Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate AO353_12330 AO353_12330 peptide ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc02121 (258 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12330 Length = 244 Score = 271 bits (692), Expect = 1e-77 Identities = 133/222 (59%), Positives = 169/222 (76%) Query: 36 DINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIVVDGIELTNDLKKIDEVRRE 95 ++ RV +GE +VV GPSGSGKST +RC+N LE G + +DG++L + ++ RRE Sbjct: 23 NVTTRVAKGEVLVVIGPSGSGKSTFLRCLNGLEAFDSGSVSIDGLQLADPKTDVNAYRRE 82 Query: 96 VGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKEAEQVAMHFLERVKIPEQALKYPGQLS 155 VGMVFQHFNLFPH+T+LEN LA VRK K+E E A+ LE+V I ++A ++P +LS Sbjct: 83 VGMVFQHFNLFPHMTVLENLCLAQKVVRKRGKQEREAKALALLEKVGIAQKAHEFPSRLS 142 Query: 156 GGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVKEVLDTMVGLAEEGMTMICVTHEMGF 215 GGQQQRVAIAR+L M PK++LFDEPTSALDPEMV EVLD M LA EGMTM+CVTHEMGF Sbjct: 143 GGQQQRVAIARALAMEPKVMLFDEPTSALDPEMVGEVLDVMKTLAVEGMTMVCVTHEMGF 202 Query: 216 ARQVANRVIFMDQGQIVEQNSPAEFFDNPQHERTKLFLSQIL 257 AR+VA+RV+F D G+++E SPAEFFD P+ R + FL Q+L Sbjct: 203 AREVADRVLFFDHGKLLEDASPAEFFDAPKDPRAQAFLRQVL 244 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: 228 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: 258 Length of database: 244 Length adjustment: 24 Effective length of query: 234 Effective length of database: 220 Effective search space: 51480 Effective search space used: 51480 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