Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate RR42_RS07815 RR42_RS07815 glutamine ABC transporter ATP-binding protein
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__Cup4G11:RR42_RS07815 Length = 243 Score = 246 bits (628), Expect = 3e-70 Identities = 137/246 (55%), Positives = 172/246 (69%), Gaps = 12/246 (4%) Query: 27 LQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLD 86 +++E + K YG H VL + RQG+V+ LIG SGSGKSTMLRCIN LEQ G IT+D Sbjct: 2 IKMEQLSKSYGAHRVLSNIDAEIRQGEVVCLIGPSGSGKSTMLRCINGLEQYQGGSITID 61 Query: 87 GISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVSAA 146 G R +P ++ +R R++MVFQ FNL+ H T LEN+ P V S A Sbjct: 62 G-------ERVNAASPG---IRQIRQRVSMVFQRFNLFPHRTALENVMEGPVHVKKESVA 111 Query: 147 EAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDPE 206 EA++RA L VGL ++A YP LSGGQQQRVAIARALAM P+ ILFDEPTSALDPE Sbjct: 112 EAKERAAEILASVGLAEKMA-HYPTQLSGGQQQRVAIARALAMRPDAILFDEPTSALDPE 170 Query: 207 LVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHG-DARILDQPNSE 265 LVGEVL V++ LAE+G TM++VTHEM FAR+VS++VLFL GR+ E G A++L QP++E Sbjct: 171 LVGEVLGVMRKLAEKGMTMVIVTHEMKFAREVSNRVLFLDGGRIAEQGPSAQVLTQPSNE 230 Query: 266 RLQQFL 271 R+Q FL Sbjct: 231 RMQDFL 236 Lambda K H 0.319 0.133 0.372 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: 215 Number of extensions: 11 Number of successful extensions: 4 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: 276 Length of database: 243 Length adjustment: 24 Effective length of query: 252 Effective length of database: 219 Effective search space: 55188 Effective search space used: 55188 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: 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