Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate WP_011654832.1 RL_RS30155 amino acid ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc02121 (258 letters) >NCBI__GCF_000009265.1:WP_011654832.1 Length = 254 Score = 337 bits (864), Expect = 1e-97 Identities = 169/242 (69%), Positives = 195/242 (80%) Query: 16 DVAIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKI 75 + I + + KWYG F LRDIN+ V GERIV+ GPSGSGKST+IRCIN LE +++G+I Sbjct: 11 ETMITMERVEKWYGAFQALRDINISVRSGERIVLCGPSGSGKSTLIRCINHLETYERGEI 70 Query: 76 VVDGIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKEAEQVAM 135 V GI L N K ID +RREVGMVFQ FNLFPHLT+L+NC LAP+ + + EAE+ A Sbjct: 71 RVGGILLGNQAKTIDAIRREVGMVFQQFNLFPHLTVLQNCMLAPMKAVGVSRAEAEERAR 130 Query: 136 HFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVKEVLDT 195 LERVKI EQA KYP QLSGGQQQRVAIAR+LCMRPK++LFDEPTSALDPEMVKEVLDT Sbjct: 131 GLLERVKILEQADKYPVQLSGGQQQRVAIARALCMRPKVMLFDEPTSALDPEMVKEVLDT 190 Query: 196 MVGLAEEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHERTKLFLSQ 255 M+ LA+EGMTMICVTHEMGFARQVA+RVIFM G IVE+ PAEFF NPQHERT+ FL + Sbjct: 191 MIALADEGMTMICVTHEMGFARQVADRVIFMASGAIVEEAPPAEFFTNPQHERTRKFLGE 250 Query: 256 IL 257 IL Sbjct: 251 IL 252 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: 244 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: 254 Length adjustment: 24 Effective length of query: 234 Effective length of database: 230 Effective search space: 53820 Effective search space used: 53820 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 Apr 09 2024. 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