+ EVLD M Sbjct: 122 LEKVNIPDKAGAYPGQLSGGQQQRVAIARGLAMKPRIMLFDEPTSALDPEMINEVLDVMR 181 Query: 198 GLAEEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHERTKLFLSQIL 257 LA EGMTM+CVTHEMGFAR+VA+RVIFMDQG +VEQN+P FF+NPQHER++ FLS+IL Sbjct: 182 QLAREGMTMVCVTHEMGFAREVADRVIFMDQGILVEQNTPDAFFNNPQHERSREFLSKIL 241 Lambda K H 0.322 0.136 0.397 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: 219 Number of extensions: 4 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: 258 Length of database: 243 Length adjustment: 24 Effective length of query: 234 Effective length of database: 219 Effective search space: 51246 Effective search space used: 51246 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 (21.9 bits) S2: 46 (22.3 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