Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate RR42_RS16370 RR42_RS16370 glutamine ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc02121 (258 letters) >FitnessBrowser__Cup4G11:RR42_RS16370 Length = 260 Score = 333 bits (855), Expect = 2e-96 Identities = 158/251 (62%), Positives = 204/251 (81%) Query: 8 PKLAVSTTDVAIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRL 67 P ++ IE+ ++KW+G+ VL +I++RV RGERIV+ GPSGSGKSTMIRCINRL Sbjct: 9 PAQDAASQPATIELRRVSKWFGETQVLSNIDMRVQRGERIVICGPSGSGKSTMIRCINRL 68 Query: 68 EEHQKGKIVVDGIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPK 127 EEHQ+G+I+V+G+ LT + I VRREVGMVFQ FNLFPHL++L+N +AP+ +R + K Sbjct: 69 EEHQQGEILVEGVSLTKSPRNISFVRREVGMVFQQFNLFPHLSVLQNLMIAPMKIRGIKK 128 Query: 128 KEAEQVAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPE 187 KEAE+ A HFLERV+I ++A +YP QLSGGQQQRVAIAR+LCM+PK++LFDEPTSALDPE Sbjct: 129 KEAEETARHFLERVRIGDKADRYPAQLSGGQQQRVAIARALCMKPKMMLFDEPTSALDPE 188 Query: 188 MVKEVLDTMVGLAEEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHE 247 M+KEVLD M+ LA +GMTM+CVTHEMGFAR VA+R++FMD+G+IVE+ P FF P+ E Sbjct: 189 MIKEVLDVMMQLARDGMTMVCVTHEMGFARTVADRILFMDKGEIVEEAQPEAFFSMPKSE 248 Query: 248 RTKLFLSQILH 258 R + FL QIL+ Sbjct: 249 RARAFLGQILN 259 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: 245 Number of extensions: 7 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: 260 Length adjustment: 24 Effective length of query: 234 Effective length of database: 236 Effective search space: 55224 Effective search space used: 55224 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: 47 (22.7 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