Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate RR42_RS34310 RR42_RS34310 amino acid ABC transporter permease
Query= uniprot:A0A1N7UBU2 (233 letters) >FitnessBrowser__Cup4G11:RR42_RS34310 Length = 222 Score = 119 bits (297), Expect = 6e-32 Identities = 81/228 (35%), Positives = 121/228 (53%), Gaps = 11/228 (4%) Query: 2 NEFLNLHGYGPMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLI 61 N F + + P+L QGA +T+++ LA LS LGL A KLS A+ L A+ +I Sbjct: 4 NFFQHAREFLPILLQGAVVTVEVTVLAFVLSSLLGLALALMKLSPARTLSWGASGAINVI 63 Query: 62 RSVPDLVLILLIFYSLQLWLNDLSEVFGWDYFEIDPFTAGVITLGFIYGAYFTENFRGAI 121 R +P +V + I++ L D + F AGVI LG Y AY ENFR I Sbjct: 64 RGLPIIVQLFYIYFVLP----DAG-------IHLTAFQAGVIGLGIAYSAYQAENFRAGI 112 Query: 122 LSVPVGQLEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDL 181 +V GQ EAA A G+ V+ PQ +R +LP GN +++LK ++LVS I ++++ Sbjct: 113 EAVDPGQREAAQAMGMRPALVMRRVILPQALRISLPPYGNTLVMMLKDSSLVSTITVAEM 172 Query: 182 VKAAQNAGKTTNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNLGIK 229 +A Q +T + + L L+YL+++ L+RLERR +G K Sbjct: 173 TRAGQLIASSTFQNMTVYTLVALLYLLMSLPLVFGLRRLERRLGVGRK 220 Lambda K H 0.327 0.141 0.428 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: 129 Number of extensions: 8 Number of successful extensions: 2 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: 233 Length of database: 222 Length adjustment: 22 Effective length of query: 211 Effective length of database: 200 Effective search space: 42200 Effective search space used: 42200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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